GenomeTools C API
This document describes the GenomeTools C API (that is, all public interfaces which are part of libgenometools).
See the index for an alphabetical list of all available interfaces.
Classes
- GtAddIntronsStream
- GtAlphabet
- GtAnnoDBGFFlike
- GtAnnoDBSchema
- GtArray
- GtArrayInStream
- GtArrayOutStream
- GtBEDInStream
- GtBioseq
- GtBittab
- GtBlock
- GtBoolMatrix
- GtBufferStream
- GtCDSStream
- GtCDSVisitor
- GtCSAStream
- GtCanvas
- GtCanvasCairoContext
- GtCanvasCairoFile
- GtCheckBoundariesVisitor
- GtCodonIterator
- GtCodonIteratorEncseq
- GtCodonIteratorSimple
- GtColor
- GtCommentNode
- GtCstrTable
- GtCustomTrack
- GtCustomTrackGcContent
- GtCustomTrackScriptWrapper
- GtDiagram
- GtDiscDistri
- GtDlist
- GtDlistelem
- GtEOFNode
- GtEncseq
- GtEncseqBuilder
- GtEncseqEncoder
- GtEncseqLoader
- GtEncseqReader
- GtError
- GtExtractFeatureStream
- GtFastaReader
- GtFeatureInStream
- GtFeatureIndex
- GtFeatureIndexMemory
- GtFeatureNode
- GtFeatureNodeIterator
- GtFeatureOutStream
- GtFeatureStream
- GtFile
- GtGFF3InStream
- GtGFF3OutStream
- GtGFF3Parser
- GtGFF3Visitor
- GtGTFInStream
- GtGTFOutStream
- GtGenomeNode
- GtGraphics
- GtGraphicsCairo
- GtHashmap
- GtIDToMD5Stream
- GtImageInfo
- GtInterFeatureStream
- GtIntervalTree
- GtIntervalTreeNode
- GtLayout
- GtLogger
- GtMD5Encoder
- GtMD5Tab
- GtMD5ToIDStream
- GtMatch
- GtMatchBlast
- GtMatchIterator
- GtMatchLAST
- GtMatchOpen
- GtMatchSW
- GtMatchVisitor
- GtMergeFeatureStream
- GtMergeStream
- GtMetaNode
- GtMutex
- GtNodeStream
- GtNodeStreamClass
- GtNodeVisitor
- GtORFIterator
- GtOption
- GtOptionParser
- GtOutputFileInfo
- GtPhase
- GtQueue
- GtRBTree
- GtRBTreeIter
- GtRDBMySQL
- GtRDBSqlite
- GtRDBVisitor
- GtRWLock
- GtRange
- GtReadmode
- GtRecMap
- GtRegionMapping
- GtRegionNode
- GtScoreMatrix
- GtScriptWrapperStream
- GtScriptWrapperVisitor
- GtSelectStream
- GtSeq
- GtSeqIterator
- GtSeqIteratorFastQ
- GtSeqIteratorSequenceBuffer
- GtSeqid2FileInfo
- GtSequenceNode
- GtSetSourceVisitor
- GtSortStream
- GtSpliceSiteInfoStream
- GtSplitter
- GtStatStream
- GtStr
- GtStrArray
- GtStrCache
- GtStrand
- GtStyle
- GtTagValueMap
- GtTextWidthCalculator
- GtTextWidthCalculatorCairo
- GtThread
- GtTimer
- GtTool
- GtToolbox
- GtTransTable
- GtTranslator
- GtTypeChecker
- GtTypeCheckerOBO
- GtUniqStream
- GtVisitorStream
- GtXRFChecker
Modules
- Array2dim
- Array3dim
- Arraydef
- Assert
- Bsearch
- BytePopcount
- ByteSelect
- ClassAlloc
- Compat
- ConsensusSplicedAlignment
- Countingsort
- Cstr
- CstrArray
- Deprecated
- Divmodmul
- Endianess
- Ensure
- FASTA
- FileAllocator
- Fileutils
- FunctionPointer
- GFF3Escaping
- GlobalChaining
- Grep
- Init
- Log
- MD5Fingerprint
- MD5Seqid
- Mathsupport
- MemoryAllocation
- Msort
- Multithread
- ORF
- POSIX
- Parseutils
- Qsort
- RegularSeqID
- Reverse
- Safearith
- SeqID2File
- Strcmp
- Symbol
- Threads
- Tooldriver
- Undef
- UnitTest
- Unused
- Version
- VersionFunc
- Warning
- XANSI
- XPOSIX
- Yarandom
Sole functions
const char*  GtGetSeqFunc(void *seqs, GtUword index)
Function used to retrieve a cleartext sequence for an index number.
GtUword      GtGetSeqLenFunc(void *seqs, GtUword index)
Function used to retrieve a sequence length for an index number.
GtFile*            gt_output_file_xopen_forcecheck(const char *path,
                                                  const char *mode, bool force,
                                                  GtError *err)
Helper function for (rare) tools which do not use the full GtOutputFileInfo
   (usually if directories are involved).
int              gt_feature_index_gfflike_get_all_features(GtFeatureIndex *gfi,
                                                          GtArray *results,
                                                          GtError *err)
Retrieves all features contained in gfi into results. Returns 0 on
   success, a negative value otherwise. The message in err is set
   accordingly.
GtNodeStream*  gt_dup_feature_stream_new(GtNodeStream*, const char *dest_type,
                                        const char *source_type)
Duplicate internal feature nodes of type source_type as features with type
   dest_type. The duplicated features does not inherit the children.
void  GtTrackSelectorFunc(GtBlock*, GtStr*, void*)
A GtTrackSelectorFunc is a callback function which sets a GtStr to a
   string to be used as a track identifier for assignment of a GtBlock
   to a given track.
int  GtTrackOrderingFunc(const char *s1, const char *s2, void *data)
A function describing the order of tracks based on their track identifier
   strings s1 and s2. Must return a negative value if the track with ID s1
   should appear before the track with ID s2 and a positive value if s1
   should appear after s2. Returning a value of 0 will result in an undefined
   ordering of s1 and s2.
Class GtAddIntronsStream
 Implements the GtNodeStream interface. A GtAddIntronsStream inserts new
   feature nodes with type intron between existing feature nodes with type
   exon. This is a special case of the GtInterFeatureStream. 
GtNodeStream*  gt_add_introns_stream_new(GtNodeStream *in_stream)
Create a GtAddIntronsStream* which inserts feature nodes of type intron
   between feature nodes of type exon it retrieves from in_stream and
   returns them.
Class GtAlphabet
The following type is for storing alphabets.
GtAlphabet*     gt_alphabet_new_dna(void)
Return a GtAlphabet object which represents a DNA alphabet.
GtAlphabet*     gt_alphabet_new_protein(void)
Return a GtAlphabet object which represents a protein alphabet.
GtAlphabet*     gt_alphabet_new_empty(void)
Return an empty GtAlphabet object.
GtAlphabet*     gt_alphabet_new_from_file(const char *filename, GtError *err)
Return a GtAlphabet object, as read from an .al1 file specified by
   filename (i.e. no al1 suffix necessary).
GtAlphabet*     gt_alphabet_new_from_file_no_suffix(const char *filename,
                                                   GtError *err)
Return a GtAlphabet object, as read from a file specified by
   filename.
GtAlphabet*     gt_alphabet_new_from_string(const char *alphadef,
                                           GtUword len, GtError *err)
Return a GtAlphabet object, as read from a string of length len
   specified by alphadef.
GtAlphabet*     gt_alphabet_new_from_sequence(const GtStrArray *filenametab,
                                             GtError *err)
Returns a new GtAlphabet object by scanning the sequence files in
   filenametab to determine whether they are DNA or protein sequences,
   and the appropriate alphabet will be used (see gt_alphabet_guess()).
   Returns NULL on error, see err for details.
GtAlphabet*     gt_alphabet_guess(const char *sequence, GtUword seqlen)
Try to guess which type the given sequence with length has (DNA or
   protein) and return an according GtAlphabet* object.
GtAlphabet*     gt_alphabet_clone(const GtAlphabet *alphabet)
Return a clone of alphabet.
bool            gt_alphabet_equals(const GtAlphabet *a, const GtAlphabet *b)
Returns TRUE if a and b are equal (i.e. have the same symbol
   mapping), FALSE otherwise.
GtAlphabet*     gt_alphabet_ref(GtAlphabet *alphabet)
Increase the reference count for alphabet and return it.
void            gt_alphabet_add_mapping(GtAlphabet *alphabet,
                                       const char *characters)
Add the mapping of all given characters to the given alphabet. The first
   character is the result of subsequent gt_alphabet_decode() calls.
void            gt_alphabet_add_wildcard(GtAlphabet *alphabet, char wildcard)
Add wildcard to the alphabet.
const GtUchar*  gt_alphabet_symbolmap(const GtAlphabet *alphabet)
Returns the array of symbols from alphabet such that the index of the
   character equals its encoding.
unsigned int    gt_alphabet_num_of_chars(const GtAlphabet *alphabet)
Returns number of characters in alphabet (excluding wildcards).
unsigned int    gt_alphabet_size(const GtAlphabet *alphabet)
Returns number of characters in alphabet (including wildcards).
const GtUchar*  gt_alphabet_characters(const GtAlphabet *alphabet)
Returns an array of the characters in alphabet.
GtUchar         gt_alphabet_wildcard_show(const GtAlphabet *alphabet)
Returns the character used in alphabet to represent wildcards in output.
unsigned int    gt_alphabet_bits_per_symbol(const GtAlphabet *alphabet)
Returns the required number of bits required to represent a symbol
   in alphabet.
void            gt_alphabet_output(const GtAlphabet *alphabet, FILE *fpout)
Writes a representation of alphabet to the file pointer fpout.
int             gt_alphabet_to_file(const GtAlphabet *alphabet,
                                   const char *indexname,
                                   GtError *err)
Writes a representation of alphabet to the .al1 output file as specified
   by indexname (i.e. without the .al1 suffix).
void            gt_alphabet_to_str(const GtAlphabet *alphabet, GtStr *dest)
Writes a representation of alphabet to the GtStr as specified
   by dest.
GtUchar         gt_alphabet_pretty_symbol(const GtAlphabet *alphabet,
                                         unsigned int currentchar)
Returns the printable character specified in alphabet for currentchar.
void            gt_alphabet_echo_pretty_symbol(const GtAlphabet *alphabet,
                                              FILE *fpout,
                                              GtUchar currentchar)
Prints the printable character specified in alphabet for currentchar on
   fpout.
bool            gt_alphabet_is_protein(const GtAlphabet *alphabet)
The following method checks if the given alphabet is the protein
   alphabet with the aminoacids A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S,
   T, V, W, Y written in lower or upper case and returns true, if this is the
   case (false otherwise).
bool            gt_alphabet_is_dna(const GtAlphabet *alphabet)
The following method checks if the given alphabet is the DNA alphabet with
   the bases A, C, G, T written in lower or upper case and returns true, if
   this is the case (false otherwise).
bool            gt_alphabet_valid_input(const GtAlphabet *alphabet, char c)
Returns true if the character c is defined in alphabet.
GtUchar         gt_alphabet_encode(const GtAlphabet *alphabet, char c)
Encode character c with given alphabet.
   Ensure that c is encodable with the given alphabet!
char            gt_alphabet_decode(const GtAlphabet *alphabet, GtUchar c)
Decode character c with given alphabet.
void            gt_alphabet_encode_seq(const GtAlphabet *alphabet, GtUchar *out,
                                      const char *in, GtUword length)
Encode sequence in of given length with alphabet and store the result
   in out. in has to be encodable with the given alphabet!
void            gt_alphabet_decode_seq_to_fp(const GtAlphabet *alphabet,
                                            FILE *fpout,
                                            const GtUchar *src,
                                            GtUword len)
Suppose the string src of length len was transformed according to the
   alphabet. The following method shows each character in src as the
   printable character specified in the transformation. The output is written
   to the given file pointer fpout.
void            gt_alphabet_decode_seq_to_cstr(const GtAlphabet *alphabet,
                                              char *dest,
                                              const GtUchar *src,
                                              GtUword len)
Suppose the string src of length len was transformed according to the
   alphabet. The following method shows each character in src as the
   printable character specified in the transformation. The output is written
   to the given string dest and terminated with '\0' at dest[len]. dest
   therefore has to be of at least len + 1 length.
GtStr*          gt_alphabet_decode_seq_to_str(const GtAlphabet *alphabet,
                                             const GtUchar *src,
                                             GtUword len)
Analog to gt_alphabet_decode_seq_to_fp() writing the output to
   a new GtStr.
void            gt_alphabet_delete(GtAlphabet *alphabet)
Decrease the reference count for alphabet or delete it, if this was the
   last reference.
Class GtAnnoDBGFFlike
 The GtAnnoDBGFFlike class implements the GtAnnoDBSchema interface,
   using a database schema specifically tailored to store GenomeTools
   annotations. 
GtAnnoDBSchema*  gt_anno_db_gfflike_new(void)
Creates a new GtAnnoDBGFFlike schema object.
Class GtAnnoDBSchema
 The GtAnnoDBSchema interface for a database-backed abstract
   GtFeatureIndex factory. 
GtFeatureIndex*  gt_anno_db_schema_get_feature_index(GtAnnoDBSchema *schema,
                                                    GtRDB *db, GtError *err)
Returns a GtFeatureIndex object representing GtRDB object db
   interpreted as having schema schema. Returns NULL if an error occurred,
   err is set accordingly.
void             gt_anno_db_schema_delete(GtAnnoDBSchema *schema)
Deletes schema and frees all associated memory.
Class GtArray
 GtArray objects are generic arrays for elements of a certain size which
   grow on demand. 
GtArray*  gt_array_new(size_t size_of_elem)
Return a new GtArray object whose elements have the size size_of_elem.
GtArray*  gt_array_ref(GtArray *array)
Increase the reference count for array and return it.
   If array is NULL, NULL is returned without any side effects.
GtArray*  gt_array_clone(const GtArray *array)
Return a clone of array.
void*     gt_array_get(const GtArray *array, GtUword index)
Return pointer to element number index of array. index has to be
   smaller than gt_array_size(array).
void*     gt_array_get_first(const GtArray *array)
Return pointer to first element of array.
void*     gt_array_get_last(const GtArray *array)
Return pointer to last element of array.
void*     gt_array_pop(GtArray *array)
Return pointer to last element of array and remove it from array.
void*     gt_array_get_space(const GtArray *array)
Return pointer to the internal space of array where the elements are
   stored.
#define gt_array_add(array, elem)
Add element elem to array. The size of elem must equal the given
   element size when the array was created and is determined automatically
   with the sizeof operator.
void      gt_array_add_elem(GtArray *array, void *elem, size_t size_of_elem)
Add element elem with size size_of_elem to array. size_of_elem must
   equal the given element size when the array was created. Usually, this
   method is not used directly and the macro gt_array_add() is used
   instead.
void      gt_array_add_array(GtArray *dest, const GtArray *src)
Add all elements of array src to the array dest. The element sizes of
   both arrays must be equal.
void      gt_array_rem(GtArray *array, GtUword index)
Remove element with number index from array in O(gt_array_size(array))
   time. index has to be smaller than gt_array_size(array).
void      gt_array_rem_span(GtArray *array, GtUword frompos,
                                 GtUword topos)
Remove elements starting with number frompos up to (and including) topos
   from array in O(gt_array_size(array)) time. frompos has to be smaller
   or equal than topos and both have to be smaller than
   gt_array_size(array).
void      gt_array_reverse(GtArray *array)
Reverse the order of the elements in array.
void      gt_array_set_size(GtArray *array, GtUword size)
Set the size of array to size. size must be smaller or equal than
   gt_array_size(array).
void      gt_array_reset(GtArray *array)
Reset the array. That is, afterwards the array has size 0.
size_t    gt_array_elem_size(const GtArray *array)
Return the size of the elements stored in array.
GtUword   gt_array_size(const GtArray *array)
Return the number of elements in array. If array equals NULL, 0 is
   returned.
void      gt_array_sort(GtArray *array, GtCompare compar)
Sort array with the given compare function compar.
void      gt_array_sort_stable(GtArray *array, GtCompare compar)
Sort array in a stable way with the given compare function compar.
void      gt_array_sort_with_data(GtArray *array, GtCompareWithData compar,
                                 void *data)
Sort array with the given compare function compar. Passes a pointer with
   userdata data to compar.
void      gt_array_sort_stable_with_data(GtArray *array,
                                        GtCompareWithData compar, void *data)
Sort array in a stable way with the given compare function compar. Passes
   a pointer with userdata data to compar.
int       gt_array_cmp(const GtArray *array_a, const GtArray *array_b)
Compare the content of array_a with the content of array_b.
   array_a and array_b must have the same gt_array_size() and
   gt_array_elem_size().
void      gt_array_prepend_array(GtArray *dest, const GtArray *src)
Prepend the items from src to dest.
void      gt_array_delete(GtArray *array)
Decrease the reference count for array or delete it, if this was the last
   reference.
Class GtArrayInStream
 Implements the GtNodeStream interface. GtArrayOutStream takes
   an array of GtGenomeNodes and delivers them when used as an input stream.
   This stream can be used to feed nodes from outside into a stream flow. 
GtNodeStream*  gt_array_in_stream_new(GtArray *nodes, GtUword *progress,
                                     GtError *err)
Creates a new GtArrayInStream, delivering nodes from nodes. Note that
   the array must contain pointers to GtGenomeNodes! For every node passed,
   the value pointed to by progress is incremented by 1.
Class GtArrayOutStream
 The GtArrayOutStream class implements the GtNodeStream interface.
   GtArrayOutStream takes nodes from an input stream and adds them to a
   GtArray. This stream can be used to obtain nodes for processing outside
   of the usual stream flow. 
GtNodeStream*  gt_array_out_stream_new(GtNodeStream *in_stream,
                                      GtArray *nodes, GtError *err)
Creates a new GtArrayInStream, storing new references to GtFeatureNodes
   from in_stream in nodes. Note that the array must be set up to contain
   pointers to GtGenomeNodes!
GtNodeStream*  gt_array_out_stream_all_new(GtNodeStream *in_stream,
                                          GtArray *nodes, GtError *err)
Like gt_array_out_stream_new(), but not restricted to feature nodes.
Class GtBEDInStream
 Implements the GtNodeStream interface. A GtBEDInStream allows one to
   parse a BED file and return it as a stream of GtGenomeNode objects. 
GtNodeStream*  gt_bed_in_stream_new(const char *filename)
Return a GtBEDInStream object which subsequently reads the BED file with
   the given filename. If filename equals NULL, the BED data is read from
   stdin.
void           gt_bed_in_stream_set_feature_type(GtBEDInStream *bed_in_stream,
                                                const char *type)
Create BED features parsed by bed_in_stream with given type (instead of
   the default "BED_feature").
void           gt_bed_in_stream_set_thick_feature_type(GtBEDInStream
                                                      *bed_in_stream,
                                                      const char *type)
Create thick BED features parsed by bed_in_stream with given type
   (instead of the default "BED_thick_feature").
void           gt_bed_in_stream_set_block_type(GtBEDInStream *bed_in_stream,
                                              const char *type)
Create BED blocks parsed by bed_in_stream with given type (instead of
   the default "BED_block").
Class GtBioseq
 GtBioseq represents a simple collection of biosequences. 
GtBioseq*    gt_bioseq_new(const char *sequence_file, GtError*)
Construct a new GtBioseq object (and create the bioseq files, if
   necessary).
GtBioseq*    gt_bioseq_new_recreate(const char *sequence_file, GtError*)
Construct a new GtBioseq object (and always create the the bioseq
   files).
GtBioseq*    gt_bioseq_new_str(GtStr* sequence_file, GtError*)
Construct a new GtBioseq object (and always create the the bioseq
   files, if necessary). Filename is given as a GtString.
void         gt_bioseq_delete(GtBioseq *bioseq)
Delete the bioseq.
void         gt_bioseq_delete_indices(GtBioseq *bioseq)
Delete the index files belonging to bioseq.
GtAlphabet*  gt_bioseq_get_alphabet(GtBioseq *bioseq)
Return the GtAlphabet associated with bioseq.
GtSeq*       gt_bioseq_get_seq(GtBioseq *bioseq, GtUword index)
Return sequence with given index as GtSeq.
GtSeq*       gt_bioseq_get_seq_range(GtBioseq*, GtUword index,
                                    GtUword start, GtUword end)
Return subsequence within the boundaries start and end of the sequence
   with given index as GtSeq.
const char*  gt_bioseq_get_description(GtBioseq*, GtUword)
Return description of the sequence with given index.
char         gt_bioseq_get_char(const GtBioseq*, GtUword index,
                               GtUword position)
Return character at position position of the sequence with given
   index.
bool         gt_bioseq_seq_has_wildcards(const GtBioseq *bioseq,
                                        GtUword idx)
Return TRUE if sequence with given index contains wildcards.
char*        gt_bioseq_get_sequence(const GtBioseq *bioseq, GtUword index)
Return sequence with given index (not '\0' terminated).
char*        gt_bioseq_get_sequence_range(const GtBioseq *bioseq, GtUword index,
                                         GtUword start,
                                         GtUword end)
Return subsequence within the boundaries start and end of the sequence
   with given index (not '\0' terminated).
GtUchar      gt_bioseq_get_encoded_char(const GtBioseq *bioseq, GtUword index,
                                       GtUword position)
Return character at position position of the sequence with given
   index. Character is encoded according to alphabet.
void         gt_bioseq_get_encoded_sequence(const GtBioseq *bioseq,
                                           GtUchar *out,
                                           GtUword index)
Writes encoded sequence with given index as to out. The sequence
   is encoded according to alphabet.
void         gt_bioseq_get_encoded_sequence_range(const GtBioseq *bioseq,
                                                 GtUchar *out,
                                                 GtUword index,
                                                 GtUword start,
                                                 GtUword end)
Return subsequence within the boundaries start and end of the sequence
   with given index (not '\0' terminated). The sequence is encoded according
   to the alphabet of bioseq.
const char*  gt_bioseq_get_md5_fingerprint(GtBioseq *bioseq, GtUword index)
Return MD5 fingerprint of sequence with given index.
const char*  gt_bioseq_filename(const GtBioseq *bioseq)
Return filename of sequence file underlying bioseq.
GtUword      gt_bioseq_get_sequence_length(const GtBioseq *bioseq,
                                          GtUword index)
Return length of the sequence with given index in bioseq.
GtUword      gt_bioseq_get_total_length(const GtBioseq *bioseq)
Return length of all sequences in bioseq.
GtUword      gt_bioseq_number_of_sequences(GtBioseq *bioseq)
Return count of all sequences in bioseq.
GtUword      gt_bioseq_md5_to_index(GtBioseq *bioseq, const char *MD5)
Return the index of the (first) sequence with given MD5 contained in
   bioseq, if it exists. Otherwise GT_UNDEF_UWORD is returned.
void         gt_bioseq_show_as_fasta(GtBioseq *bioseq, GtUword width,
                                    GtFile *outfp)
Shows a bioseq on outfp (in fasta format).
   If width is != 0 the sequences are formatted accordingly.
void         gt_bioseq_show_sequence_as_fasta(GtBioseq *bioseq, GtUword seqnum,
                                             GtUword width, GtFile *outfp)
Shows a sequence with number seqnum from a bioseq on outfp (in fasta
   format). If width is != 0 the sequences are formatted accordingly.
void         gt_bioseq_show_gc_content(GtBioseq*, GtFile *outfp)
Shows GC-content on outfp (for DNA files).
void         gt_bioseq_show_stat(GtBioseq *bioseq, GtFile *outfp)
Shows bioseq statistics (on outfp).
void         gt_bioseq_show_seqlengthdistri(GtBioseq *bioseq, GtFile *outfp)
Shows bioseq sequence length distribution (on outfp).
Class GtBittab
Implements arbitrary-length bit arrays and various operations on them.
GtBittab*  gt_bittab_new(GtUword num_of_bits)
Return a new GtBittab of length num_of_bits, initialised to 0.
   num_of_bits has to be > 0
void       gt_bittab_set_bit(GtBittab *bittab, GtUword i)
Set bit i in bittab to 1.
void       gt_bittab_unset_bit(GtBittab *bittab, GtUword i)
Set bit i in bittab to 0.
void       gt_bittab_complement(GtBittab *bittab_a, const GtBittab *bittab_b)
Set bittab_a to be the complement of bittab_b.
void       gt_bittab_equal(GtBittab *bittab_a, const GtBittab *bittab_b)
Set bittab_a to be equal to bittab_b.
void       gt_bittab_and(GtBittab *bittab_a, const GtBittab *bittab_b,
                        const GtBittab *bittab_c)
Set bittab_a to be the bitwise AND of bittab_b and bittab_c.
void       gt_bittab_or(GtBittab *bittab_a, const GtBittab *bittab_b,
                       const GtBittab *bittab_c)
Set bittab_a to be the bitwise OR of bittab_b and bittab_c.
void       gt_bittab_nand(GtBittab *bittab_a, const GtBittab *bittab_b,
                         const GtBittab *bittab_c)
Set bittab_a to be bittab_b NAND bittab_c.
void       gt_bittab_and_equal(GtBittab *bittab_a, const GtBittab *bittab_b)
Set bittab_a to be the bitwise AND of bittab_a and bittab_b.
void       gt_bittab_or_equal(GtBittab *bittab_a, const GtBittab *bittab_b)
Set bittab_a to be the bitwise OR of bittab_a and bittab_b.
void       gt_bittab_shift_left_equal(GtBittab *bittab)
Shift bittab by one position to the left.
void       gt_bittab_shift_right_equal(GtBittab *bittab)
Shift bittab by one position to the right.
void       gt_bittab_unset(GtBittab *bittab)
Set all bits in bittab to 0.
void       gt_bittab_show(const GtBittab *bittab, FILE *fp)
Output a representation of bittab to fp.
void       gt_bittab_get_all_bitnums(const GtBittab *bittab, GtArray *array)
Fill array with the indices of all set bits in bittab.
bool       gt_bittab_bit_is_set(const GtBittab *bittab, GtUword i)
Return true if bit i is set in bittab.
bool       gt_bittab_cmp(const GtBittab *bittab_a, const GtBittab *bittab_b)
Return true if bittab_a and bittab_b are identical.
GtUword    gt_bittab_get_first_bitnum(const GtBittab *bittab)
Return the index of the first set bit in bittab.
GtUword    gt_bittab_get_last_bitnum(const GtBittab *bittab)
Return the index of the last set bit in bittab.
GtUword    gt_bittab_get_next_bitnum(const GtBittab *bittab, GtUword i)
Return the index of the next set bit in bittab with an index greater
   than i.
GtUword    gt_bittab_count_set_bits(const GtBittab *bittab)
Return the number of set bits in bittab.
GtUword    gt_bittab_size(GtBittab *bittab)
Return the total number of bits of bittab.
void       gt_bittab_delete(GtBittab *bittab)
Delete bittab.
Class GtBlock
 The GtBlock class represents a portion of screen space which relates to
   a specific ``top-level'' feature (and maybe its collapsed child features).
   It is the smallest layoutable unit in AnnotationSketch and has a caption
   (which may be displayed above the block rendering). 
GtBlock*               gt_block_new(void)
Creates a new GtBlock object.
GtBlock*               gt_block_ref(GtBlock*)
Increases the reference count.
GtBlock*               gt_block_new_from_node(GtFeatureNode *node)
Create a new GtBlock object, setting block parameters (such as strand,
   range) from a given node template.
GtRange                gt_block_get_range(const GtBlock*)
Returns the base range of the GtBlock's top level element.
GtRange*               gt_block_get_range_ptr(const GtBlock *block)
Returns a pointer to the base range of the GtBlock's top level element.
bool                   gt_block_has_only_one_fullsize_element(const GtBlock*)
Checks whether a GtBlock is occupied completely by a single element.
void                   gt_block_merge(GtBlock*, GtBlock*)
Merges the contents of two GtBlocks into the first one.
GtBlock*               gt_block_clone(GtBlock*)
Returns an independent copy of a GtBlock.
void                   gt_block_set_caption_visibility(GtBlock*, bool)
Set whether a block caption should be displayed or not.
bool                   gt_block_caption_is_visible(const GtBlock*)
Returns whether a block caption should be displayed or not.
void                   gt_block_set_caption(GtBlock*, GtStr *caption)
Sets the GtBlock's caption to caption.
GtStr*                 gt_block_get_caption(const GtBlock*)
Returns the GtBlock's caption.
void                   gt_block_set_strand(GtBlock*, GtStrand strand)
Sets the GtBlock's strand to strand.
GtStrand               gt_block_get_strand(const GtBlock*)
Returns the GtBlock's strand.
GtFeatureNode*         gt_block_get_top_level_feature(const GtBlock*)
Returns the GtBlock's top level feature as a GtFeatureNode object.
GtUword          gt_block_get_size(const GtBlock*)
Returns the number of elements in the GtBlock.
const char*            gt_block_get_type(const GtBlock*)
Returns the feature type of the GtBlock.
void                   gt_block_delete(GtBlock*)
Deletes a GtBlock.
Class GtBoolMatrix
 GtBoolMatrix implements a two-dimensional matrix containing boolean
   values. 
GtBoolMatrix*  gt_bool_matrix_new(void)
Create a new, empty GtBoolMatrix.
bool           gt_bool_matrix_get(GtBoolMatrix *bm, GtUword firstdim,
                                 GtUword seconddim)
Returns the value at position firstdim, seconddim from bm.
void           gt_bool_matrix_set(GtBoolMatrix *bm, GtUword firstdim,
                                 GtUword seconddim, bool b)
Sets the value at position firstdim, seconddim in bm to b.
GtUword        gt_bool_matrix_get_first_column(const GtBoolMatrix *bm,
                                              GtUword firstdim)
Returns the first value from column position firstdim from bm.
GtUword        gt_bool_matrix_get_last_column(const GtBoolMatrix *bm,
                                             GtUword firstdim)
Returns the last value from column position firstdim from bm.
GtUword        gt_bool_matrix_get_next_column(const GtBoolMatrix *bm,
                                             GtUword firstdim,
                                             GtUword i)
Returns the next value from column position firstdim from bm,
   with i being the current position.
void           gt_bool_matrix_delete(GtBoolMatrix *bm)
Deletes bm.
Class GtBufferStream
 The GtBufferStream is a GtNodeStream that buffers GtGenomeNodes. 
GtNodeStream*             gt_buffer_stream_new(GtNodeStream *in_stream)
Create a new GtBufferStream, reading from in_stream. The stream is
   initially configured to buffer nodes read from the input until
   gt_buffer_stream_dequeue() switches it to dequeue mode. In this mode,
   calls to gt_node_stream_next() will deliver the stored nodes in FIFO
   order.
void                      gt_buffer_stream_dequeue(GtBufferStream *bs)
Switch stream bs to dequeue mode.
Class GtCDSStream
 Implements the GtNodeStream interface. A GtCDSStream determines the
   coding sequence (CDS) for sequences determined by feature nodes of type
   exon and adds them as feature nodes of type CDS. 
GtNodeStream*  gt_cds_stream_new(GtNodeStream *in_stream,
                                GtRegionMapping *region_mapping,
                                unsigned int minorflen, const char *source,
                                bool start_codon, bool final_stop_codon,
                                bool generic_star_codons)
Create a GtCDSStream* which determines the coding sequence (CDS) for
   sequences determined by feature nodes of type exon it retrieves from
   in_stream, adds them as feature nodes of type CDS and returns all
   nodes. region_mapping is used to map the sequence IDs of the feature nodes
   to the regions of the actual sequences. minorflen is the minimum length an
   ORF must have in order to be added. The CDS features are created with the
   given source. If start_codon equals true an ORF must begin with a start
   codon, otherwise it can start at any position. If final_stop_codon equals
   true the final ORF must end with a stop codon. If generic_start_codons
   equals true, the start codons of the standard translation scheme are used
   as start codons (otherwise the amino acid 'M' is regarded as a start codon).
Class GtCDSVisitor
 GtCDSVisitor is a GtNodeVisitor that adds CDS features for the
   longest ORFs in a GtFeatureNode. 
GtNodeVisitor*             gt_cds_visitor_new(GtRegionMapping *region_mapping,
                                             unsigned int minorflen,
                                             GtStr *source, bool start_codon,
                                             bool final_stop_codon,
                                             bool generic_start_codons)
Create a new GtCDSVisitor with the given region_mapping for sequence,
   minorflen minimum ORF length, source as the source string.
   If start_codon is true a frame has to start with a start codon,
   otherwise a frame can start everywhere (i.e., at the first amino acid or
   after a stop codon). If final_stop_codon is true the last ORF must
   end with a stop codon, otherwise it can be ``open''.
   Takes ownership of region_mapping.
void                       gt_cds_visitor_set_region_mapping(GtCDSVisitor
                                                            *cds_visitor,
                                                            GtRegionMapping
                                                            *region_mapping)
Sets region_mapping to be the region mapping specifying the sequence for
   cds_visitor. Does not take ownership of region_mapping.
Class GtCSAStream
 Implements the GtNodeStream interface. A GtCSAStream takes spliced
   alignments and transforms them into consensus spliced alignments. 
GtNodeStream*  gt_csa_stream_new(GtNodeStream *in_stream,
                                GtUword join_length)
Create a GtCSAStream* which takes spliced alignments from its in_stream
   (which are at most join_length many bases apart), transforms them into
   consensus spliced alignments, and returns them.
Class GtCanvas
 The GtCanvas class is an abstraction of a stateful drawing surface.
   Constructors must be implemented in subclasses as different arguments are
   required for drawing to specific graphics back-ends. 
GtUword  gt_canvas_get_height(GtCanvas *canvas)
Returns the height of the given canvas.
void     gt_canvas_delete(GtCanvas *canvas)
Delete the given canvas.
Class GtCanvasCairoContext
 Implements the GtCanvas interface using a Cairo context (cairo_t)
   as input. This Canvas uses the GtGraphicsCairo class.
   Drawing to a cairo_t allows the use of the  AnnotationSketch engine
   in any Cairo-based graphical application. 
GtCanvas*  gt_canvas_cairo_context_new(GtStyle *style, cairo_t *context,
                                      double offsetpos,
                                      GtUword width,
                                      GtUword height,
                                      GtImageInfo *image_info,
                                      GtError *err)
Create a new GtCanvas object tied to the cairo_t context, width and
   height using the given style. The optional image_info is
   filled when the created Canvas object is used to render a GtDiagram object.
   offsetpos determines where to start drawing on the surface.
Class GtCanvasCairoFile
 Implements the GtCanvas interface.
   This Canvas uses the GtGraphicsCairo class.  
GtCanvas*  gt_canvas_cairo_file_new(GtStyle *style,
                                   GtGraphicsOutType output_type,
                                   GtUword width,
                                   GtUword height,
                                   GtImageInfo *image_info,
                                   GtError *err)
Create a new GtCanvasCairoFile object with given output_type and
   width using the configuration given in style. The optional image_info
   is filled when the created object is used to render a GtDiagram object.
   Possible GtGraphicsOutType values are GRAPHICS_PNG, GRAPHICS_PS,
   GRAPHICS_PDF and GRAPHICS_SVG. Dependent on the local Cairo installation,
   not all of them may be available.
int      gt_canvas_cairo_file_to_file(GtCanvasCairoFile *canvas,
                                     const char *filename, GtError *err)
Write rendered canvas to the file with name filename. If this
   method returns a value other than 0, check err for an error message.
int      gt_canvas_cairo_file_to_stream(GtCanvasCairoFile *canvas,
                                       GtStr *stream)
Append rendered canvas image data to given stream.
Class GtCheckBoundariesVisitor
 Implements the GtNodeVisitor interface. 
GtNodeVisitor*  gt_check_boundaries_visitor_new(void)
Creates a new GtCheckBoundariesVisitor object.
Class GtCodonIterator
 The GtCodonIterator interface. 
GtUword           gt_codon_iterator_current_position(GtCodonIterator
                                                          *codon_iterator)
Return the current reading offset of codin_iterator, starting from the
   position in the sequence given at iterator instantiation time.
GtUword           gt_codon_iterator_length(GtCodonIterator
                                                *codon_iterator)
Return the length of the substring to scan, given at instantiation time.
void                    gt_codon_iterator_rewind(GtCodonIterator
                                                *codon_iterator)
Rewind the codon_iterator to point again to the position in the sequence
   given at iterator instantiation time.
GtCodonIteratorStatus   gt_codon_iterator_next(GtCodonIterator *codon_iterator,
                                              char *n1, char *n2, char *n3,
                                              unsigned int *frame,
                                              GtError *err)
Sets the values of n1, n2 and n3 to the codon beginning at the current
   reading position of codon_iterator and then advances the reading position
   by one. The current reading frame shift (0, 1 or 2) is for the current codon
   is written to the position pointed to by frame.
   This function returns one of three status codes:
   GT_CODON_ITERATOR_OK    : a codon was read successfully,
   GT_CODON_ITERATOR_END   : no codon was read because the end of the scan
                             region has been reached,
   GT_CODON_ITERATOR_ERROR : no codon was read because an error occurred during
                             sequence access. See err for details.
void                    gt_codon_iterator_delete(GtCodonIterator
                                                *codon_iterator)
Delete codon_iterator.
Class GtCodonIteratorEncseq
GtCodonIterator*             gt_codon_iterator_encseq_new(GtEncseq *encseq,
                                                         GtUword startpos,
                                                         GtUword length,
                                                         GtError *err)
Creates a new GtCodonIterator traversing encseq over a length of len
   starting at concatenated position startpos. If an error occurs, NULL is
   returned and err is set accordingly.
GtCodonIterator*             gt_codon_iterator_encseq_new_with_readmode(
                                                        GtEncseq *encseq,
                                                        GtUword startpos,
                                                        GtUword length,
                                                        GtReadmode readmode,
                                                        GtError *err)
Creates a new GtCodonIterator traversing encseq over a length of len
   starting at concatenated position startpos. readmode specified reading
   direction. If an error occurs, NULL is returned and err is set
   accordingly.
Class GtCodonIteratorSimple
GtCodonIterator*             gt_codon_iterator_simple_new(const char *seq,
                                                         GtUword len,
                                                         GtError *err)
Creates a new GtCodonIterator traversing seq over a length of len.
   If an error occurs, NULL is returned and err is set accordingly.
Class GtColor
 The GtColor class holds a RGB color definition. 
GtColor*  gt_color_new(double red, double green, double blue, double alpha)
Create a new GtColor object with the color given by the red, green,
   and blue arguments. The value for each color channel must be between 0
   and 1.
void       gt_color_set(GtColor *color, double red, double green, double blue,
                       double alpha)
Change the color of the color object to the color given by the red,
   green, and blue arguments. The value for each color channel must be
   between 0 and 1.
bool       gt_color_equals(const GtColor *c1, const GtColor *c2)
Returns true if the colors c1 and c2 are equal.
void       gt_color_delete(GtColor *color)
Delete the color object.
Class GtCommentNode
 Implements the GtGenomeNode interface. Comment nodes correspond to comment
   lines in GFF3 files (i.e., lines which start with a single ``#''). 
GtGenomeNode*             gt_comment_node_new(const char *comment)
Return a new GtCommentNode object representing a comment. Please note
   that the single leading ``#'' which denotes comment lines in GFF3 files
   should not be part of comment.
const char*               gt_comment_node_get_comment(const GtCommentNode
                                                     *comment_node)
Return the comment stored in comment_node.
GtCommentNode*            gt_comment_node_try_cast(GtGenomeNode *gn)
Test whether the given genome node is a comment node. If so, a pointer to the meta node is returned. If not, NULL is returned. Note that in most cases, one should implement a GtNodeVisitor to handle processing of different GtGenomeNode types.
GtCommentNode*            gt_comment_node_cast(GtGenomeNode *gn)
Test whether the given genome node is a comment node. If so, a pointer to the meta node is returned. If not, an assertion fails.
Class GtCstrTable
Implements a table of C strings.
GtCstrTable*   gt_cstr_table_new(void)
Return a new GtCstrTable object.
void           gt_cstr_table_add(GtCstrTable *table, const char *cstr)
Add cstr to table. table must not already contain cstr!
const char*    gt_cstr_table_get(const GtCstrTable *table, const char *cstr)
If a C string equal to cstr is contained in table, it is returned.
   Otherwise NULL is returned.
GtStrArray*    gt_cstr_table_get_all(const GtCstrTable *table)
Return a GtStrArray* which contains all cstrs added to table in
   alphabetical order. The caller is responsible to free it!
void           gt_cstr_table_remove(GtCstrTable *table, const char *cstr)
Remove cstr from table.
void           gt_cstr_table_reset(GtCstrTable *table)
Reset table (that is, remove all contained C strings).
void           gt_cstr_table_delete(GtCstrTable *table)
Delete C string table.
Class GtCustomTrack
 The GtCustomTrack interface allows the GtCanvas to call user-defined
   drawing functions on a GtGraphics object. Please refer to the specific
   implementations' documentation for more information on a particular
   custom track. 
GtCustomTrack*  gt_custom_track_ref(GtCustomTrack *ctrack)
Increase the reference count for ctrack.
void            gt_custom_track_delete(GtCustomTrack *ctrack)
Delete the given ctrack.
Class GtCustomTrackGcContent
 Implements the GtCustomTrack interface. This custom track draws a plot of
   the GC content of a given sequence in the displayed range. As a window
   size for GC content calculation, windowsize is used. 
GtCustomTrack*  gt_custom_track_gc_content_new(const char *seq,
                                              GtUword seqlen,
                                              GtUword windowsize,
                                              GtUword height,
                                              double avg,
                                              bool show_scale)
Creates a new GtCustomTrackGcContent for sequence seq with length
   seqlen of height height with windowsize windowsize.
   A horizontal line is drawn for the percentage value avg,
   with avg between 0 and 1. If show_scale is set to true, then a vertical
   scale rule is drawn at the left end of the curve.
Class GtCustomTrackScriptWrapper
 Implements the GtCustomTrack interface. This custom track is
   only used to store pointers to external callbacks, e.g. written in a
   scripting language. This class does not store any state, relying on the
   developer of the external custom track class to do so.  
GtCustomTrack*  gt_custom_track_script_wrapper_new(GtCtScriptRenderFunc
                                                             render_func,
                                                  GtCtScriptGetHeightFunc
                                                             get_height_func,
                                                  GtCtScriptGetTitleFunc
                                                             get_title_func,
                                                  GtCtScriptFreeFunc
                                                             free_func)
Creates a new GtCustomTrackScriptWrapper object.
Class GtDiagram
 The GtDiagram class acts as a representation of a sequence annotation
   diagram independent of any output format. Besides annotation features as
   annotation graphs, it can contain one or more custom tracks. A individual
   graphical representation of the GtDiagram contents is created by creating a
   GtLayout object using the GtDiagram and then calling
   gt_layout_sketch() with an appropriate GtCanvas object. 
GtDiagram*  gt_diagram_new(GtFeatureIndex *feature_index, const char *seqid,
                          const GtRange *range, GtStyle *style, GtError*)
Create a new GtDiagram object representing the feature nodes in
   feature_index in region seqid overlapping with range. The GtStyle
   object style will be used to determine collapsing options during the
   layout process.
GtDiagram*  gt_diagram_new_from_array(GtArray *features, const GtRange *range,
                                     GtStyle *style)
Create a new GtDiagram object representing the feature nodes in
   features. The features must overlap with range. The GtStyle
   object style will be used to determine collapsing options during the
   layout process.
GtRange     gt_diagram_get_range(const GtDiagram *diagram)
Returns the sequence position range represented by the diagram.
void        gt_diagram_set_track_selector_func(GtDiagram*, GtTrackSelectorFunc,
                                              void*)
Assigns a GtTrackSelectorFunc to use to assign blocks to tracks. If none is set, or set to NULL, then track types are used as track keys (default behavior).
void        gt_diagram_reset_track_selector_func(GtDiagram *diagram)
Resets the track selection behavior of this GtDiagram back to the
   default.
void        gt_diagram_add_custom_track(GtDiagram*, GtCustomTrack*)
Registers a new custom track in the diagram.
void        gt_diagram_delete(GtDiagram*)
Delete the diagram and all its components.
Class GtDiscDistri
 The GtDiscDistri class represents a discrete distribution of integer
   values. 
void  GtDiscDistriIterFunc(GtUword key,
                                     GtUint64 value,
                                     void *data)
Callback function called during iteration over each item of the
   distribution, where key is the counted value and value is the count.
GtDiscDistri*  gt_disc_distri_new(void)
Creates a new, empty GtDiscDistri.
void           gt_disc_distri_add(GtDiscDistri *d, GtUword key)
Adds one count of key to d.
void           gt_disc_distri_add_multi(GtDiscDistri *d, GtUword key,
                                       GtUint64 occurrences)
Adds occurrences counts of key to d.
GtUint64       gt_disc_distri_get(const GtDiscDistri *d, GtUword key)
Return the current count of key as stored in d.
void           gt_disc_distri_show(const GtDiscDistri *d, GtFile *outfp)
Prints the current state of d to outfile. If outfp is NULL,
   stdout will be used for output.
void           gt_disc_distri_foreach(const GtDiscDistri *d,
                                     GtDiscDistriIterFunc func,
                                     void *data)
Iterate over all non-empty entries in d, calling func for each one,
   from the smallest to the largest key. The data pointer can be used to pass
   arbitrary data to func.
void           gt_disc_distri_foreach_in_reverse_order(const GtDiscDistri *d,
                                                      GtDiscDistriIterFunc func,
                                                      void *data)
Same as foreach, but from the longest to the smallest key.
Class GtDlist
 A double-linked list which is sorted according to a GtCompare compare
   function (qsort(3)-like, only if one was supplied to the constructor). 
GtDlist*      gt_dlist_new(GtCompare compar)
Return a new GtDlist object sorted according to compar function. If
   compar equals NULL, no sorting is enforced.
GtDlist*      gt_dlist_new_with_data(GtCompareWithData compar, void *data)
Return a new GtDlist object sorted according to compar function. If
   compar equals NULL, no sorting is enforced. Use data to supply
   additional data to the comparator function.
GtDlistelem*  gt_dlist_first(const GtDlist *dlist)
Return the first GtDlistelem object in dlist.
GtDlistelem*  gt_dlist_last(const GtDlist *dlist)
Return the last GtDlistelem object in dlist.
GtDlistelem*  gt_dlist_find(const GtDlist *dlist, void *data)
Return the first GtDlistelem object in dlist which contains data
   identical to data. Takes O(n) time.
GtUword       gt_dlist_size(const GtDlist *dlist)
Return the number of GtDlistelem objects in dlist.
void          gt_dlist_add(GtDlist *dlist, void *data)
Add a new GtDlistelem object containing data to dlist.
   Usually O(n), but O(1) if data is added in sorted order.
void          gt_dlist_remove(GtDlist *dlist, GtDlistelem *dlistelem)
Remove dlistelem from dlist and free it.
int           gt_dlist_example(GtError *err)
Example for usage of the GtDlist class.
void          gt_dlist_delete(GtDlist *dlist)
Delete dlist.
Class GtDlistelem
GtDlistelem*  gt_dlistelem_next(const GtDlistelem *dlistelem)
Return the successor of dlistelem, or NULL if the element is the last
   one in the GtDlist.
GtDlistelem*  gt_dlistelem_previous(const GtDlistelem *dlistelem)
Return the predecessor of dlistelem, or NULL if the element is the
   first one in the GtDlist.
void*         gt_dlistelem_get_data(const GtDlistelem *dlistelem)
Return the data pointer attached to dlistelem.
Class GtEOFNode
 Implements the GtGenomeNode interface. EOF nodes mark the barrier between
   separate input files in an GFF3 stream. 
GtGenomeNode*             gt_eof_node_new(void)
Create a new GtEOFNode* representing an EOF marker.
GtEOFNode*                gt_eof_node_try_cast(GtGenomeNode *gn)
Test whether the given genome node is an EOF node. If so, a pointer to the EOF node is returned. If not, NULL is returned. Note that in most cases, one should implement a GtNodeVisitor to handle processing of different GtGenomeNode types.
Class GtEncseq
 The GtEncseq class represents a concatenated collection of sequences from
   one or more input files in a bit-compressed encoding. It is stored in a
   number of mmap()able files, depending on which features it is meant to
   support.
   The main compressed sequence information is stored in an encoded sequence
   table, with the file suffix '.esq'. This table is the minimum requirement
   for the GtEncseq structure and must always be present. In addition, if
   support for multiple sequences is desired, a sequence separator position
   table with the '.ssp' suffix is required. If support for sequence
   descriptions is required, two additional tables are needed: a description
   table with the suffix '.des' and a description separator table with the
   file suffix '.sds'. Creation and requirement of these tables can be switched
   on and off using API functions as outlined below.
   The GtEncseq represents the stored sequences as one concatenated string.
   It allows access to the sequences by providing start positions and lengths
   for each sequence, making it possible to extract encoded substrings into a
   given buffer, as well as accessing single characters both in a random and a
   sequential fashion. 
const char*        gt_encseq_indexname(const GtEncseq *encseq)
Returns the indexname (as given at loading time) of encseq or the string
   "generated" if the GtEncseq was build in memory only.
GtUword            gt_encseq_total_length(const GtEncseq *encseq)
Returns the total number of characters in all sequences of encseq,
   including separators and wildcards.
GtUword            gt_encseq_num_of_sequences(const GtEncseq *encseq)
Returns the total number of sequences contained in encseq.
GtUchar            gt_encseq_get_encoded_char(const GtEncseq *encseq,
                                             GtUword pos,
                                             GtReadmode readmode)
Returns the encoded representation of the character at position pos of
   encseq read in the direction as indicated by readmode.
char               gt_encseq_get_decoded_char(const GtEncseq *encseq,
                                             GtUword pos,
                                             GtReadmode readmode)
Returns the decoded representation of the character at position pos of
   encseq read in the direction as indicated by readmode.
bool               gt_encseq_position_is_separator(const GtEncseq *encseq,
                                                  GtUword pos,
                                                  GtReadmode readmode)
Returns true iff pos is a separator position of encseq
   read in the direction as indicated by readmode.
bool               gt_encseq_position_is_wildcard(const GtEncseq *encseq,
                                                 GtUword pos,
                                                 GtReadmode readmode)
Returns true iff pos is a wildcard in encseq
   read in the direction as indicated by readmode.
GtEncseq*          gt_encseq_ref(GtEncseq *encseq)
Increases the reference count of encseq.
GtEncseqReader*    gt_encseq_create_reader_with_readmode(const GtEncseq *encseq,
                                                        GtReadmode readmode,
                                                        GtUword startpos)
Returns a new GtEncseqReader for encseq, starting from position
   startpos. Also supports reading the sequence from the reverse and
   delivering (reverse) complement characters on DNA alphabets using the
   readmode option. Please make sure that the GT_READMODE_COMPL and
   GT_READMODE_REVCOMPL readmodes are only used on DNA alphabets.
void               gt_encseq_extract_encoded(const GtEncseq *encseq,
                                            GtUchar *buffer,
                                            GtUword frompos,
                                            GtUword topos)
Stores the encoded representation of the substring from 0-based position
   frompos to position topos of encseq. The result is written to the
   location pointed to by buffer, which must be large enough to hold the
   result.
void               gt_encseq_extract_decoded(const GtEncseq *encseq,
                                            char *buffer,
                                            GtUword frompos,
                                            GtUword topos)
Stores the decoded version of the substring from 0-based position frompos
   to position topos of encseq. If the extracted region contains a separator
   character, it will be represented by non-printable GT_SEPARATOR constant.
   The caller is responsible to handle this case. The result of the extraction
   is written to the location pointed to by buffer, which must be sufficiently
   large to hold the result.
GtUword            gt_encseq_seqlength(const GtEncseq *encseq,
                                      GtUword seqnum)
Returns the length of the seqnum-th sequence in the encseq.
   Requires multiple sequence support enabled in encseq.
GtUword            gt_encseq_min_seq_length(const GtEncseq *encseq)
Returns the length of the shortest sequence in the encseq.
GtUword            gt_encseq_max_seq_length(const GtEncseq *encseq)
Returns the length of the longest sequence in the encseq.
bool               gt_encseq_has_multiseq_support(const GtEncseq *encseq)
Returns true if encseq has multiple sequence support.
bool               gt_encseq_has_description_support(const GtEncseq *encseq)
Returns true if encseq has description support.
bool               gt_encseq_has_md5_support(const GtEncseq *encseq)
Returns true if encseq has MD5 support.
GtUword            gt_encseq_seqstartpos(const GtEncseq *encseq,
                                        GtUword seqnum)
Returns the start position of the seqnum-th sequence in the encseq.
   Requires multiple sequence support enabled in encseq.
GtUword            gt_encseq_seqnum(const GtEncseq *encseq,
                                   GtUword position)
Returns the sequence number from the given position for a given
   GtEncseq encseq.
const char*        gt_encseq_description(const GtEncseq *encseq,
                                        GtUword *desclen,
                                        GtUword seqnum)
Returns a pointer to the description of the seqnum-th sequence in the
   encseq. The length of the returned string is written to the
   location pointed at by desclen.
   The returned description pointer is not \0-terminated!
   Requires description support enabled in encseq.
const GtStrArray*  gt_encseq_filenames(const GtEncseq *encseq)
Returns a GtStrArray of the names of the original sequence files
   contained in encseq.
GtUword            gt_encseq_num_of_files(const GtEncseq *encseq)
Returns the number of files contained in encseq.
GtUint64           gt_encseq_effective_filelength(const GtEncseq *encseq,
                                                 GtUword filenum)
Returns the effective length (sum of sequence lengths and separators
   between them) of the filenum-th file contained in encseq.
GtUword            gt_encseq_filestartpos(const GtEncseq *encseq,
                                         GtUword filenum)
Returns the start position of the sequences of the  filenum-th file in the
   encseq. Requires multiple file support enabled in encseq.
GtUword            gt_encseq_filenum(const GtEncseq *encseq,
                                    GtUword position)
Returns the file number from the given position for a given
   GtEncseq encseq.
GtUword            gt_encseq_filenum_first_seqnum(const GtEncseq *encseq,
                                                 GtUword filenum)
Returns the first sequence number of the sequences in file filenum for a
   given GtEncseq encseq.
GtAlphabet*        gt_encseq_alphabet(const GtEncseq *encseq)
Returns the GtAlphabet associated with encseq.
int                gt_encseq_mirror(GtEncseq *encseq, GtError *err)
Extends encseq  by virtual reverse complement sequences.
   Returns 0 if mirroring has been successfully enabled, otherwise -1.
   err is set accordingly.
void               gt_encseq_unmirror(GtEncseq *encseq)
Removes virtual reverse complement sequences added by
   gt_encseq_mirror().
bool               gt_encseq_is_mirrored(const GtEncseq *encseq)
Returns true if encseq contains virtual reverse complement sequences as
   added by gt_encseq_mirror().
GtUword            gt_encseq_version(const GtEncseq *encseq)
Returns the version number of the file representation of encseq if it
   exists, or 0 if it was not mapped from a file.
bool               gt_encseq_is_64_bit(const GtEncseq *encseq)
Returns TRUE if encseq was created on a 64-bit system.
void               gt_encseq_delete(GtEncseq *encseq)
Deletes encseq and frees all associated space.
Class GtEncseqBuilder
 The GtEncseqBuilder class creates GtEncseq objects by constructing
   uncompressed, encoded string copies in memory. 
GtEncseqBuilder*   gt_encseq_builder_new(GtAlphabet *alpha)
Creates a new GtEncseqBuilder using the alphabet alpha as a basis for
   on-the-fly encoding of sequences in memory.
void               gt_encseq_builder_enable_description_support(
                                                           GtEncseqBuilder *eb)
Enables support for retrieving descriptions from the encoded sequence
   to be built by eb. Requires additional memory to hold the descriptions and
   a position index.
   Activated by default.
void               gt_encseq_builder_disable_description_support(
                                                           GtEncseqBuilder *eb)
Disables support for retrieving descriptions from the encoded sequence
   to be built by eb. Disabling this support will result in an error when
   trying to call the method gt_encseq_description() on the
   GtEncseq object created by eb.
void               gt_encseq_builder_enable_multiseq_support(
                                                           GtEncseqBuilder *eb)
Enables support for random access to multiple sequences in the encoded
   sequence to be built by eb. Requires additional memory for an index of
   starting positions. Activated by default.
void               gt_encseq_builder_disable_multiseq_support(
                                                           GtEncseqBuilder *eb)
Disables support for random access to multiple sequences in the encoded
   sequence to be built by eb. Disabling this support will result in an
   error when trying to call the method gt_encseq_seqlength() or
   gt_encseq_seqstartpos() on the GtEncseq object created by eb.
void               gt_encseq_builder_create_esq_tab(GtEncseqBuilder *eb)
Enables creation of the .esq table containing the encoded sequence itself. Naturally, enabled by default.
void               gt_encseq_builder_do_not_create_esq_tab(GtEncseqBuilder *eb)
Disables creation of the .esq table.
void               gt_encseq_builder_create_des_tab(GtEncseqBuilder *eb)
Enables creation of the .des table containing sequence descriptions.
void               gt_encseq_builder_do_not_create_des_tab(GtEncseqBuilder *eb)
Disables creation of the .des table.
void               gt_encseq_builder_create_ssp_tab(GtEncseqBuilder *eb)
Enables creation of the .ssp table containing indexes for multiple sequences.
void               gt_encseq_builder_do_not_create_ssp_tab(GtEncseqBuilder *eb)
Disables creation of the .ssp table.
void               gt_encseq_builder_create_sds_tab(GtEncseqBuilder *eb)
Enables creation of the .sds table containing indexes for sequence descriptions.
void               gt_encseq_builder_do_not_create_sds_tab(GtEncseqBuilder *eb)
Disables creation of the .sds table.
void               gt_encseq_builder_add_cstr(GtEncseqBuilder *eb,
                                             const char *str,
                                             GtUword strlen,
                                             const char *desc)
Adds a sequence given as a C string str of length strlen to the
   encoded sequence to be built by eb. Additionally, a description can be
   given (desc). If description support is enabled, this must not be NULL.
   A copy will be made during the addition process and the sequence will
   be encoded using the alphabet set at the construction time of eb. Thus it
   must only contain symbols compatible with the alphabet.
void               gt_encseq_builder_add_str(GtEncseqBuilder *eb, GtStr *str,
                                           const char *desc)
Adds a sequence given as a GtStr str to the encoded sequence to be built
   by eb. Additionally, a description can be given. If description support
   is enabled, desc must not be NULL.
   A copy will be made during the addition process and the sequence will
   be encoded using the alphabet set at the construction time of eb. Thus it
   must only contain symbols compatible with the alphabet.
void               gt_encseq_builder_add_encoded(GtEncseqBuilder *eb,
                                               const GtUchar *str,
                                               GtUword strlen,
                                               const char *desc)
Adds a sequence given as a pre-encoded string  str of length strlen to
   the encoded sequence to be built by eb. str must be encoded using the
   alphabet set at the construction time of eb. str is not allowed to
   include sequence separators. Does not take ownership of str.
   Additionally, a description desc can be given. If description support
   is enabled, this must not be NULL.
void               gt_encseq_builder_add_encoded_own(GtEncseqBuilder *eb,
                                                   const GtUchar *str,
                                                   GtUword strlen,
                                                   const char *desc)
Adds a sequence given as a pre-encoded string  str of length strlen to
   the encoded sequence to be built by eb. str must be encoded using the
   alphabet set at the construction time of eb.
   Always creates a copy of str, so it can be used with memory that is to be
   freed immediately after adding.
   Additionally, a description desc can be given. If description support
   is enabled, this must not be NULL.
void               gt_encseq_builder_add_multiple_encoded(GtEncseqBuilder *eb,
                                                         const GtUchar *str,
                                                         GtUword strlen)
Adds a sequence given as a pre-encoded string  str of length strlen to
   the encoded sequence to be built by eb. str must be encoded using the
   alphabet set at the construction time of eb. str may include
   sequence separators. Does not take ownership of str.
void               gt_encseq_builder_set_logger(GtEncseqBuilder*, GtLogger *l)
Sets the logger to use by ee during encoding to l. Default is NULL (no
   logging).
GtEncseq*          gt_encseq_builder_build(GtEncseqBuilder *eb, GtError *err)
Creates a new GtEncseq from the sequences added to eb.
   Returns a GtEncseq instance on success, or NULL on error.
   If an error occurred, err is set accordingly.
   The state of eb is reset to empty after successful creation of a new
   GtEncseq (like having called gt_encseq_builder_reset()).
void               gt_encseq_builder_reset(GtEncseqBuilder *eb)
Clears all added sequences and descriptions, resetting eb to a state
   similar to the state immediately after its initial creation.
void               gt_encseq_builder_delete(GtEncseqBuilder *eb)
Deletes eb.
Class GtEncseqEncoder
 The GtEncseqEncoder class creates objects encapsulating a parameter
   set for conversion from sequence files into encoded sequence files on
   secondary storage. 
GtEncseqEncoder*   gt_encseq_encoder_new(void)
Creates a new GtEncseqEncoder.
void               gt_encseq_encoder_set_timer(GtEncseqEncoder *ee, GtTimer *t)
Sets t to be the timer for ee. Default is NULL (no progress
reporting).
GtTimer*           gt_encseq_encoder_get_timer(const GtEncseqEncoder *ee)
Returns the timer set for ee.
int                gt_encseq_encoder_use_representation(GtEncseqEncoder *ee,
                                                      const char *sat,
                                                      GtError *err)
Sets the representation of ee to sat which must be one of 'direct',
   'bytecompress', 'bit', 'uchar', 'ushort' or 'uint32'. Returns 0 on success,
   and a negative value on error (err is set accordingly).
GtStr*             gt_encseq_encoder_representation(const GtEncseqEncoder *ee)
Returns the representation requested for ee.
int                gt_encseq_encoder_use_symbolmap_file(GtEncseqEncoder *ee,
                                                      const char *smap,
                                                      GtError *err)
Sets the symbol map file to use in ee to smap which must a valid
   alphabet description file. Returns 0 on success, and a negative value on
   error (err is set accordingly). Default is NULL (no alphabet
   transformation).
const char*        gt_encseq_encoder_symbolmap_file(const GtEncseqEncoder *ee)
Returns the symbol map file requested for ee.
void               gt_encseq_encoder_set_logger(GtEncseqEncoder *ee,
                                              GtLogger *l)
Sets the logger to use by ee during encoding to l. Default is NULL (no
   logging).
void               gt_encseq_encoder_enable_description_support(
                                                           GtEncseqEncoder *ee)
Enables support for retrieving descriptions from the encoded sequence
   encoded by ee. That is, the .des and .sds tables are created.
   This is a prerequisite for being able to activate description support in
   gt_encseq_loader_require_description_support(). Activated by default.
void               gt_encseq_encoder_disable_description_support(
                                                           GtEncseqEncoder *ee)
Disables support for retrieving descriptions from the encoded sequence
   encoded by ee. That is, the .des and .sds tables are not created.
   Encoded sequences created without this support will not be able to be
   loaded via a GtEncseqLoader with
   gt_encseq_loader_require_description_support() enabled.
void               gt_encseq_encoder_enable_multiseq_support(
                                                           GtEncseqEncoder *ee)
Enables support for random access to multiple sequences in the encoded
   sequence encoded by ee. That is, the .ssp table is created.
   This is a prerequisite for being able to activate description support in
   gt_encseq_loader_require_multiseq_support(). Activated by default.
void               gt_encseq_encoder_disable_multiseq_support(
                                                           GtEncseqEncoder *ee)
Disables support for random access to multiple sequences in the encoded
   sequence encoded by ee. That is, the .ssp table is not created.
   Encoded sequences created without this support will not be able to be
   loaded via a GtEncseqLoader with
   gt_encseq_loader_require_multiseq_support() enabled.
void               gt_encseq_encoder_enable_lossless_support(
                                                           GtEncseqEncoder *ee)
Enables support for lossless reproduction of the original sequence, regardless of alphabet transformations that may apply. Deactivated by default.
void               gt_encseq_encoder_disable_lossless_support(
                                                           GtEncseqEncoder *ee)
Enables support for lossless reproduction of the original sequence,
   regardless of alphabet transformations that may apply. Encoded sequences
   created without this support will not be able to be loaded via a
   GtEncseqLoader with gt_encseq_loader_require_lossless_support()
   enabled.
void               gt_encseq_encoder_enable_md5_support(GtEncseqEncoder *ee)
Enables support for quick MD5 indexing of the sequences in ee. Activated by
   default.
void               gt_encseq_encoder_disable_md5_support(GtEncseqEncoder *ee)
Enables support for quick MD5 indexing of the sequences in ee. Encoded
   sequences created without this support will not be able to be loaded via
   a GtEncseqLoader with gt_encseq_loader_require_md5_support() enabled.
void               gt_encseq_encoder_create_des_tab(GtEncseqEncoder *ee)
Enables creation of the .des table containing sequence descriptions. Enabled by default.
void               gt_encseq_encoder_do_not_create_des_tab(GtEncseqEncoder *ee)
Disables creation of the .des table.
bool               gt_encseq_encoder_des_tab_requested(
                                                     const GtEncseqEncoder *ee)
Returns true if the creation of the .des table has been requested,
   false otherwise.
void               gt_encseq_encoder_create_ssp_tab(GtEncseqEncoder *ee)
Enables creation of the .ssp table containing indexes for multiple sequences. Enabled by default.
void               gt_encseq_encoder_do_not_create_ssp_tab(GtEncseqEncoder *ee)
Disables creation of the .ssp table.
bool               gt_encseq_encoder_ssp_tab_requested(
                                                     const GtEncseqEncoder *ee)
Returns true if the creation of the .ssp table has been requested,
   false otherwise.
void               gt_encseq_encoder_create_sds_tab(GtEncseqEncoder *ee)
Enables creation of the .sds table containing indexes for sequence descriptions. Enabled by default.
void               gt_encseq_encoder_do_not_create_sds_tab(GtEncseqEncoder *ee)
Disables creation of the .sds table.
bool               gt_encseq_encoder_sds_tab_requested(
                                                     const GtEncseqEncoder *ee)
Returns true if the creation of the .sds table has been requested,
   false otherwise.
void               gt_encseq_encoder_create_md5_tab(GtEncseqEncoder *ee)
Enables creation of the .md5 table containing MD5 sums. Enabled by default.
void               gt_encseq_encoder_do_not_create_md5_tab(GtEncseqEncoder *ee)
Disables creation of the .md5 table.
bool               gt_encseq_encoder_md5_tab_requested(
                                                     const GtEncseqEncoder *ee)
Returns true if the creation of the .md5 table has been requested,
   false otherwise.
void               gt_encseq_encoder_set_input_dna(GtEncseqEncoder *ee)
Sets the sequence input type for ee to DNA.
bool               gt_encseq_encoder_is_input_dna(GtEncseqEncoder *ee)
Returns true if the input sequence has been defined as being DNA.
void               gt_encseq_encoder_set_input_protein(GtEncseqEncoder *ee)
Sets the sequence input type for ee to protein/amino acids.
bool               gt_encseq_encoder_is_input_protein(GtEncseqEncoder *ee)
Returns true if the input sequence has been defined as being protein.
void               gt_encseq_encoder_clip_desc(GtEncseqEncoder *ee)
Makes ee ignore all description suffixes after the first whitespace
   character per description (as defined via isspace(3)).
bool               gt_encseq_encoder_are_descs_clipped(GtEncseqEncoder *ee)
Returns true if ee clips all descriptions after the first whitespace.
void               gt_encseq_encoder_enable_dust(GtEncseqEncoder *ee, bool echo,
                                                GtUword ws, double thresh,
                                                GtUword linker)
Enables masking of low-complexity regions according to the dust algorithm.
int                gt_encseq_encoder_encode(GtEncseqEncoder *ee,
                                          GtStrArray *seqfiles,
                                          const char *indexname,
                                          GtError *err)
Encodes the sequence files given in seqfiles using the settings in ee
   and indexname as the prefix for the index tables. Returns 0 on success, or
   a negative value on error (err is set accordingly).
void               gt_encseq_encoder_delete(GtEncseqEncoder *ee)
Deletes ee.
Class GtEncseqLoader
 The GtEncseqLoader class creates GtEncseq objects by mapping index files
   from secondary storage into memory. 
GtEncseqLoader*    gt_encseq_loader_new(void)
Creates a new GtEncseqLoader.
void               gt_encseq_loader_enable_autosupport(GtEncseqLoader *el)
Enables auto-discovery of supported features when loading an encoded
   sequence. That is, if a file with indexname.suffix exists which
   is named like a table file, it is loaded automatically.
   Use gt_encseq_has_multiseq_support() etc. to query for these capabilities.
void               gt_encseq_loader_disable_autosupport(GtEncseqLoader *el)
Disables auto-discovery of supported features.
void               gt_encseq_loader_require_description_support(
                                                            GtEncseqLoader *el)
Enables support for retrieving descriptions from the encoded sequence
   to be loaded by el. That is, the .des and .sds tables must be present.
   For example, these tables are created by having enabled the
   gt_encseq_encoder_enable_description_support() option when encoding.
   Activated by default.
void               gt_encseq_loader_drop_description_support(GtEncseqLoader *el)
Disables support for retrieving descriptions from the encoded sequence
   to be loaded by el. That is, the .des and .sds tables need not be present.
   However, disabling this support will result in an error when trying to call
   the method gt_encseq_description() on the GtEncseq
   object created by el.
void               gt_encseq_loader_require_multiseq_support(GtEncseqLoader *el)
Enables support for random access to multiple sequences in the encoded
   sequence to be loaded by el. That is, the .ssp table must be present.
   For example, this table is created by having enabled the
   gt_encseq_encoder_enable_multiseq_support() option when encoding.
   Activated by default.
void               gt_encseq_loader_drop_multiseq_support(GtEncseqLoader *el)
Disables support for random access to multiple sequences in the encoded
   sequence to be loaded by el. That is, the .ssp table needs not be present.
   However, disabling this support will result in an error when trying to call
   the method gt_encseq_seqlength() and gt_encseq_seqstartpos() on
   the GtEncseq object created by el.
void               gt_encseq_loader_require_lossless_support(GtEncseqLoader *el)
Enables support for lossless reproduction of the original sequence
   in the encoded sequence to be loaded by el. That is, the .ois table
   must be present.
   For example, this table is created by having enabled the
   gt_encseq_encoder_enable_lossless_support() option when encoding.
   Deactivated by default.
void               gt_encseq_loader_drop_lossless_support(GtEncseqLoader *el)
Disables support for lossless reproduction of the original sequence
   in the encoded sequence to be loaded by el. That is, the .ois table
   needs not be present.
   However, disabling this support may result in a reduced alphabet
   representation when accessing decoded characters.
void               gt_encseq_loader_require_md5_support(GtEncseqLoader *el)
Enables support for quick retrieval of the MD5 sums for the sequences in the
   encoded sequence to be loaded by el. That is, the .md5 table must be
   present. For example, this table is created by having enabled the
   gt_encseq_encoder_enable_md5_support() option when encoding.
   Activated by default.
void               gt_encseq_loader_drop_md5_support(GtEncseqLoader *el)
Disables support for quick retrieval of the MD5 sums for the sequences in the
   encoded sequence to be loaded by el. That is, the .md5 table needs not be
   present.
void               gt_encseq_loader_require_des_tab(GtEncseqLoader *el)
Requires presence of the .des table containing sequence descriptions. Enabled by default.
void               gt_encseq_loader_do_not_require_des_tab(GtEncseqLoader *el)
Disables requirement of the .des table for loading a GtEncseq
   using el.
bool               gt_encseq_loader_des_tab_required(const GtEncseqLoader *el)
Returns true if a .des table must be present for loading to succeed.
void               gt_encseq_loader_require_ssp_tab(GtEncseqLoader *el)
Requires presence of the .ssp table containing indexes for multiple sequences. Enabled by default.
void               gt_encseq_loader_do_not_require_ssp_tab(GtEncseqLoader *el)
Disables requirement of the .ssp table for loading a GtEncseq
   using el.
bool               gt_encseq_loader_ssp_tab_required(const GtEncseqLoader *el)
Returns true if a .ssp table must be present for loading to succeed.
void               gt_encseq_loader_require_sds_tab(GtEncseqLoader *el)
Requires presence of the .sds table containing indexes for sequence descriptions. Enabled by default.
void               gt_encseq_loader_do_not_require_sds_tab(GtEncseqLoader *el)
Disables requirement of the .sds table for loading a GtEncseq
   using el.
bool               gt_encseq_loader_sds_tab_required(const GtEncseqLoader *el)
Returns true if a .sds table must be present for loading to succeed.
void               gt_encseq_loader_set_logger(GtEncseqLoader *el, GtLogger *l)
Sets the logger to use by ee during encoding to l. Default is NULL (no
   logging).
void               gt_encseq_loader_mirror(GtEncseqLoader *el)
Enables loading of a sequence using el with mirroring enabled from the
   start. Identical to invoking gt_encseq_mirror() directly after loading.
void               gt_encseq_loader_do_not_mirror(GtEncseqLoader *el)
Disables loading of a sequence using el with mirroring enabled right from
   the start.
GtEncseq*          gt_encseq_loader_load(GtEncseqLoader *el,
                                        const char *indexname,
                                        GtError *err)
Attempts to map the index files as specified by indexname using the options
   set in el using this interface. Returns a GtEncseq instance
   on success, or NULL on error. If an error occurred, err is set
   accordingly.
void               gt_encseq_loader_delete(GtEncseqLoader *el)
Deletes el.
Class GtEncseqReader
 The GtEncseqReader class represents the current state of a
   sequential scan of a GtEncseq region as an iterator. 
void               gt_encseq_reader_reinit_with_readmode(GtEncseqReader *esr,
                                                      const GtEncseq *encseq,
                                                      GtReadmode readmode,
                                                      GtUword startpos)
Reinitializes the given esr with the values as described in
   gt_encseq_create_reader_with_readmode().
GtUchar            gt_encseq_reader_next_encoded_char(GtEncseqReader *esr)
Returns the next encoded character from current position of esr, advancing
   the iterator by one position.
char               gt_encseq_reader_next_decoded_char(GtEncseqReader *esr)
Returns the next decoded character from current position of esr, advancing
   the iterator by one position.
void               gt_encseq_reader_delete(GtEncseqReader *esr)
Deletes esr, freeing all associated space.
Class GtError
   This class is used for the handling of user errors in GenomeTools.
   Thereby, the actual GtError object is used to store the error message
   while it is signaled by the return value of the called function, if an error
   occurred.
   By convention in GenomeTools, the GtError object is always passed into
   a function as the last parameter and -1 (or NULL for constructors) is used
   as return value to indicate that an error occurred.
   Success is usually indicated by 0 as return value or via a non-NULL object
   pointer for constructors.
   It is possible to use NULL as an GtError object, if one is not interested
   in the actual error message.
   Functions which do not get an GtError object cannot fail due to a user
   error and it is not necessary to check their return code for an error
   condition.
GtError*    gt_error_new(void)
Return a new GtError object
#define gt_error_check(err)
Insert an assertion to check that the error err is not set or is NULL.
   This macro should be used at the beginning of every routine which has an
   GtError* argument to make sure the error propagation has been coded
   correctly.
void         gt_error_set(GtError *err, const char *format, ...)
Set the error message stored in err according to format (as in
   printf(3)).
void         gt_error_vset(GtError *err, const char *format, va_list ap)
Set the error message stored in err according to format (as in
   vprintf(3)).
void         gt_error_set_nonvariadic(GtError *err, const char *msg)
Set the error message stored in err to msg.
bool         gt_error_is_set(const GtError *err)
Return true if the error err is set, false otherwise.
void         gt_error_unset(GtError *err)
Unset the error err.
const char*  gt_error_get(const GtError *err)
Return the error string stored in err (the error must be set).
void         gt_error_set_progname(GtError *err, const char *progname)
Sets the program name assigned to err to progname.
const char*  gt_error_get_progname(const GtError *err)
Returns the program name assigned to err.
void         gt_error_delete(GtError *err)
Delete the error object err.
Class GtExtractFeatureStream
 Implements the GtNodeStream interface. A GtExtractFeatureStream extracts
   the corresponding sequences of features. 
GtNodeStream*  gt_extract_feature_stream_new(GtNodeStream *in_stream,
                                            GtRegionMapping *region_Mapping,
                                            const char *type, bool join,
                                            bool translate, bool seqid,
                                            bool target, GtUword width,
                                            GtFile *outfp)
Create a GtExtractFeatureStream* which extracts the corresponding sequences
   of feature nodes (of the given type) it retrieves from in_stream and
   writes them in FASTA format (with the given width) to outfp. If join is
   true, features of the given type are joined together before the sequence
   is extracted. If translate is true, the sequences are translated into
   amino acid sequences before they are written to outfp. If seqid is true
   the sequence IDs of the extracted features are added to the FASTA header.
   If target is true the target IDs of the extracted features are added to
   the FASTA header. Takes ownership of region_mapping!
Class GtFastaReader
 GtFastaReader is an interface to iteratively process the sequences in
   a FASTA file, with multiple implementations. 
int  GtFastaReaderProcDescription(const char *description,
                                            GtUword length, void *data,
                                            GtError*)
Gets called for each description (the start of a fasta entry).
int  GtFastaReaderProcSequencePart(const char *seqpart,
                                             GtUword length, void *data,
                                             GtError*)
Gets called for each sequence part of a fasta entry.
int  GtFastaReaderProcSequenceLength(GtUword, void *data,
                                               GtError*)
Gets called after a fasta entry has been read.
int           gt_fasta_reader_run(GtFastaReader *fr,
                                 GtFastaReaderProcDescription,
                                 GtFastaReaderProcSequencePart,
                                 GtFastaReaderProcSequenceLength, void *data,
                                 GtError*)
Run fr with the given handler functions and data for common storage.
   A value less than zero is returned on error and err is set accordingly.
void          gt_fasta_reader_delete(GtFastaReader *fr)
Delete fr.
Class GtFeatureInStream
GtNodeStream*  gt_feature_in_stream_new(GtFeatureIndex *fi)
Create a new GtFeatureInStream using the given GtFeatureIndex as the
   source of a node stream.
void  gt_feature_in_stream_use_orig_ranges(GtFeatureInStream *stream)
Instruct stream to deliver GtRegionNode objects whose ranges are
   specified such as with ##sequence-region pragmas, rather than those
   inferred from the features. Specifically, use
   gt_feature_index_get_orig_range_for_seqid on the underlying feature
   index rather than the default gt_feature_index_get_range_for_seqid.
Class GtFeatureIndex
 This interface represents a searchable container for GtFeatureNode objects,
   typically root nodes of larger structures. How storage and searching takes
   place is left to the discretion of the implementing class.
   Output from a gt_feature_index_get_features_*() method should always
   be sorted by feature start position. 
int          gt_feature_index_add_region_node(GtFeatureIndex *feature_index,
                                             GtRegionNode *region_node,
                                             GtError *err)
Add region_node to feature_index.
int          gt_feature_index_add_feature_node(GtFeatureIndex *feature_index,
                                              GtFeatureNode *feature_node,
                                              GtError *err)
Add feature_node to feature_index, associating it with a sequence
   region denoted by its identifier string.
int          gt_feature_index_remove_node(GtFeatureIndex *feature_index,
                                         GtFeatureNode *node,
                                         GtError *err)
Removes node genome_node from feature_index.
int          gt_feature_index_add_gff3file(GtFeatureIndex *feature_index,
                                          const char *gff3file, GtError *err)
Add all features contained in gff3file to feature_index, if gff3file is
   valid. Otherwise, feature_index is not changed and err is set.
GtArray*     gt_feature_index_get_features_for_seqid(GtFeatureIndex*,
                                                    const char *seqid,
                                                    GtError *err)
Returns an array of GtFeatureNodes associated with a given sequence region
   identifier seqid.
int          gt_feature_index_get_features_for_range(GtFeatureIndex
                                                    *feature_index,
                                                    GtArray *results,
                                                    const char *seqid,
                                                    const GtRange *range,
                                                    GtError*)
Look up genome features in feature_index for sequence region seqid in
   range and store them in results.
char*        gt_feature_index_get_first_seqid(const GtFeatureIndex
                                             *feature_index,
                                             GtError *err)
Returns the first sequence region identifier added to feature_index.
GtStrArray*  gt_feature_index_get_seqids(const GtFeatureIndex *feature_index,
                                        GtError *err)
Returns a GtStrArray of all sequence region identifiers contained in
   feature_index (in alphabetical order).
int          gt_feature_index_get_range_for_seqid(GtFeatureIndex *feature_index,
                                                 GtRange *range,
                                                 const char *seqid,
                                                 GtError *err)
Writes the range of all features contained in the feature_index for
   region identifier seqid to the GtRange pointer range.
int          gt_feature_index_get_orig_range_for_seqid(GtFeatureIndex
                                                                *feature_index,
                                                      GtRange *range,
                                                      const char *seqid,
                                                      GtError *err)
Writes the range of the whole sequence region contained in the
   feature_index for region identifier seqid to the GtRange
   pointer range.
int          gt_feature_index_has_seqid(const GtFeatureIndex *feature_index,
                                       bool *has_seqid,
                                       const char *seqid,
                                       GtError *err)
Returns has_seqid  to true if the sequence region identified by seqid
   has been registered in the feature_index.
int          gt_feature_index_save(GtFeatureIndex *feature_index, GtError *err)
Calls the save function for the given feature_index. The save functions
   must be defined, otherwise the method fails with an assertion (for example,
   the memory based feature index does not have a save function) .
void         gt_feature_index_delete(GtFeatureIndex*)
Deletes the feature_index and all its referenced features.
Class GtFeatureIndexMemory
 The GtFeatureIndexMemory class implements a GtFeatureIndex in memory.
   Features are organized by region node. Each region node collects its
   feature nodes in an interval tree structure, which allows for efficient
   range queries. 
GtFeatureIndex*  gt_feature_index_memory_new(void)
Creates a new GtFeatureIndexMemory object.
GtFeatureNode*   gt_feature_index_memory_get_node_by_ptr(GtFeatureIndexMemory*,
                                                        GtFeatureNode *ptr,
                                                        GtError *err)
Returns ptr if it is a valid node indexed in GtFeatureIndexMemory.
   Otherwise NULL is returned and err is set accordingly.
Class GtFeatureNode
 Implements the GtGenomeNode interface. A single feature node corresponds
   to a GFF3 feature line (i.e., a line which does not start with #).
   Part-of relationships (which are realized in GFF3 with the Parent and ID
   attributes) are realized in the C API with the
   gt_feature_node_add_child() method.
Besides the ``mere'' feature nodes two ``special'' feature nodes exist: multi-features and pseudo-features.
Multi-features represent features which span multiple lines (it is indicated in GFF3 files by the fact, that each line has the same ID attribute).
   To check if a feature is a multi-feature use the method
   gt_feature_node_is_multi().
   Multi-features are connected via a ``representative''. That is, two features
   are part of the same multi-feature if they have the same representative.
   The feature node representative can be be retrieved via the
   gt_feature_node_get_multi_representative() method.
Pseudo-features became a technical necessity to be able to pass related top-level features as a single entity through the streaming machinery. There are two cases in which a pseudo-feature has to be introduced.
First, if a multi-feature has no parent. In this case all features which comprise the multi-feature become the children of a pseudo-feature.
Second, if two or more top-level features have the same children (and are thereby connected). In this case all these top-level features become the children of a pseudo-feature.
It should be clear from the explanation above that pseudo-features make only sense as top-level features (a fact which is enforced in the code).
Pseudo-features are typically ignored during a traversal to give the illusion that they do not exist.
GtGenomeNode*   gt_feature_node_new(GtStr *seqid, const char *type,
                                   GtUword start, GtUword end,
                                   GtStrand strand)
Return an new GtFeatureNode object on sequence with ID seqid and type
   type which lies from start to end on strand strand.
   The GtFeatureNode* stores a new reference to seqid, so make sure you do
   not modify the original seqid afterwards!
   start and end always refer to the forward strand, therefore start has
   to be smaller or equal than end.
GtGenomeNode*   gt_feature_node_new_pseudo(GtStr *seqid, GtUword start,
                                          GtUword end, GtStrand strand)
Return a new pseudo-GtFeatureNode object on sequence with ID seqid which
   lies from start to end on strand strand. Pseudo-features do not have a
   type.  The GtFeatureNode  stores a new reference to seqid, so make sure
   you do not modify the original seqid afterwards.  start and end always
   refer to the forward strand, therefore start has to be smaller or equal
   than end.
GtGenomeNode*   gt_feature_node_new_pseudo_template(GtFeatureNode *feature_node)
Return a new pseudo-GtFeatureNode object which uses feature_node as
   template.  That is, the sequence ID, range, strand, and source are taken from
   feature_node.
GtGenomeNode*   gt_feature_node_new_standard_gene(void)
Return the ``standard gene'' (mainly for testing purposes).
void            gt_feature_node_add_child(GtFeatureNode *parent,
                                         GtFeatureNode *child)
Add child feature node to parent feature node.
   parent takes ownership of child.
const char*     gt_feature_node_get_source(const GtFeatureNode *feature_node)
Return the source of feature_node. If no source has been set, "." is
   returned. Corresponds to column 2 of GFF3 feature lines.
void            gt_feature_node_set_source(GtFeatureNode *feature_node,
                                          GtStr *source)
Set the source of feature_node. Stores a new reference to source.
   Corresponds to column 2 of GFF3 feature lines.
bool            gt_feature_node_has_source(const GtFeatureNode *feature_node)
Return true if feature_node has a defined source (i.e., on different
   from "."). false otherwise.
const char*     gt_feature_node_get_type(const GtFeatureNode *feature_node)
Return the type of feature_node. Corresponds to column 3 of GFF3 feature
   lines.
void            gt_feature_node_set_type(GtFeatureNode *feature_node,
                                        const char *type)
Set the type of feature_node to type.
bool            gt_feature_node_has_type(GtFeatureNode *feature_node,
                                        const char *type)
Return true if feature_node has given type, false otherwise.
GtUword         gt_feature_node_number_of_children(const GtFeatureNode
                                                  *feature_node)
Return the number of children for given feature_node.
GtUword         gt_feature_node_number_of_children_of_type(const GtFeatureNode
                                                          *parent,
                                                          const GtFeatureNode
                                                          *node)
Return the number of children of type node
   for given GtFeatureNode parent.
bool            gt_feature_node_score_is_defined(const GtFeatureNode
                                                *feature_node)
Return true if the score of feature_node is defined, false
   otherwise.
float           gt_feature_node_get_score(const GtFeatureNode *feature_node)
Return the score of feature_node. The score has to be defined.
   Corresponds to column 6 of GFF3 feature lines.
void            gt_feature_node_set_score(GtFeatureNode *feature_node,
                                         float score)
Set the score of feature_node to score.
void            gt_feature_node_unset_score(GtFeatureNode *feature_node)
Unset the score of feature_node.
GtStrand        gt_feature_node_get_strand(const GtFeatureNode *feature_node)
Return the strand of feature_node. Corresponds to column 7 of GFF3
   feature lines.
void            gt_feature_node_set_strand(GtFeatureNode *feature_node,
                                          GtStrand strand)
Set the strand of feature_node to strand.
GtPhase         gt_feature_node_get_phase(const GtFeatureNode *feature_node)
Return the phase of feature_node. Corresponds to column 8 of GFF3 feature
   lines.
void            gt_feature_node_set_phase(GtFeatureNode *feature_node,
                                         GtPhase phase)
Set the phase of feature_node to phase.
const char*     gt_feature_node_get_attribute(const GtFeatureNode *feature_node,
                                             const char *name)
Return the attribute of feature_node with the given name.
   If no such attribute has been added, NULL is returned.
   The attributes are stored in column 9 of GFF3 feature lines.
GtStrArray*     gt_feature_node_get_attribute_list(const GtFeatureNode
                                                  *feature_node)
Return a string array containing the used attribute names of feature_node.
   The caller is responsible to free the returned GtStrArray*.
void            gt_feature_node_add_attribute(GtFeatureNode *feature_node,
                                             const char *tag,
                                             const char *value)
Add attribute tag=value to feature_node. tag and value must at
   least have length 1. feature_node must not contain an attribute with the
   given tag already. You should not add Parent and ID attributes, use
   gt_feature_node_add_child() to denote part-of relationships.
void            gt_feature_node_set_attribute(GtFeatureNode* feature_node,
                                             const char *tag,
                                             const char *value)
Set attribute tag to new value in feature_node, if it exists already.
   Otherwise the attribute tag=value is added to feature_node.
   tag and value must at least have length 1.
   You should not set Parent and ID attributes, use
   gt_feature_node_add_child() to denote part-of relationships.
void            gt_feature_node_remove_attribute(GtFeatureNode* feature_node,
                                                const char *tag)
Remove attribute tag from feature_node. feature_node must contain an
   attribute with the given tag already! You should not remove Parent and ID
   attributes.
void  GtFeatureNodeAttributeIterFunc(const char *attr_name,
                                               const char *attr_value,
                                               void *data)
Delivers the key (in attr_name)and value (in attr_value) of an
   attribute. The data parameter carries over arbitrary user data from the
   gt_feature_node_foreach_attribute call.
void            gt_feature_node_foreach_attribute(GtFeatureNode *feature_node,
                                            GtFeatureNodeAttributeIterFunc func,
                                            void *data)
Calls func for each attribute in feature_node. Use data to forward
   arbitrary data during traversal.
bool            gt_feature_node_is_multi(const GtFeatureNode *feature_node)
Return true if feature_node is a multi-feature, false otherwise.
bool            gt_feature_node_is_pseudo(const GtFeatureNode *feature_node)
Return true if feature_node is a pseudo-feature, false otherwise.
void            gt_feature_node_make_multi_representative(GtFeatureNode
                                                         *feature_node)
Make feature_node the representative of a multi-feature.
   Thereby feature_node becomes a multi-feature.
void            gt_feature_node_set_multi_representative(GtFeatureNode
                                                        *feature_node,
                                                        GtFeatureNode
                                                        *representative)
Set the multi-feature representative of feature_node to representative.
   Thereby feature_node becomes a multi-feature.
void            gt_feature_node_unset_multi(GtFeatureNode *feature_node)
Unset the multi-feature status of feature_node and remove its multi-feature
   representative.
GtFeatureNode*  gt_feature_node_get_multi_representative(GtFeatureNode
                                                        *feature_node)
Return the representative of the multi-feature feature_node.
bool            gt_feature_node_is_similar(const GtFeatureNode *feature_node_a,
                                          const GtFeatureNode *feature_node_b)
Returns true, if the given feature_node_a has the same seqid, feature
   type, range, strand, and phase as feature_node_b.
   Returns false otherwise.
void            gt_feature_node_mark(GtFeatureNode*)
Marks the given feature_node.
void            gt_feature_node_unmark(GtFeatureNode*)
If the given feature_node is marked it will be unmarked.
bool            gt_feature_node_contains_marked(GtFeatureNode *feature_node)
Returns true if the given feature_node graph contains a marked node.
bool            gt_feature_node_is_marked(const GtFeatureNode *feature_node)
Returns true if the (top-level) feature_node is marked.
void            gt_feature_node_remove_leaf(GtFeatureNode *tree,
                                           GtFeatureNode *leafn)
Removes the parent-child relationship between the leaf node leafn and a
   parent node tree. tree needs not be the direct parent of the leafn.
   Note that leafn is freed, use gt_genome_node_ref() to increase the
   reference count if deletion is not wanted. As a side effect, the tree
   property of tree is set back to an undefined state.
GtFeatureNode*  gt_feature_node_try_cast(GtGenomeNode *gn)
Test whether the given genome node is a feature node. If so, a pointer to the feature node is returned. If not, NULL is returned. Note that in most cases, one should implement a GtNodeVisitor to handle processing of different GtGenomeNode types.
GtFeatureNode*  gt_feature_node_cast(GtGenomeNode *gn)
Test whether the given genome node is a feature node. If so, a pointer to the feature node is returned. If not, an assertion fails.
Class GtFeatureNodeIterator
GtFeatureNodeIterator*  gt_feature_node_iterator_new(const GtFeatureNode
                                                    *feature_node)
Return a new GtFeatureNodeIterator* which performs a depth-first
   traversal of feature_node (including feature_node itself).
   It ignores pseudo-features.
GtFeatureNodeIterator*  gt_feature_node_iterator_new_direct(const GtFeatureNode
                                                           *feature_node)
Return a new GtFeatureNodeIterator* which iterates over all direct
   children of feature_node (without feature_node itself).
GtFeatureNode*          gt_feature_node_iterator_next(GtFeatureNodeIterator
                                                     *feature_node_iterator)
Return the next GtFeatureNode* in feature_node_iterator or NULL if none
   exists.
void                    gt_feature_node_iterator_delete(GtFeatureNodeIterator
                                                       *feature_node_iterator)
Delete feature_node_iterator.
Class GtFeatureOutStream
GtNodeStream*  gt_feature_out_stream_new(GtNodeStream*, GtFeatureIndex *fi)
Create a new GtFeatureOutStream which writes all passed nodes to
   GtFeatureIndex fi.
Class GtFeatureStream
GtNodeStream*  gt_feature_stream_new(GtNodeStream*, GtFeatureIndex *fi)
Create a new GtFeatureStream which writes all passed nodes to
   GtFeatureIndex fi. Note: The GtFeatureStream class is now deprecated.
   Please use the GtFeatureOutStream class instead.
Class GtFile
 This class defines (generic) files in GenomeTools. A generic file is is a
   file which either uncompressed or compressed (with gzip or bzip2).
   A NULL-pointer as generic file implies stdout. 
GtFile*      gt_file_new(const char *path, const char *mode, GtError *err)
Return a new GtFile object for the given path and open the underlying
   file handle with given mode. Returns NULL and sets err accordingly, if
   the file path could not be opened. The compression mode is determined by
   the ending of path (gzip compression if it ends with '.gz', bzip2
   compression if it ends with '.bz2', and uncompressed otherwise).
GtFile*      gt_file_ref(GtFile *file)
Increments the reference count of file.
GtFile*      gt_file_new_from_fileptr(FILE *fp)
Create a new GtFile object from a normal file pointer fp.
void         gt_file_xprintf(GtFile *file, const char *format, ...)
printf(3) for generic file.
void         gt_file_xfputs(const char *cstr, GtFile *file)
Write \0-terminated C string cstr to file. Similar to fputs(3), but
   terminates on error.
void         gt_file_xfputc(int c, GtFile *file)
Write single character c to file. Similar to fputc(3), but terminates
   on error.
int          gt_file_xfgetc(GtFile *file)
Return next character from file or EOF, if end-of-file is reached.
int          gt_file_xread(GtFile *file, void *buf, size_t nbytes)
Read up to nbytes from generic file and store result in buf, returns
   bytes read.
void         gt_file_xwrite(GtFile *file, void *buf, size_t nbytes)
Write nbytes from buf to given generic file.
void         gt_file_xrewind(GtFile *file)
Rewind the generic file.
GtFileMode   gt_file_mode_determine(const char *path)
Returns GT_FILE_MODE_GZIP if file with path ends with '.gz',
   GT_FILE_MODE_BZIP2 if it ends with '.bz2', and GT_FILE_MODE_UNCOMPRESSED
   otherwise.
const char*  gt_file_mode_suffix(GtFileMode mode)
Returns ".gz" if mode is GFM_GZIP, ".bz2" if mode is GFM_BZIP2, and ""
   otherwise.
size_t       gt_file_basename_length(const char *path)
Returns the length of the ``basename'' of path. That is, the length of path
   without '.gz' or '.bz2' suffixes.
GtFile*      gt_file_open(GtFileMode, const char *path, const char *mode,
                         GtError*)
Create a new GtFile object and open the underlying file handle, returns
   NULL and sets err if the file path could not be opened.
GtFile*      gt_file_xopen_file_mode(GtFileMode file_mode, const char *path,
                                    const char *mode)
Create a new GtFile object and open the underlying file handle, abort if
   the file path does not exist. The file_mode has to be given
   explicitly.
GtFile*      gt_file_xopen(const char *path, const char *mode)
Create a new GtFile object and open the underlying file handle. Aborts if
   the file path could not be opened. The GtFileMode is determined
   automatically via gt_file_mode_determine(path).
GtFileMode   gt_file_mode(const GtFile *file)
Returns the mode of the given file.
void         gt_file_unget_char(GtFile *file, char c)
Unget character c to file (which obviously cannot be NULL).
   Can only be used once at a time.
void         gt_file_delete(GtFile *file)
Close the underlying file handle and destroy the file object.
void         gt_file_delete_without_handle(GtFile*)
Destroy the file handle object, but do not close the underlying handle.
Class GtGFF3InStream
 Implements the GtNodeStream interface. A GtGFF3InStream parses GFF3 files
   and returns them as a stream of GtGenomeNode objects. 
GtNodeStream*  gt_gff3_in_stream_new_unsorted(int num_of_files,
                                             const char **filenames)
Return a GtGFF3InStream object which subsequently reads the num_of_files
   many GFF3 files denoted in filenames. The GFF3 files do not have to be
   sorted. If num_of_files is 0 or a file name is "-", it is read from
   stdin. The memory footprint is O(file size) in the worst-case.
GtNodeStream*  gt_gff3_in_stream_new_sorted(const char *filename)
Create a GtGFF3InStream* which reads the sorted GFF3 file denoted by
   filename. If filename is NULL, it is read from stdin.
   The memory footprint is O(1) on average.
void           gt_gff3_in_stream_check_id_attributes(GtGFF3InStream
                                                               *gff3_in_stream)
Make sure all ID attributes which are parsed by gff3_in_stream are correct.
   Increases the memory footprint to O(file size).
void           gt_gff3_in_stream_enable_tidy_mode(GtGFF3InStream
                                                               *gff3_in_stream)
Enable tidy mode for gff3_in_stream. That is, the GFF3 parser tries to tidy
   up features which would normally lead to an error.
void           gt_gff3_in_stream_enable_strict_mode(GtGFF3InStream
                                                               *gff3_in_stream)
Enable strict mode for gff3_in_stream.
void           gt_gff3_in_stream_show_progress_bar(GtGFF3InStream
                                                               *gff3_in_stream)
Show progress bar on stdout to convey the progress of parsing the GFF3
   files underlying gff3_in_stream.
GtStrArray*    gt_gff3_in_stream_get_used_types(GtNodeStream *gff3_in_stream)
Returns a GtStrArray* which contains all type names in alphabetical order
   which have been parsed by gff3_in_stream. The caller is responsible to
   free it!
void           gt_gff3_in_stream_set_type_checker(GtNodeStream *gff3_in_stream,
                                                 GtTypeChecker *type_checker)
Sets type_checker to be the type checker used in gff3_in_stream. That
   is, it will be queried when the validity of SO types is to be determined.
Class GtGFF3OutStream
 Implements the GtNodeStream interface. A GtGFF3OutStream produces GFF3
   output.
   It automatically inserts termination lines at the appropriate places. 
GtNodeStream*  gt_gff3_out_stream_new(GtNodeStream *in_stream, GtFile *outfp)
Create a GtGFF3OutStream* which uses in_stream as input.
   It shows the nodes passed through it as GFF3 on outfp.
void           gt_gff3_out_stream_set_fasta_width(GtGFF3OutStream
                                                 *gff3_out_stream,
                                                 GtUword fasta_width)
Set the width with which the FASTA sequences of GtSequenceNodes passed
   through gff3_out_stream are shown to fasta_width.
   Per default, each FASTA entry is shown on a single line.
void           gt_gff3_out_stream_retain_id_attributes(GtGFF3OutStream
                                                      *gff3_out_stream)
If this method is called upon gff3_out_stream, use the original ID
   attributes provided in the input (instead of creating new ones, which
   is the default). Memory consumption for gff3_out_stream is raised from O(1)
   to O(input_size), because bookkeeping of used IDs becomes necessary to
   avoid ID collisions.
Class GtGFF3Parser
 A GtGFF3Parser can be used to parse GFF3 files and convert them into
   GtGenomeNode objects. If the GFF3 files do not contain the encouraged
   sequence-region meta directives, the GFF3 parser introduces the corresponding
   region nodes automatically. This is a low-level class and it is usually not
   used directly. Normally, a GtGFF3InStream is used to parse GFF3 files. 
GtGFF3Parser*  gt_gff3_parser_new(GtTypeChecker *type_checker)
Return a new GtGFF3Parser object with optional type_checker. If a
   type_checker was given, the GtGFF3Parser stores a new reference to it
   internally and uses the type_checker to check types during parsing.
void           gt_gff3_parser_check_id_attributes(GtGFF3Parser *gff3_parser)
Enable ID attribute checking in gff3_parser. Thereby, the memory
   consumption of the gff3_parser becomes proportional to the input file
   size(s).
void           gt_gff3_parser_check_region_boundaries(GtGFF3Parser *gff3_parser)
Enable sequence region boundary checking in gff3_parser. That is,
   encountering features outside the sequence region boundaries will result in
   an error.
void           gt_gff3_parser_do_not_check_region_boundaries(GtGFF3Parser
                                                                  *gff3_parser)
Disable sequence region boundary checking in gff3_parser. That is,
   features outside the sequence region boundaries will be permitted.
void           gt_gff3_parser_set_offset(GtGFF3Parser *gff3_parser,
                                        GtWord offset)
Transform all features parsed by gff3_parser by the given offset.
void           gt_gff3_parser_set_type_checker(GtGFF3Parser *gff3_parser,
                                              GtTypeChecker *type_checker)
Set type_checker used by gff3_parser.
void           gt_gff3_parser_set_xrf_checker(GtGFF3Parser *gff3_parser,
                                             GtXRFChecker *xrf_checker)
Set xrf_checker used by gff3_parser.
void           gt_gff3_parser_enable_tidy_mode(GtGFF3Parser *gff3_parser)
Enable the tidy mode in gff3_parser. In tidy mode the gff3_parser parser
   tries to tidy up features which would normally lead to a parse error.
int            gt_gff3_parser_parse_genome_nodes(GtGFF3Parser *gff3_parser,
                                                int *status_code,
                                                GtQueue *genome_nodes,
                                                GtCstrTable *used_types,
                                                GtStr *filenamestr,
                                                GtUint64 *line_number,
                                                GtFile *fpin,
                                                GtError *err)
Use gff3_parser to parse genome nodes from file pointer fpin.
   status_code is set to 0 if at least one genome node was created (and stored
   in genome_nodes) and to EOF if no further genome nodes could be parsed
   from fpin. Every encountered (genome feature) type is recorded in the
   C string table used_types. The parser uses the given filenamestr to
   store the file name of fpin in the created genome nodes or to give the
   correct filename in error messages, if necessary.
   line_number is increased accordingly during parsing and has to be set to 0
   before parsing a new fpin.
   If an error occurs during parsing this method returns -1 and sets err
   accordingly.
void           gt_gff3_parser_reset(GtGFF3Parser *gff3_parser)
Reset the gff3_parser (necessary if the input file is switched).
void           gt_gff3_parser_delete(GtGFF3Parser *gff3_parser)
Delete the gff3_parser.
Class GtGFF3Visitor
 Implements the GtNodeVisitor interface with a visitor that produces GFF3
   output. This is a low-level class and it is usually not used directly.
   Normally, a GtGFF3OutStream is used to produce GFF3 output. 
GtNodeVisitor*  gt_gff3_visitor_new(GtFile *outfp)
Create a new GtNodeVisitor* which writes the output it produces to the
   given output file pointer outfp. If outfp is NULL, the output is
   written to stdout.
void            gt_gff3_visitor_set_fasta_width(GtGFF3Visitor *gff3_visitor,
                                               GtUword fasta_width)
Set the width with which the FASTA sequences of GtSequenceNodes visited
   by gff3_visitor are shown to fasta_width.
   Per default, each FASTA entry is shown on a single line.
void            gt_gff3_visitor_retain_id_attributes(GtGFF3Visitor
                                                    *gff3_visitor)
Retain the original ID attributes (instead of creating new ones), if
   possible.  Memory consumption for gff3_visitor is raised from O(1) to
   O(input_size), because bookkeeping of used IDs becomes necessary to avoid
   ID collisions.
Class GtGTFInStream
 Implements the GtNodeStream interface. A GtGTFInStream parses a GTF2.2
   file and returns it as a stream of GtGenomeNode objects. 
GtNodeStream*  gt_gtf_in_stream_new(const char *filename)
Create a GtGTFInStream* which subsequently reads the GTF file with the
   given filename. If filename equals NULL, the GTF data is read from
   stdin.
Class GtGTFOutStream
 Implements the GtNodeStream interface. A GtGTFOutStream produces GTF2.2
   output. 
GtNodeStream*  gt_gtf_out_stream_new(GtNodeStream *in_stream, GtFile *outfp)
Create a GtNodeStream* which uses in_stream as input.
   It shows the nodes passed through it as GTF2.2 on outfp.
Class GtGenomeNode
 The GtGenomeNode interface. The different implementation of the
   GtGenomeNode interface represent different parts of genome annotations (as
   they are usually found in GFF3 files). 
GtGenomeNode*  gt_genome_node_ref(GtGenomeNode *genome_node)
Increase the reference count for genome_node and return it.
   genome_node must not be NULL.
GtStr*         gt_genome_node_get_seqid(GtGenomeNode *genome_node)
Return the sequence ID of genome_node.
   Corresponds to column 1 of GFF3 feature lines.
GtRange        gt_genome_node_get_range(GtGenomeNode *genome_node)
Return the genomic range of of genome_node.
   Corresponds to columns 4 and 5 of GFF3 feature lines.
GtUword        gt_genome_node_get_start(GtGenomeNode *genome_node)
Return the start of genome_node.
   Corresponds to column 4 of GFF3 feature lines.
GtUword        gt_genome_node_get_end(GtGenomeNode *genome_node)
Return the end of genome_node.
   Corresponds to column 5 of GFF3 feature lines.
GtUword        gt_genome_node_get_length(GtGenomeNode *genome_node)
Return the length of genome_node.
   Computed from column 4 and 5 of GFF3 feature lines.
const char*    gt_genome_node_get_filename(const GtGenomeNode* genome_node)
Return the filename the genome_node was read from.
   If the node did not originate from a file, an appropriate string is
   returned.
unsigned int   gt_genome_node_get_line_number(const GtGenomeNode*)
Return the line of the source file the genome_node was encountered on
   (if the node was read from a file, otherwise 0 is returned).
void           gt_genome_node_set_range(GtGenomeNode *genome_node,
                                       const GtRange *range)
Set the genomic range of genome_node to given range.
void           gt_genome_node_add_user_data(GtGenomeNode *genome_node,
                                           const char *key, void *data,
                                           GtFree free_func)
Attach a pointer to data to the genome_node using a given string as
   key. free_func is the optional destructor for data.
void*          gt_genome_node_get_user_data(const GtGenomeNode *genome_node,
                                           const char *key)
Return the pointer attached to the genome_node for a given key.
void           gt_genome_node_release_user_data(GtGenomeNode *genome_node,
                                               const char *key)
Call the destructor function associated with the user data attached to
   genome_node under the key on the attached data.
int            gt_genome_node_cmp(GtGenomeNode *genome_node_a,
                                 GtGenomeNode *genome_node_b)
Compare genome_node_a with genome_node_b and return the result (similar
   to strcmp(3)). This method is the criterion used to sort genome nodes.
void           gt_genome_nodes_sort(GtArray *nodes)
Sort node array nodes
void           gt_genome_nodes_sort_stable(GtArray *nodes)
Sort node array nodes in a stable way
int            gt_genome_node_accept(GtGenomeNode *genome_node,
                                    GtNodeVisitor *node_visitor, GtError *err)
Let genome_node accept the node_visitor.
   In the case of an error, -1 is returned and err is set accordingly.
void           gt_genome_nodes_show(GtArray *nodes, GtFile *outfp)
Outputs the nodes nodes to the output outfp.
void           gt_genome_node_delete(GtGenomeNode *genome_node)
Decrease the reference count for genome_node or delete it, if this was the
   last reference.
Class GtGraphics
 The GtGraphics interface acts as a low-level abstraction of a drawing
   surface. It is used as a common drawing object in GtCanvas and
   GtCustomTrack implementations and supports a variety of drawing operations
   for both text and basic primitive shapes. 
void    gt_graphics_draw_text(GtGraphics*, double x, double y, const char*)
Draws text in black to the right of (x,y). The coordinate y is used as
   a baseline.
void    gt_graphics_draw_text_clip(GtGraphics*, double x, double y, const char*)
Draws text in black to the right of (x,y). The coordinate y is used as
   a baseline. If the text exceeds the margins, it is clipped.
#define gt_graphics_draw_text_left(g,x,y,t)
Synonym to gt_graphics_draw_text()
void    gt_graphics_draw_text_centered(GtGraphics*, double x, double y,
                                      const char*)
Draws text in black centered at (x,y). The coordinate y is used as a
   baseline.
void    gt_graphics_draw_text_right(GtGraphics*, double x, double y,
                                   const char*)
Draws text in black to the left of (x,y). The coordinate y is used as a
   baseline.
void    gt_graphics_draw_colored_text(GtGraphics*, double x, double y,
                                     GtColor, const char*)
Draws text in a given GtColor to the right of (x,y). The coordinate y
   is used as a baseline.
double  gt_graphics_get_text_height(GtGraphics*)
Returns the height of a capital letter in pixels/points.
int  gt_graphics_set_background_color(GtGraphics*, GtColor)
Sets the background color of the GtGraphics to a specific color.
   Note that this may only be supported for bitmap output formats.
double  gt_graphics_get_text_width(GtGraphics*, const char *text)
Returns the width of the given string in pixels/points.
void    gt_graphics_set_font(GtGraphics *g, const char *family,
                            FontSlant slant, FontWeight weight, double size)
Sets basic font family, slant and weight options. Font families are implementation-specific, e.g. in Cairo there is no operation to list available family names on the system, but the standard CSS2 generic family names, ("serif", "sans-serif", "cursive", "fantasy", "monospace"), are likely to work as expected.
double  gt_graphics_get_image_width(GtGraphics*)
Returns the width of the image in pixels/points.
double  gt_graphics_get_image_height(GtGraphics*)
Returns the height of the image in pixels/points.
void    gt_graphics_set_margins(GtGraphics*, double margin_x,
                                  double margin_y)
Set margins (space to the image boundaries that are clear of elements)
   in the graphics.
   margin_x denotes the Margin to the left and right, in pixels.
   margin_y denotes the Margin to the top and bottom, in pixels.
double  gt_graphics_get_xmargins(GtGraphics*)
Returns the horizontal margins in pixels/points.
double  gt_graphics_get_ymargins(GtGraphics*)
Returns the vertical margins in pixels/points.
void    gt_graphics_draw_horizontal_line(GtGraphics *g, double x, double y,
                                        GtColor color, double width,
                                        double stroke_width)
Draws a horizontal line of length width beginning at the given coordinates
   to the right in the color color with stroke width stroke_width.
void    gt_graphics_draw_vertical_line(GtGraphics *g, double x, double y,
                                      GtColor color, double length,
                                      double stroke_width)
Draws a vertical line of length length beginning at the given coordinates
   downwards in the color color with stroke width stroke_width.
void    gt_graphics_draw_line(GtGraphics *g, double x, double y,
                             double xto, double yto, GtColor color,
                             double stroke_width)
Draws a line beginning at (x,y) to (xto,yto) in the color color
   with stroke width stroke_width.
void    gt_graphics_draw_box(GtGraphics*, double x, double y, double width,
                            double height, GtColor fill_color,
                            ArrowStatus arrow_status, double arrow_width,
                            double stroke_width, GtColor stroke_color,
                            bool dashed)
Draws a arrow-like box glyph at (x,y) where these are the top left
   coordinates. The box extends width pixels (incl. arrowhead) into the x
   direction and height pixels into the y direction. It will be filled with
   fill_color and stroked with width stroke_width and color stroke_color.
   The width of the arrowhead is given by the arrow_width parameter.
   The arrow_status parameter determines whether an arrowhead will be drawn
   at the left or right end, both ends, or none.
   If dashed is set to true, then the outline will be dashed instead of
   solid.
void    gt_graphics_draw_dashes(GtGraphics*, double x, double y,
                                  double width, double height,
                                  ArrowStatus arrow_status, double arrow_width,
                                  double stroke_width, GtColor stroke_color)
Draws a transparent box with a dashed line at the center at (x,y)
   (where these are the top left coordinates). The box extends width pixels
   (incl. arrowhead) into the x direction and height pixels into the y
   direction. It will be stroked with width stroke_width and color
   stroke_color. The width of the arrowhead is given by the arrow_width
   parameter. The arrow_status parameter determines whether an arrowhead will
   be drawn at the left or right end, both ends, or none.
void    gt_graphics_draw_caret(GtGraphics*, double x, double y, double width,
                              double height, ArrowStatus arrow_status,
                              double arrow_width,  double stroke_width,
                              GtColor stroke_color)
Draws a caret (``hat'') style glyph at (x,y) (where these are the top
   left coordinates). The box extends width pixels (incl. arrowhead) into the
   x direction and height pixels into the y direction. It will be stroked
   with width stroke_width and color stroke_color. The width of the
   arrowhead is given by the arrow_width parameter. The arrow_status
   parameter determines whether an arrowhead will be drawn at the left or right
   end, both ends, or none.
void    gt_graphics_draw_rectangle(GtGraphics*, double x, double y,
                                  bool filled, GtColor fill_color,
                                  bool stroked, GtColor stroke_color,
                                  double stroke_width, double width,
                                  double height)
Draws a rectangle at (x,y) where these are the top left coordinates.
   The rectangle extends width pixels (incl. arrowhead) into the x
   direction and height pixels into the y direction. It will be filled with
   fill_color if filled is set to true and stroked with width stroke_width
   and color stroke_color if stroked is set to true.
void    gt_graphics_draw_arrowhead(GtGraphics*, double x, double y, GtColor,
                                  ArrowStatus arrow_status)
Draws an arrowhead at (x,y) where these are the top left coordinates.
   The direction is determined by the arrow_status parameter.
void    gt_graphics_draw_curve_data(GtGraphics *g, double x, double y,
                                   GtColor color,
                                   double data[], GtUword ndata,
                                   GtRange valrange, GtUword height)
Draws a curve over the full visible image width (without margins) at
   (x,y) where these are the top left coordinates. As input, the array of
   double values data with ndata data points is used. The valrange gives
   the minimum and maximum value of the displayed data. If a value outside the
   data range is encountered, the drawing will be stopped at this data point.
int     gt_graphics_save_to_file(const GtGraphics*, const char *filename,
                                GtError*)
Write out the GtGraphics object to the given file with filename.
void    gt_graphics_save_to_stream(const GtGraphics*, GtStr *stream)
Write out the GtGraphics object to the given stream.
void    gt_graphics_delete(GtGraphics*)
Deletes the the GtGraphics object.
Class GtGraphicsCairo
 Implements the GtGraphics interface.
   This implementation uses the Cairo 2D vector graphics library as a
   drawing back-end. 
GtGraphics*   gt_graphics_cairo_new(GtGraphicsOutType type, unsigned int width,
                                   unsigned int height)
Creates a new GtGraphics object using the Cairo backend. The object
   is meant for writing a new image of width width and height height
   to a file or stream. Use type to define the output format.
GtGraphics*   gt_graphics_cairo_new_from_context(cairo_t *context,
                                                unsigned int width,
                                                unsigned int height)
Creates a new GtGraphics object using the Cairo backend. The object
   is meant for writing on an existing cairo_t context within the boundaries
   of width width and height height.
void          gt_graphics_cairo_draw_curve_data(GtGraphics *gg,
                                               double x, double y,
                                               GtColor color, double data[],
                                               GtUword ndata, GtRange valrange,
                                               GtUword height)
Draws a curve in gg at the position x,y for ndata data points as
   given in data. The data points must be in the range valrange and the
   resulting graph has the height height in type-dependent units
   (e.g. pixels).
Class GtHashmap
A hashmap allowing to index any kind of pointer (as a value). As keys, strings or any other pointer can be used.
int  GtHashmapVisitFunc(void *key, void *value, void *data,
                                  GtError *err)
Callback function when using the gt_hashmap_foreach*() functions.
   Must return a status code (0 = continue iteration, 1 = stop iteration,
   2 = deleted element, 3 = modified key, 4 = redo iteration).
   Gets called with the key and value of the current hashmap member, and the
   err object given in the original gt_hashmap_foreach*() call.
GtHashmap*  gt_hashmap_new(GtHashType keyhashtype, GtFree keyfree,
                          GtFree valuefree)
Creates a new GtHashmap object of type keyhashtype. If keyfree and/or
   valuefree are given, they will be used to free the hashmap members
   when the GtHashmap is deleted. keyhashtype defines how to hash the
   keys given when using the GtHashmap.
   GT_HASH_DIRECT uses the key pointer as a basis for the hash function.
   Equal pointers will refer to the same value. If GT_HASH_STRING is used, the
   keys will be  evaluated as strings and keys will be considered equal if the
   strings are identical, regardless of their address in memory
GtHashmap*  gt_hashmap_new_no_ma(GtHashType keyhashtype, GtFree keyfree,
                                GtFree valuefree)
Like gt_hashmap_new(), but without using GenomeTools' memory allocator.
GtHashmap*  gt_hashmap_ref(GtHashmap *hm)
Increase the reference count of hm.
void*       gt_hashmap_get(GtHashmap *hashmap, const void *key)
Return the value stored in hashmap for key or NULL if no such key
   exists.
void*       gt_hashmap_get_key(GtHashmap *hm, const void *key)
Returns the key stored in hm for key or NULL if no such key exists.
void        gt_hashmap_add(GtHashmap *hashmap, void *key, void *value)
Set the value stored in hashmap for key to value, overwriting the prior
   value for that key if present.
void        gt_hashmap_remove(GtHashmap *hashmap, const void *key)
Remove the member with key key from hashmap.
int         gt_hashmap_foreach_ordered(GtHashmap *hashmap,
                                      GtHashmapVisitFunc func,
                                      void *data, GtCompare cmp, GtError *err)
Iterate over hashmap in order given by compare function cmp.
   For each member, func is called (see interface).
int         gt_hashmap_foreach(GtHashmap *hashmap, GtHashmapVisitFunc func,
                              void *data, GtError *err)
Iterate over hashmap in arbitrary order.
   For each member, func is called (see interface).
int         gt_hashmap_foreach_in_key_order(GtHashmap *hashmap,
                                           GtHashmapVisitFunc func,
                                           void *data, GtError *err)
Iterate over hashmap in either alphabetical order (if GtHashType was
   specified as GT_HASH_STRING) or numerical order (if GtHashType was
   specified as GT_HASH_DIRECT).
void        gt_hashmap_reset(GtHashmap *hashmap)
Reset hashmap by unsetting values for all keys, calling the free function
   if necessary.
void        gt_hashmap_delete(GtHashmap *hashmap)
Delete hashmap, calling the free function if necessary.
Class GtIDToMD5Stream
 Implements the GtNodeStream interface. A GtIDToMD5Stream converts
   ``regular'' sequence IDs to MD5 fingerprints. 
GtNodeStream*  gt_id_to_md5_stream_new(GtNodeStream *in_stream,
                                      GtRegionMapping *region_mapping,
                                      bool substitute_target_ids)
Create a GtIDToMD5Stream object which converts ``regular'' sequence IDs
   from nodes it retrieves from its in_stream to MD5 fingerprints (with the
   help of the given region_mapping). If substitute_target_ids is true, the
   IDs of Target attributes are also converted to MD5 fingerprints.
   Takes ownership of region_mapping!
Class GtImageInfo
 The GtImageInfo class is a container for 2D coordinate to GtFeatureNode
   mappings which could, for example, be used to associate sections of a
   rendered image with GUI widgets or HTML imagemap areas. This information is
   given in the form of GtRecMap objects. They are created during the
   image rendering process and stored inside a GtImageInfo object for later
   retrieval. Additionally, the rendered width of an image can be obtained via
   a GtImageInfo method. 
GtImageInfo*      gt_image_info_new(void)
Creates a new GtImageInfo object.
unsigned int      gt_image_info_get_height(GtImageInfo *image_info)
Returns the height of the rendered image (in pixels or points).
GtUword     gt_image_info_num_of_rec_maps(GtImageInfo *image_info)
Returns the total number of mappings in image_info.
const GtRecMap*   gt_image_info_get_rec_map(GtImageInfo *image_info,
                                           GtUword i)
Returns the i-th GtRecMap mapping in image_info.
void              gt_image_info_delete(GtImageInfo *image_info)
Deletes image_info and all the GtRecMap objects created by it.
Class GtInterFeatureStream
 Implements the GtNodeStream interface. A GtInterFeatureStream inserts new
   feature nodes between existing feature nodes of a certain type. 
GtNodeStream*  gt_inter_feature_stream_new(GtNodeStream *in_stream,
                                          const char *outside_type,
                                          const char *inter_type)
Create a GtInterFeatureStream* which inserts feature nodes of type
   inter_type between the feature nodes of type outside_type it retrieves
   from in_stream and returns them.
Class GtIntervalTree
This is an interval tree data structure, implemented according to Cormen et al., Introduction to Algorithms, 2nd edition, MIT Press, Cambridge, MA, USA, 2001
GtIntervalTree*      gt_interval_tree_new(GtFree)
Creates a new GtIntervalTree. If a GtFree function is given as an
   argument, it is applied on the data pointers in all inserted nodes when the
   GtIntervalTree is deleted.
GtUword        gt_interval_tree_size(GtIntervalTree*)
Returns the number of elements in the GtIntervalTree.
GtIntervalTreeNode*  gt_interval_tree_find_first_overlapping(GtIntervalTree*,
                                                            GtUword start,
                                                            GtUword end)
Returns the first node in the GtIntervalTree which overlaps the given
   range (from start to end).
void                 gt_interval_tree_insert(GtIntervalTree *tree,
                                            GtIntervalTreeNode *node)
Inserts node node into tree.
void                 gt_interval_tree_find_all_overlapping(GtIntervalTree*,
                                                          GtUword start,
                                                          GtUword end,
                                                          GtArray*)
Collects data pointers of all GtIntervalTreeNodes in the tree which
   overlap with the query range (from start to end) in a GtArray.
void                 gt_interval_tree_iterate_overlapping(GtIntervalTree *it,
                                                GtIntervalTreeIteratorFunc func,
                                                GtUword start,
                                                GtUword end,
                                                void *data)
Call func for all GtIntervalTreeNodes in the tree which overlap with
   the query range (from start to end). Use data to pass in arbitrary
   user data.
int                  gt_interval_tree_traverse(GtIntervalTree*,
                                              GtIntervalTreeIteratorFunc func,
                                              void *data)
Traverses the GtIntervalTree in a depth-first fashion, applying func to
   each node encountered. The data pointer can be used to reference arbitrary
   data needed in the GtIntervalTreeIteratorFunc.
void                 gt_interval_tree_remove(GtIntervalTree*,
                                            GtIntervalTreeNode *node)
Removes the entry referenced by node from the GtIntervalTree.
   The data attached to node is freed according to the free function defined
   in the tree.
   Note that the memory pointed to by node can be re-used internally,
   referencing other data in the tree. Make sure to handle this pointer as
   expired after calling gt_interval_tree_remove()!
void                 gt_interval_tree_delete(GtIntervalTree*)
Deletes a GtIntervalTree. If a GtFree function was set in the tree
   constructor, data pointers specified in the nodes are freed using the given
   GtFree function.
Class GtIntervalTreeNode
GtIntervalTreeNode*  gt_interval_tree_node_new(void *data,
                                              GtUword low,
                                              GtUword high)
Creates a new GtIntervalTreeNode. Transfers ownership of data to interval
   tree if inserted into a GtIntervalTree in which a
   GtIntervalTreeDataFreeFunc is set.
void*                gt_interval_tree_node_get_data(GtIntervalTreeNode* node)
Returns a pointer to the data associated with node node.
Class GtLayout
 The GtLayout class represents contents (tracks) of a GtDiagram broken up
   into lines such that a given horizontal space allotment given in pixels
   or points is used up most efficiently. This is done using the GtLineBreaker
   and GtTextWidthCalculator classes. As defaults, Cairo-based instances of
   these classes are used but can be specified separately.
   A GtLayout can be queried for the height of the laid out representation and
   finally be rendered to a GtCanvas. 
GtLayout*      gt_layout_new(GtDiagram *diagram, unsigned int width, GtStyle*,
                            GtError*)
Creates a new GtLayout object for the contents of diagram.
   The layout is done for a target image width of width and using the rules in
   GtStyle object style.
GtLayout*      gt_layout_new_with_twc(GtDiagram*,
                                     unsigned int width,
                                     GtStyle*,
                                     GtTextWidthCalculator*,
                                     GtError*)
Like gt_layout_new(), but allows use of a different GtTextWidthCalculator
   implementation.
void           gt_layout_set_track_ordering_func(GtLayout *layout,
                                                GtTrackOrderingFunc func,
                                                void *data)
Sets the GtTrackOrderingFunc comparator function func which defines an
   order on the tracks contained in layout. This determines the order in
   which the tracks are drawn vertically.
   Additional data necessary in the comparator function can be given in data,
   the caller is responsible to free it.
int            gt_layout_get_height(GtLayout *layout,
                                   GtUword *result,
                                   GtError *err)
Calculates the height of layout in pixels. The height value is written to
   the location pointed to by result. If an error occurs during the
   calculation, this function returns -1 and err is set accordingly.
   Returns 0 on success.
int            gt_layout_sketch(GtLayout *layout, GtCanvas *target_canvas,
                               GtError*)
Renders layout on the target_canvas.
void           gt_layout_delete(GtLayout*)
Destroys a layout.
Class GtLogger
GtLogger*  gt_logger_new(bool enabled, const char *prefix, FILE *target)
Creates a new GtLogger, with logging enabled or not,
   and prefixing all log entries with prefix (e.g. "debug").
   The log output is terminated by a newline. All log output will
   be written to target.
void       gt_logger_enable(GtLogger *logger)
Enable logging on logger.
void       gt_logger_disable(GtLogger *logger)
Disable logging on logger.
bool       gt_logger_enabled(GtLogger *logger)
Return true if logging is enabled on logger, false otherwise.
FILE*      gt_logger_target(GtLogger *logger)
Return logging target of logger.
void       gt_logger_set_target(GtLogger *logger, FILE *fp)
Set logging target of logger to fp.
void       gt_logger_log_force(GtLogger *logger, const char *format, ...)
Log to target regardless of logging status.
void       gt_logger_log(GtLogger *logger, const char *format, ...)
Log to target depending on logging status.
void       gt_logger_log_va_force(GtLogger *logger, const char *format, va_list)
Log to target regardless of logging status, using a va_list argument.
void       gt_logger_log_va(GtLogger *logger, const char *format, va_list)
Log to target depending on logging status, using a va_list argument.
void       gt_logger_delete(GtLogger *logger)
Delete logger.
Class GtMD5Encoder
 The GtMD5Encoder class implements a stateful encoder for MD5 hashes
   for strings build by iterative addition of blocks. 
GtMD5Encoder*  gt_md5_encoder_new(void)
Returns a new GtMD5Encoder object.
void           gt_md5_encoder_add_block(GtMD5Encoder *enc, const char *message,
                                       GtUword len)
Processes message of length len (max. block length 64 bytes) to be
   incorporated in the hash currently represented by enc.
void           gt_md5_encoder_finish(GtMD5Encoder *enc, unsigned char *output,
                                    char *outstr)
Finishes enc to produce the final MD5 value, written to the 16-byte array
   output. If outstr is not NULL, a \0-terminated string representation of
   the hash will be written to the 32-byte string buffer it points to.
void           gt_md5_encoder_reset(GtMD5Encoder *enc)
Discards the current state of enc and resets it to represent the MD5 hash
   of the empty string.
void           gt_md5_encoder_delete(GtMD5Encoder *enc)
Deletes enc and frees all associated space.
Class GtMD5Tab
 GtMd5Tab is a table referencing sequences in a sequence collection. 
GtMD5Tab*      gt_md5_tab_new(const char *sequence_file, void *seqs,
                             GtGetSeqFunc get_seq, GtGetSeqLenFunc get_seq_len,
                             GtUword num_of_seqs, bool use_cache_file,
                             bool use_file_locking)
Create a new MD5 table object for sequences contained in sequence_file.
   The sequences have to be stored in seqs (num_of_seqs many) and have to be
   accessible via the functions get_seq and get_seq_len. If use_cache_file
   is true, the MD5 sums are read from a cache file (named
   "sequence_fileGT_MD5TAB_FILE_SUFFIX"), if it exists or written to it, if
   it doesn't exist. If use_cache_file is false, no cache file is read or
   written. If use_file_locking is true, file locking is used to access the
   cache file (recommended).
GtMD5Tab*      gt_md5_tab_new_from_cache_file(const char *cache_file,
                                             GtUword num_of_seqs,
                                             bool use_file_locking,
                                             GtError *err)
Create a new MD5 table object for sequences directly from a cache_file,
   containing MD5 sums for num_of_seqs many sequences. If use_file_locking
   is true, file locking is used to access the cache file (recommended).
   Returns NULL if an error occurred opening the cache file, err is set
   accordingly.
GtMD5Tab*      gt_md5_tab_ref(GtMD5Tab *md5_tab)
Increment reference count for md5_tab.
void           gt_md5_tab_disable_file_locking(GtMD5Tab *md5_tab)
Do not use file locking for md5_tab.
const char*    gt_md5_tab_get(const GtMD5Tab*, GtUword index)
Return the MD5 sum for sequence index.
GtUword        gt_md5_tab_map(GtMD5Tab*, const char *md5)
Map md5 back to sequence index.
GtUword        gt_md5_tab_size(const GtMD5Tab *md5_tab)
Return the size of the md5_tab.
void           gt_md5_tab_delete(GtMD5Tab *md5_tab)
Decrement reference count for or delete md5_tab.
Class GtMD5ToIDStream
 Implements the GtNodeStream interface. A GtMD5ToIDStream converts MD5
   fingerprints used as sequence IDs to ``regular'' ones. 
GtNodeStream*  gt_md5_to_id_stream_new(GtNodeStream *in_stream,
                                      GtRegionMapping *region_mapping)
Create a GtMD5toIDStream* which converts MD5 sequence IDs from nodes it
   retrieves from its in_stream to ``regular'' ones (with the help of the
   given region_mapping). Takes ownership of region_mapping!
Class GtMatch
 The GtMatch interface defines a generic set of functions for a data
   structure designed to hold matches, that is, two similar locations on two
   sequences which are further described by additional data specific to the
   matching engine. Matches have a direction, e.g. direct or reverse
   (palindromic). 
void              gt_match_set_seqid1(GtMatch *match, const char *seqid)
Sets the sequence ID of the first sequence involved in the match match to
   seqid. The string seqid must be null-terminated.
void              gt_match_set_seqid1_nt(GtMatch *match, const char *seqid,
                                        GtUword len)
Sets the sequence ID of the first sequence involved in the match match to
   seqid. The string seqid needs not be null-terminated, its length is
   given by len.
void              gt_match_set_seqid2(GtMatch *match, const char *seqid)
Sets the sequence ID of the second sequence involved in the match match to
   seqid. The string seqid must be null-terminated.
void              gt_match_set_seqid2_nt(GtMatch *match, const char *seqid,
                                        GtUword len)
Sets the sequence ID of the second sequence involved in the match match to
   seqid. The string seqid needs not be null-terminated, its length is
   given by len.
const char*       gt_match_get_seqid1(const GtMatch *match)
Returns the sequence ID of the first sequence involved in the match
   match.
const char*       gt_match_get_seqid2(const GtMatch *match)
Returns the sequence ID of the second sequence involved in the match
   match.
void              gt_match_set_range_seq1(GtMatch *match, GtUword start,
                                         GtUword end)
Sets the range of the first sequence involved in the match match to
   start-end.
void              gt_match_set_range_seq2(GtMatch *match, GtUword start,
                                         GtUword end)
Sets the range of the second sequence involved in the match match to
   start-end.
void              gt_match_get_range_seq1(const GtMatch *match, GtRange *range)
Writes the range of the first sequence involved in the match match to the
   location pointed to by range.
   Note: depending on how the matches were produced the resulting range might
   differ. e.g. Blast hit ranges are 1-Based, not zero based and inclusive i.e.
   range.end is the last position that is part of the match.
void              gt_match_get_range_seq2(const GtMatch *match, GtRange *range)
Writes the range of the second sequence involved in the match match to the
   location pointed to by range.
   Note: depending on how the matches were produced the resulting range might
   differ. e.g. Blast hit ranges are 1-Based, not zero based and inclusive i.e.
   range.end is the last position that is part of the match.
GtMatchDirection  gt_match_get_direction(const GtMatch *match)
Returns the match direction of match.
void              gt_match_delete(GtMatch *match)
Deletes the match match, freeing all associated memory.
Class GtMatchBlast
GtMatch*  gt_match_blast_new(char *seqid1,
                            char *seqid2,
                            GtUword start_seq1,
                            GtUword start_seq2,
                            GtUword end_seq1,
                            GtUword end_seq2,
                            double evalue,
                            float bitscore,
                            GtUword ali_l,
                            double similarity,
                            GtMatchDirection dir)
Creates a new GtMatch object meant to store results in the BLAST
   format. That is, it stores double values evalue for match E-values,
   bitscores and the alignment length ali_l in addition to the generic
   match contents seqid1, seqid2, start_seq1, start_seq2, end_seq1,
   and end_seq2.
GtMatch*  gt_match_blast_new_extended(char *seqid1,
                                     char *seqid2,
                                     GtUword start_seq1,
                                     GtUword end_seq1,
                                     GtUword start_seq2,
                                     GtUword end_seq2,
                                     double evalue,
                                     float bitscore,
                                     GtUword length,
                                     double similarity,
                                     GtUword mm_num,
                                     GtUword gap_open_num,
                                     GtMatchDirection dir)
Creates a new GtMatch object meant to store results in the BLAST
   format. That is, it stores double values evalue for match E-values,
   bitscores and the alignment length ali_l in addition to the generic
   match contents seqid1, seqid2, start_seq1, start_seq2, end_seq1,
   and end_seq2. In addition to gt_match_blast_new it also stores
   the number of mismatches and the number of gap
void  gt_match_blast_set_evalue(GtMatchBlast *mb, double evalue)
Sets evalue to be the E-value in mb.
void  gt_match_blast_set_bitscore(GtMatchBlast *mb, float bits)
Sets bits to be the bit-score in mb.
void  gt_match_blast_set_align_length(GtMatchBlast *mb, GtUword length)
Sets length to be the alignment length in mb.
void  gt_match_blast_set_similarity(GtMatchBlast *mb, double similarity)
Sets similarity to be the match similarity in mb.
void  gt_match_blast_set_mismatches(GtMatchBlast *mb, GtUword mm_num)
Sets num to be the number of mismatches in mb.
void  gt_match_blast_set_gapopen(GtMatchBlast *mb, GtUword gap_open_num)
Sets num to be the number of gap openings in mb.
double  gt_match_blast_get_evalue(GtMatchBlast *mb)
Returns the E-value stored in mb.
float  gt_match_blast_get_bitscore(GtMatchBlast *mb)
Returns the bit-score value stored in mb.
GtUword  gt_match_blast_get_align_length(GtMatchBlast *mb)
Returns the alignment length stored in mb.
double  gt_match_blast_get_similarity(GtMatchBlast *mb)
Returns the alignment similarity stored in mb.
GtUword  gt_match_blast_get_mismatches(GtMatchBlast *mb)
Returns the number of mismatches stored in mb.
GtUword  gt_match_blast_get_gapopen(GtMatchBlast *mb)
Returns the number of gap openings stored in mb.
Class GtMatchIterator
GtMatchIteratorStatus  gt_match_iterator_next(GtMatchIterator *mp,
                                             GtMatch **match, GtError *err)
Advances mp by one, returning the next match.
   Writes a pointer to the next match to the position pointed to by match.
   Returns GT_MATCHER_STATUS_OK when the match could be delivered and there are
   more matches to come, GT_MATCHER_STATUS_END when no more matches are
   available, and GT_MATCHER_STATUS_ERROR if an error occurred. err is set
   accordingly.
void                   gt_match_iterator_delete(GtMatchIterator *mp)
Deletes mp, freeing all associated space.
Class GtMatchLAST
 The GtMatchLAST class, implementing the GtMatch interface, is meant to
    store results given in the format as output by LAST. 
GtMatch*       gt_match_last_new(const char *seqid1,
                                const char *seqid2,
                                GtUword score,
                                GtUword seqno1,
                                GtUword seqno2,
                                GtUword start_seq1,
                                GtUword start_seq2,
                                GtUword end_seq1,
                                GtUword end_seq2,
                                GtMatchDirection dir)
Creates a new GtMatch object meant to store results from the
   LAST software.
GtUword  gt_match_last_get_seqno1(const GtMatchLAST *ml)
Returns the sequence number of the match ms in the first sequence set.
GtUword  gt_match_last_get_seqno2(const GtMatchLAST *ml)
Returns the sequence number of the match ms in the second sequence set.
GtUword  gt_match_last_get_score(const GtMatchLAST *ml)
Returns the LAST score of the match ms.
Class GtMatchOpen
 The GtMatchOpen class, implementing the GtMatch interface, is meant to
    store results in the OpenMatch format, e.g. as output by Vmatch. 
GtMatch*  gt_match_open_new(char *seqid1,
                           char *seqid2,
                           GtUword start_seq1,
                           GtUword start_seq2,
                           GtUword end_seq1,
                           GtUword end_seq2,
                           GtWord weight,
                           GtMatchDirection dir)
Creates a new GtMatchOpen object, storing long values weight in addition
   to the generic match contents seqid1, seqid2, start_seq1, start_seq2,
   end_seq1, and end_seq2.
void  gt_match_open_set_weight(GtMatchOpen *mo, GtWord weight)
Sets weight to be the weight value in mo.
GtWord  gt_match_open_get_weight(GtMatchOpen *mo)
Returns the weight value stored in mo.
Class GtMatchSW
 The GtMatchSW class, implementing the GtMatch interface, is meant to
    store results from Smith-Waterman matching (using the swalign module). 
GtMatch*       gt_match_sw_new(const char *seqid1,
                              const char *seqid2,
                              GtUword seqno1,
                              GtUword seqno2,
                              GtUword length,
                              GtUword edist,
                              GtUword start_seq1,
                              GtUword start_seq2,
                              GtUword end_seq1,
                              GtUword end_seq2,
                              GtMatchDirection dir)
Creates a new GtMatch object, storing the alignment length length,
   the edit distance edist and the sequence numbers in the sequence
   collections in addition to the generic match contents seqid1, seqid2,
   start_seq1, start_seq2, end_seq1 and end_seq2.
GtUword  gt_match_sw_get_seqno1(const GtMatchSW *ms)
Returns the sequence number of the match ms in the first sequence set.
GtUword  gt_match_sw_get_seqno2(const GtMatchSW *ms)
Returns the sequence number of the match ms in the second sequence set.
GtUword  gt_match_sw_get_alignment_length(const GtMatchSW *ms)
Returns the alignment length of the match ms.
GtUword  gt_match_sw_get_edist(const GtMatchSW *ms)
Returns the edit distance of the match ms.
Class GtMatchVisitor
 The GtMatchVisitor class allows one to distinguish a GtMatch
   implementation, e.g. BLAST or OpenMatch, and to call different
   code for each implementation. 
int  gt_match_visitor_visit_match_blast(GtMatchVisitor *match_visitor,
                                       GtMatchBlast *match_blast,
                                       GtError *err)
Visit match_blast with match_visitor.
int  gt_match_visitor_visit_match_open(GtMatchVisitor *match_visitor,
                                      GtMatchOpen *match_open,
                                      GtError *err)
Visit match_open with match_visitor.
void  gt_match_visitor_delete(GtMatchVisitor *match_visitor)
Deletes match_visitor freeing all associated space.
Class GtMergeFeatureStream
 Implements the GtNodeStream interface. A GtMergeFeatureStream merges
   adjacent features of the same type. 
GtNodeStream*  gt_merge_feature_stream_new(GtNodeStream *in_stream)
Create a GtMergeFeatureStream* which merges adjacent features of the same
   type it retrieves from in_stream and returns them (and all other unmodified
   features).
Class GtMergeStream
 Implements the GtNodeStream interface. A GtMergeStream allows one to
   merge a set of sorted streams in a sorted fashion. 
GtNodeStream*  gt_merge_stream_new(const GtArray *node_streams)
Create a GtMergeStream* which merges the given (sorted) node_streams in a
   sorted fashion.
Class GtMetaNode
 Implements the GtGenomeNode interface. Meta nodes correspond to meta
   lines in GFF3 files (i.e., lines which start with  ``##'') which are not
   sequence-region lines. 
GtGenomeNode*             gt_meta_node_new(const char *meta_directive,
                                          const char *meta_data)
Return a new GtMetaNode object representing a meta_directive with the
   corresponding meta_data. Please note that the leading ``##'' which
   denotes meta lines in GFF3 files should not be part of the
   meta_directive.
   The meta_directive must not be NULL, the meta_data can be NULL.
const char*               gt_meta_node_get_directive(const GtMetaNode
                                                    *meta_node)
Return the meta directive stored in meta_node.
const char*               gt_meta_node_get_data(const GtMetaNode *meta_node)
Return the meta data stored in meta_node. Can return NULL!
GtMetaNode*               gt_meta_node_try_cast(GtGenomeNode *gn)
Test whether the given genome node is a meta node. If so, a pointer to the meta node is returned. If not, NULL is returned. Note that in most cases, one should implement a GtNodeVisitor to handle processing of different GtGenomeNode types.
GtMetaNode*               gt_meta_node_cast(GtGenomeNode *gn)
Test whether the given genome node is a meta node. If so, a pointer to the meta node is returned. If not, an assertion fails.
Class GtMutex
 The GtMutex class represents a simple mutex structure. 
GtMutex*   gt_mutex_new(void)
Return a new GtMutex* object.
void       gt_mutex_delete(GtMutex *mutex)
Delete the given mutex.
#define gt_mutex_lock(mutex)
Lock the given mutex.
#define gt_mutex_unlock(mutex)
Unlock the given mutex.
Class GtNodeStream
 The GtNodeStream interface. GtNodeStream objects process GtGenomeNode
   objects in a pull-based architecture and can be chained together. 
GtNodeStream*  gt_node_stream_ref(GtNodeStream *node_stream)
Increase the reference count for node_stream and return it.
int            gt_node_stream_next(GtNodeStream *node_stream,
                                  GtGenomeNode **genome_node,
                                  GtError *err)
Try to get the the next GtGenomeNode from node_stream and store it in
   genome_node (transfers ownership to genome_node).
   If no error occurs, 0 is returned and genome_node contains either the next
   GtGenomeNode or NULL, if the node_stream is exhausted.
   If an error occurs, -1 is returned and err is set accordingly (the status
   of genome_node is undefined, but no ownership transfer occurred).
int            gt_node_stream_pull(GtNodeStream *node_stream, GtError *err)
Calls gt_node_stream_next() on node_stream repeatedly until the
   node_stream is exhausted (0 is returned) or an error occurs (-1 is returned
   and err is set). All retrieved GtGenomeNodes are deleted automatically
   with calls to gt_genome_node_delete().
   This method is basically a convenience method which simplifies calls to
   gt_node_stream_next() in a loop where the retrieved GtGenomeNode objects
   are not processed any further.
bool           gt_node_stream_is_sorted(GtNodeStream *node_stream)
Return true if node_stream is a sorted stream, false otherwise.
void           gt_node_stream_delete(GtNodeStream *node_stream)
Decrease the reference count for node_stream or delete it, if this was the
   last reference.
void  GtNodeStreamFreeFunc(GtNodeStream*)
Callback function. Performs the necessary steps to delete implementation-specific memory in the stream implementation.
int   GtNodeStreamNextFunc(GtNodeStream*, GtGenomeNode**, GtError*)
Callback function. May receive a GtGenomeNode from its predecessor and
   must write a node reference or NULL to the node pointer.
GtNodeStream*       gt_node_stream_create(const GtNodeStreamClass
                                         *node_stream_class,
                                         bool ensure_sorting)
Create a new object of the given node_stream_class. If ensure_sorting is
   true, it is enforced that all genome node objects pulled from this class
   are sorted. That is, for consecutive nodes a and b obtained from the
   given node_stream_class the return code of gt_genome_node_compare(a,b)
   has to be smaller or equal than 0. If this condition is not met, an assertion
   fails.
void*               gt_node_stream_cast(const GtNodeStreamClass
                                       *node_stream_class,
                                       GtNodeStream *node_stream)
Cast node_stream to the given node_stream_class.
   That is, if node_stream is not from the given node_stream_class, an
   assertion will fail.
Class GtNodeStreamClass
const
GtNodeStreamClass*  gt_node_stream_class_new(size_t size,
                                            GtNodeStreamFreeFunc free,
                                            GtNodeStreamNextFunc next)
Create a new node stream class (that is, a class which implements the node
   stream interface). size denotes the size of objects of the new node stream
   class. The optional free method is called once, if an object of the new
   class is deleted. The mandatory next method has to implement the
   gt_node_stream_next() semantic for the new class.
Class GtNodeVisitor
 The GtNodeVisitor interface, a visitor for GtGenomeNode objects. 
int    gt_node_visitor_visit_comment_node(GtNodeVisitor *node_visitor,
                                         GtCommentNode *comment_node,
                                         GtError *err)
Visit comment_node with node_visitor.
int    gt_node_visitor_visit_feature_node(GtNodeVisitor *node_visitor,
                                         GtFeatureNode *feature_node,
                                         GtError *err)
Visit feature_node with node_visitor.
int    gt_node_visitor_visit_meta_node(GtNodeVisitor *node_visitor,
                                      GtMetaNode *meta_node,
                                      GtError *err)
Visit meta_node with node_visitor.
int    gt_node_visitor_visit_region_node(GtNodeVisitor *node_visitor,
                                        GtRegionNode *region_node,
                                        GtError *err)
Visit region_node with node_visitor.
int    gt_node_visitor_visit_sequence_node(GtNodeVisitor *node_visitor,
                                          GtSequenceNode *sequence_node,
                                          GtError *err)
Visit sequence_node with node_visitor.
void   gt_node_visitor_delete(GtNodeVisitor *node_visitor)
Delete node_visitor.
Class GtORFIterator
 The GtORFIterator class is used to enumerate open reading frames (ORFs)
   in codon streams as delivered by a GtCodonIterator using a translation
   process as defined by a GtTranslator. 
GtORFIterator*       gt_orf_iterator_new(GtCodonIterator *ci,
                                        GtTranslator *translator)
Return a new GtORFIterator* using the codons delivered by ci and
   translated by translator.
GtORFIteratorStatus  gt_orf_iterator_next(GtORFIterator *orf_iterator,
                                         GtRange *orf_rng,
                                         unsigned int *orf_frame,
                                         GtError *err)
Sets the values of orf_rng.start, orf_rng.end and orf_frame to the
   current reading position of ci if a START/STOP codon is found. The frame
   in which the ORF is located is written to the position pointed to by
   orf_frame. This function returns one of three status codes:
   GT_ORF_ITERATOR_OK if an ORF was detected successfully(START/STOP AA pair),
   GT_ORF_ITERATOR_END if no ORF was detected because the end of the scan
                           region has been reached, or
   GT_ORF_ITERATOR_ERROR if no ORF was detected because an error occurred
                           during sequence access. See err for details.
void                 gt_orf_iterator_delete(GtORFIterator *orf_iterator)
Delete orf_iterator and frees all associated memory.
Class GtOption
 GtOption objects represent command line options (which are used in
   a GtOptionParser).
   Option descriptions are automatically formatted to
   GT_OPTION_PARSER_TERMINAL_WIDTH, but it is possible to embed newlines into
   the descriptions to manually affect the formatting. 
GtOption*        gt_option_new_bool(const char *option_string,
                                   const char *description,
                                   bool *value, bool default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
GtOption*        gt_option_new_double(const char *option_string,
                                     const char *description, double *value,
                                     double default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
GtOption*        gt_option_new_double_min(const char *option_string,
                                         const char *description, double *value,
                                         double default_value,
                                         double minimum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value.
GtOption*        gt_option_new_double_min_max(const char *option_string,
                                             const char *description,
                                             double *value,
                                             double default_value,
                                             double minimum_value,
                                             double maximum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value and at most
  the maximum_value.
GtOption*        gt_option_new_probability(const char *option_string,
                                          const char *description,
                                          double *value,
                                          double default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at larger or equal than 0.0 and smaller or
  equal than 1.0.
GtOption*        gt_option_new_int(const char *option_string,
                                  const char *description,
                                  int *value, int default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
GtOption*        gt_option_new_int_min(const char *option_string,
                                      const char *description, int *value,
                                      int default_value, int minimum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value.
GtOption*        gt_option_new_int_max(const char *option_string,
                                      const char *description, int *value,
                                      int default_value, int maximum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at most have the maximum_value.
GtOption*        gt_option_new_int_min_max(const char *option_string,
                                          const char *description,
                                          int *value, int default_value,
                                          int minimum_value, int maximum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value and at most
  the maximum_value.
GtOption*        gt_option_new_uint(const char *option_string,
                                   const char *description,
                                   unsigned int *value,
                                   unsigned int default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
GtOption*        gt_option_new_uint_min(const char *option_string,
                                       const char *description,
                                       unsigned int *value,
                                       unsigned int default_value,
                                       unsigned int minimum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value.
GtOption*        gt_option_new_uint_max(const char *option_string,
                                       const char *description,
                                       unsigned int *value,
                                       unsigned int default_value,
                                       unsigned int maximum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at most have the maximum_value.
GtOption*        gt_option_new_uint_min_max(const char *option_string,
                                           const char *description,
                                           unsigned int *value,
                                           unsigned int default_value,
                                           unsigned int minimum_value,
                                           unsigned int maximum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value and at most
  the maximum_value.
GtOption*        gt_option_new_word(const char *option_string,
                                   const char *description,
                                   GtWord *value, GtWord default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
GtOption*        gt_option_new_uword(const char *option_string,
                                    const char *description,
                                    GtUword *value,
                                    GtUword default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
GtOption*        gt_option_new_uword_min(const char *option_string,
                                        const char *description,
                                        GtUword *value,
                                        GtUword default_value,
                                        GtUword minimum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value.
GtOption*        gt_option_new_uword_min_max(const char *option_string,
                                            const char *description,
                                            GtUword *value,
                                            GtUword default_value,
                                            GtUword minimum_value,
                                            GtUword maximum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The argument to this option must at least have the minimum_value and at most
  the maximum_value.
GtOption*        gt_option_new_long(const char *option_string,
                                   const char *description,
                                   GtWord *value, GtWord default_value)
Deprecated. Usage identical to gt_option_new_word.
GtOption*        gt_option_new_ulong(const char *option_string,
                                    const char *description,
                                    GtUword *value,
                                    GtUword default_value)
Deprecated. Usage identical to gt_option_new_uword.
GtOption*        gt_option_new_ulong_min(const char *option_string,
                                        const char *description,
                                        GtUword *value,
                                        GtUword default_value,
                                        GtUword minimum_value)
Deprecated. Usage identical to gt_option_new_uword_min.
GtOption*        gt_option_new_ulong_min_max(const char *option_string,
                                            const char *description,
                                            GtUword *value,
                                            GtUword default_value,
                                            GtUword minimum_value,
                                            GtUword maximum_value)
Deprecated. Usage identical to gt_option_new_uword_min_max.
GtOption*        gt_option_new_range(const char *option_string,
                                    const char *description,
                                    GtRange *value, GtRange *default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
   If default_value equals NULL, GT_UNDEF_WORD will be used as the default
   start and end point of value.
GtOption*        gt_option_new_range_min_max(const char *option_string,
                                            const char *description,
                                            GtRange *value,
                                            GtRange *default_value,
                                            GtUword minimum_value,
                                            GtUword maximum_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
  The first argument to this option (which will be used as the start) must at
  least have the minimum_value and the second argument (which will be used as
  the end) at most the maximum_value.
GtOption*        gt_option_new_string(const char *option_string,
                                     const char *description,
                                     GtStr *value, const char *default_value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing is stored in value.
GtOption*        gt_option_new_string_array(const char *option_string,
                                           const char *description,
                                           GtStrArray *value)
Return a new GtOption with the given option_string, description, and
   default_value. The result of the option parsing are stored in value.
GtOption*        gt_option_new_choice(const char *option_string,
                                     const char *description, GtStr *value,
                                     const char *default_value,
                                     const char **domain)
Return a GtOption with the given option_string, description, and
   default_value which allows only arguments given in the NULL-terminated
   domain (default_value must be an entry of domain or NULL).
GtOption*        gt_option_new_filename(const char *option_string,
                                       const char *description,
                                       GtStr *filename)
Return a new GtOption with the given option_string, description. The
   result of the option parsing is stored in the GtStr object filename.
   filename may not be NULL!
GtOption*        gt_option_new_filename_array(const char *option_string,
                                             const char *description,
                                             GtStrArray *filename_array)
Return a new GtOption with the given option_string, description, and
   default_value. The results of the option parsing are stored in value.
GtOption*        gt_option_new_debug(bool *value)
Return a new debug GtOption object: -debug, "enable debugging output",
   default is false. The result of the option parsing is stored in value
GtOption*        gt_option_new_verbose(bool *value)
Return a new verbose GtOption object: -v, "be verbose",
   default is false. The result of the option parsing is stored in value
GtOption*        gt_option_new_width(GtUword *value)
Return a new width GtOption object: -width, "set output width for FASTA
   sequence printing (0 disables formatting)", default is 0.
   The result of the option parsing is stored in value
GtOption*        gt_option_ref(GtOption *option)
Increase the reference count for option and return it.
const char*      gt_option_get_name(const GtOption * option)
Return the name of option
void             gt_option_is_mandatory(GtOption *option)
Make option mandatory.
void             gt_option_is_mandatory_either(GtOption *option_a,
                                              const GtOption *option_b)
Make it mandatory, that either option_a or option_b is used.
void             gt_option_is_mandatory_either_3(GtOption *option_a,
                                                const GtOption *option_b,
                                                const GtOption *option_c)
Make it mandatory, that one of the options option_a, option_b, or
   option_c is used.
void             gt_option_is_mandatory_either_4(GtOption *option_a,
                                                const GtOption *option_b,
                                                const GtOption *option_c,
                                                const GtOption *option_d)
Make it mandatory, that one of the options option_a, option_b, option_c
   or option_d is used.
void             gt_option_is_extended_option(GtOption *option)
Set that option is only shown in the output of -help+.
void             gt_option_is_development_option(GtOption *option)
Set that option is only shown in the output of -helpdev.
void             gt_option_imply(GtOption *option_a, const GtOption *option_b)
Make option_a imply option_b.
void             gt_option_imply_either_2(GtOption *option_a,
                                         const GtOption *option_b,
                                         const GtOption *option_c)
Make option_a imply either option_b or option_c
void             gt_option_imply_either_3(GtOption *option_a,
                                         const GtOption *option_b,
                                         const GtOption *option_c,
                                         const GtOption *option_d)
Make option_a imply either option_b, option_c or option_d
void             gt_option_exclude(GtOption *option_a, GtOption *option_b)
Set that the options option_a and option_b exclude each other.
void             gt_option_hide_default(GtOption *option)
Hide the default value of option in -help output.
void             gt_option_argument_is_optional(GtOption *option)
Set that the argument to option is optional
bool             gt_option_is_set(const GtOption *option)
Return true if option was set, false otherwise.
void             gt_option_delete(GtOption*)
Delete option.
int  gt_option_parse_spacespec(GtUword *maximumspace,
                              const char *optname,
                              const GtStr *memlimit,
                              GtError *err)
Parse the argument to option -memlimit. Could be made into a special parser, but I do not know how. SK. 2011-09-19
Class GtOptionParser
 GtOptionParser objects can be used to parse command line options. 
#define GT_OPTION_PARSER_TERMINAL_WIDTH
The default terminal width used in the output of the GtOptionParser.
GtOptionParser*  gt_option_parser_new(const char *synopsis,
                                     const char *one_liner)
Return a new GtOptionParser object. The synopsis should summarize the
   command line arguments and mandatory arguments in a single line.
   The one_liner should describe the program for which the GtOptionParser is
   used in a single line and must have an upper case letter at the start and a
   '.' at the end.
void             gt_option_parser_add_option(GtOptionParser *option_parser,
                                            GtOption *option)
Add option to option_parser. Takes ownership of option.
GtOption*        gt_option_parser_get_option(GtOptionParser *option_parser,
                                            const char *option_string)
Return the GtOption object if an option named option_string is present in
   option_parser, and NULL if no such option exists.
void             gt_option_parser_refer_to_manual(GtOptionParser *option_parser)
Refer to manual at the end of -help output of opion_parser.
void             gt_option_parser_set_comment_func(GtOptionParser *option_parser,
                                                  GtShowCommentFunc
                                                  comment_func,
                                                  void *data)
Set comment_func in option_parser (data is passed along).
void             gt_option_parser_set_version_func(GtOptionParser *option_parser,
                                                  GtShowVersionFunc
                                                  version_func)
Set the version function used by option_parser to version_func.
   This version function takes precedence to the one supplied to
   gt_option_parser_parse().
void             gt_option_parser_set_mail_address(GtOptionParser*,
                                                  const char *mail_address)
Set the mail_address used in the final "Report bugs to" line of the -help
   output. It should be of the form 
void             gt_option_parser_register_hook(GtOptionParser *option_parser,
                                               GtOptionParserHookFunc
                                               hook_function,
                                               void *data)
Register a hook_function with option_parser. All registered hook
   functions are called at the end of gt_option_parser_parse().
   This allows one to have a module which registers a bunch of options in the
   option parser and automatically performs necessary postprocessing after the
   option parsing has been done via the hook function.
void             gt_option_parser_set_min_args(GtOptionParser *option_parser,
                                              unsigned int minimum)
The minimum number of additional command line arguments option_parser
   must parse in order to succeed.
void             gt_option_parser_set_max_args(GtOptionParser *option_parser,
                                              unsigned int maximum)
The maximum number of additional command line arguments option_parser
   must parse in order to succeed.
void             gt_option_parser_set_min_max_args(GtOptionParser *option_parser,
                                                  unsigned int minimum,
                                                  unsigned int maximum)
The minimum and maximum number of additional command line arguments
   option_parser must parse in order to succeed.
GtOPrval         gt_option_parser_parse(GtOptionParser *option_parser,
                                       int *parsed_args,
                                       int argc, const char **argv,
                                       GtShowVersionFunc version_func,
                                       GtError *err)
Use option_parser to parse options given in argument vector argv (with
   argc many arguments). The number of parsed arguments is stored in
   parsed_args. version_func is used for the output of option -version.
   In case of error, GT_OPTION_PARSER_ERROR is returned and err is set
   accordingly.
void             gt_option_parser_reset(GtOptionParser *op)
Reset all options set in op to the default values specified at
   option parser creation time.
void             gt_option_parser_delete(GtOptionParser *option_parser)
Delete option_parser.
Class GtOutputFileInfo
 The GtOutputFileInfo class encapsulates output options. 
GtOutputFileInfo*  gt_output_file_info_new(void)
Create a new GtOutputFileInfo object.
void               gt_output_file_info_register_options(
                                            GtOutputFileInfo *output_file_info,
                                            GtOptionParser *option_parser,
                                            GtFile **outfp)
Registers the options `-o', `-gzip', `-bzip2' and `-force' in
   option_parser. Options chosen during option parsing will be stored in
   output_file_info and the output file will be accessible using *outfp.
   If no option is given, default *outfp will use stdout.
   Caller retains ownership of *outfp.
void               gt_output_file_info_delete(
                                            GtOutputFileInfo *output_file_info)
Deletes output_file_info and frees all associated memory.
Class GtPhase
 This enum type defines the possible phases. The following phases are
   defined: GT_PHASE_ZERO, GT_PHASE_ONE, GT_PHASE_TWO, and
   GT_PHASE_UNDEFINED. 
#define GT_PHASE_CHARS
Use this string to map phase enum types to their corresponding character.
GtPhase  gt_phase_get(char phase_char)
Map phase_char to the corresponding phase enum type.
   An assertion will fail if phase_char is not a valid one.
Class GtQueue
 GtQueue objects are generic queues which can be used to process objects of
   any type in an First-In-First-Out (FIFO) fashion. 
GtQueue*       gt_queue_new(void)
Return a new GtQueue object.
void           gt_queue_add(GtQueue *queue, void *elem)
Add elem to queue (enqueue in computer science terminology).
void*          gt_queue_get(GtQueue *queue)
Remove the first element from non-empty queue and return it (dequeue in
   computer science terminology).
void*          gt_queue_head(GtQueue *queue)
Return the first element in non-empty queue without removing it.
void           gt_queue_remove(GtQueue *queue, void *elem)
Remove elem from queue (elem has to be in queue).
   Thereby queue is traversed in reverse order, leading to
   O(gt_queue_size(queue)) worst-case running time.
GtUword  gt_queue_size(const GtQueue *queue)
Return the number of elements in queue.
void           gt_queue_delete(GtQueue *queue)
Delete queue. Elements contained in queue are not freed!
Class GtRBTree
 The GtRBTree class. Fast logarithmic data structure. This implementation
   does not allow storage of duplicates. 
GtRBTree*       gt_rbtree_new(GtCompareWithData cmp, GtRBTreeFreeFunc free,
                             void *info)
Returns a new GtRBTree object. free might be NULL and will be used
   to free key-object otherwise. info is the data for the cmp-function.
void            gt_rbtree_clear(GtRBTree *tree)
Deletes all tree elements
void*           gt_rbtree_find(const GtRBTree *tree, void *key)
Returns key if element was found in tree and NULL if not
void            gt_rbtree_insert(GtRBTree *tree, void *key)
inserts key into tree. If key is already present in tree, it will not
   be changed.
void*           gt_rbtree_search(GtRBTree *tree, void *key, bool *nodecreated)
Returns key, if key is not present in tree
   it will be inserted and nodecreated set accordingly
int             gt_rbtree_erase(GtRBTree *tree, void *key)
Remove key from tree, returns -1 if no such key exists and 0 on success
Class GtRBTreeIter
GtRBTreeIter*   gt_rbtree_iter_new_from_first(const GtRBTree *tree)
Creates an iterator from the first (smallest) element.
GtRBTreeIter*   gt_rbtree_iter_new_from_last(const GtRBTree *tree)
Creates an iterator from the last (largest) element
void            gt_rbtree_iter_reset_from_first(GtRBTreeIter *trav)
Resets the iterator to the first (smallest) element.
void            gt_rbtree_iter_reset_from_last(GtRBTreeIter *trav)
Resets the iterator to the last (largest) element.
void*           gt_rbtree_iter_next(GtRBTreeIter *trav)
Return next (larger) key, NULL if iterator reached end.
void*           gt_rbtree_iter_prev(GtRBTreeIter *trav)
Return previous (smaller) key, NULL if iterator reached end.
void            gt_rbtree_iter_delete(GtRBTreeIter *trav)
free all memory of trav
Class GtRDBMySQL
 The GtRDBMySQL class implements the GtRDB interface using the
   MySQL client backend. This implementation is only available if
   compiled with the option ``with-mysql=yes''. 
GtRDB*  gt_rdb_mysql_new(const char *server, unsigned int port,
                        const char *database, const char *username,
                        const char *password, GtError *err)
Creates a new GtRDBSqlite object from the database accessible on server
   port port, selecting the database database using the credentials given
   by username and password. Returns NULL on error, err is set
   accordingly.
Class GtRDBSqlite
 The GtRDBSqlite class implements the GtRDB interface using the
   SQLite embedded database backend. This implementation is only available if
   compiled with the option ``with-sqlite=yes''. 
GtRDB*  gt_rdb_sqlite_new(const char *dbpath, GtError *err)
Creates a new GtRDBSqlite object from the database file located at
   dbpath. Returns NULL on error, err is set accordingly.
Class GtRDBVisitor
 The GtRDBVisitor interface, a visitor for GtRDB objects. 
int    gt_rdb_visitor_visit_sqlite(GtRDBVisitor *rdbv, GtRDBSqlite *rdbs,
                                  GtError *err)
Visit a SQLite database rdbs with rdbv. Returns 0 on success,
   a negative value otherwise, and err is set accordingly.
int    gt_rdb_visitor_visit_mysql(GtRDBVisitor *rdbv, GtRDBMySQL *rdbm,
                                 GtError *err)
Visit a MySQL database rdbm with rdbv. Returns 0 on success,
   a negative value otherwise, and err is set accordingly.
void   gt_rdb_visitor_delete(GtRDBVisitor *rdbv)
Delete rdbv.
Class GtRWLock
 The GtRWLock class represents a read/write lock. 
GtRWLock*  gt_rwlock_new(void)
Return a new GtRWLock* object.
void       gt_rwlock_delete(GtRWLock *rwlock)
Delete the given rwlock.
#define gt_rwlock_rdlock(rwlock)
Acquire a read lock for rwlock.
#define gt_rwlock_wrlock(rwlock)
Acquire a write lock for rwlock.
#define gt_rwlock_unlock(rwlock)
Unlock the given rwlock.
Class GtRange
 The GtRange class is used to represent genomic ranges in GenomeTools.
   Thereby, the start must always be smaller or equal than the end. 
int      gt_range_compare(const GtRange *range_a, const GtRange *range_b)
Compare range_a and range_b. Returns 0 if range_a equals range_b, -1
   if range_a starts before range_b or (for equal starts) range_a ends
   before range_b, and 1 else.
int      gt_range_compare_with_delta(const GtRange *range_a,
                                    const GtRange *range_b,
                                    GtUword delta)
Compare range_a and range_b with given delta.
   Returns 0 if range_a equals range_b modulo delta (i.e., the start and
   end points of range_a and range_b are at most delta bases apart), -1
   if range_a starts before range_b or (for equal starts) range_a ends
   before range_b, and 1 else.
bool     gt_range_overlap(const GtRange *range_a, const GtRange *range_b)
Returns true if range_a and range_b overlap, false otherwise.
bool     gt_range_overlap_delta(const GtRange *range_a,
                               const GtRange *range_b,
                               GtUword delta)
Returns true if range_a and range_b overlap at least delta many
   positions, false otherwise.
bool     gt_range_contains(const GtRange *range_a, const GtRange *range_b)
Returns true if range_b is contained in range_a, false otherwise.
bool     gt_range_within(const GtRange *range, GtUword point)
Returns true if point lies within range, false otherwise.
GtRange  gt_range_join(const GtRange *range_a, const GtRange *range_b)
Join range_a and range_b and return the result.
GtRange  gt_range_offset(const GtRange *range, GtWord offset)
Transform start and end of range by offset and return the result.
GtUword  gt_range_length(const GtRange *range)
Returns the length of the given range.
GtRange  gt_range_reorder(GtRange range)
Reorder range.
void     gt_ranges_sort(GtArray *ranges)
Sort an array ranges of ranges.
void     gt_ranges_sort_by_length_stable(GtArray *ranges)
Sort an array ranges of ranges by length.
bool     gt_ranges_are_sorted(const GtArray *ranges)
RetuUE if the ranges in ranges are sorted.
bool     gt_ranges_do_not_overlap(const GtArray *ranges)
Returns TRUE if the ranges in ranges do not overlap.
bool     gt_ranges_are_sorted_and_do_not_overlap(const GtArray *ranges)
Retuns TRUE if the ranges in ranges are sorted and do not overlap.
bool     gt_ranges_are_equal(const GtArray *ranges_a,
                                  const GtArray *ranges_b)
Returns TRUE if the ranges in ranges_a and ranges_b are equal.
void     gt_ranges_uniq(GtArray*, const GtArray*)
Takes a sorted array of ranges and runs the equivalent of uniq on it.
void     gt_ranges_uniq_in_place(GtArray*)
Similar to the previous function, just in place.
GtArray*  gt_ranges_uniq_count(GtArray*, const GtArray*)
Similar to gt_ranges_uniq(), additionally returns an array which contains the
   counts of the occurrences of each elem in the original array.
GtArray*  gt_ranges_uniq_in_place_count(GtArray*)
Similar to the previous function, just in place.S
bool     gt_ranges_are_consecutive(const GtArray *ranges)
Returns TRUE if the ranges in ranges are consecutive.
GtUword  gt_ranges_total_length(const GtArray *ranges)
Returns the sum of the length of the ranges in ranges.
GtUword  gt_ranges_spanned_length(const GtArray *ranges)
Returns the length of the boundaries of the ranges in ranges.
void     gt_ranges_copy_to_opposite_strand(GtArray *outranges,
                                          const GtArray *inranges,
                                          GtUword gen_total_length,
                                          GtUword gen_offset)
Copies ranges inranges to the 'opposite' strand, the result being in
   outranges.
bool     gt_ranges_borders_are_in_region(GtArray *ranges,
                                        const GtRange *region)
Returns TRUE if all ranges in ranges are within the region.
void     gt_ranges_show(GtArray *ranges, GtFile *outfp)
Prints a representation of the ranges ranges to outfp.
Class GtReadmode
 This enum type defines the possible reamodes, namely GT_READMODE_FORWARD,
   GT_READMODE_REVERSE, GT_READMODE_COMPL, and GT_READMODE_REVCOMPL. 
const char*  gt_readmode_show(GtReadmode readmode)
Returns the descriptive string for readmode.
int          gt_readmode_parse(const char *string, GtError *err)
Returns the GtReadmode for the description string, which must be one
   of "fwd","rev","cpl" or "rcl". If string does not equal any of them,
   -1 is returned and err is set accordingly.
GtReadmode  gt_readmode_inverse_dir(GtReadmode readmode)
invert the direction of a readmode: fwd => rev, rev => fwd, cpl => rcl, rcl => cpl
Class GtRecMap
 A GtRecMap object contains a mapping from a 2D coordinate pair
   which identifies a rectangle in a rendered image to the GtFeatureNode it
  represents. The rectangle is defined by the coordinates of its upper left
  (``northwest'') and lower right (``southeast'') points.
  GtRecMap objects are created by an GtImageInfo object which is filled
  during the generation of an image by AnnotationSketch. 
GtRecMap*             gt_rec_map_new(double nw_x, double nw_y, double se_x,
                                    double se_y, GtFeatureNode *f)
Creates a new GtRecMap for feature f with the given coordinates.
GtRecMap*             gt_rec_map_ref(GtRecMap *rm)
Increases the reference count of rm.
double                gt_rec_map_get_northwest_x(const GtRecMap*)
Retrieve x value of the the upper left point of the rectangle.
double                gt_rec_map_get_northwest_y(const GtRecMap*)
Retrieve y value of the the upper left point of the rectangle.
double                gt_rec_map_get_southeast_x(const GtRecMap*)
Retrieve x value of the the lower right point of the rectangle.
double                gt_rec_map_get_southeast_y(const GtRecMap*)
Retrieve y value of the the lower right point of the rectangle.
const GtFeatureNode*  gt_rec_map_get_genome_feature(const GtRecMap*)
Retrieve GtFeatureNode associated with this rectangle.
bool                  gt_rec_map_has_omitted_children(const GtRecMap*)
Returns true if the rectangle represents a block root whose elements
   have not been drawn due to size restrictions.
void                  gt_rec_map_delete(GtRecMap*)
Deletes a GtRecMap and frees all associated memory.
Class GtRegionMapping
 A GtRegionMapping objects maps sequence-regions to the corresponding
   entries of sequence files. 
GtRegionMapping*  gt_region_mapping_new_mapping(GtStr *mapping_filename,
                                               GtError *err)
Return a new GtRegionMapping object for the mapping file with the given
   mapping_filename. In the case of an error, NULL is returned and err is
   set accordingly.
GtRegionMapping*  gt_region_mapping_new_seqfiles(GtStrArray *sequence_filenames,
                                                bool matchdesc, bool usedesc)
Return a new GtRegionMapping object for the sequence files given in
   sequence_filenames. If matchdesc is true, the sequence descriptions
   from the input files are matched for the desired sequence IDs (in GFF3).
   If usedesc is true, the sequence descriptions are used to map the
   sequence IDs (in GFF3) to actual sequence entries. If a description contains
   a sequence range (e.g., III:1000001..2000000), the first part is used as
   sequence ID ('III') and the first range position as offset ('1000001').
   matchdesc and usedesc cannot be true at the same time.
GtRegionMapping*  gt_region_mapping_new_encseq(GtEncseq *encseq, bool matchdesc,
                                              bool usedesc)
Like gt_region_mapping_new_seqfiles(), but using encseq as a sequence
   source.
GtRegionMapping*  gt_region_mapping_new_rawseq(const char *rawseq,
                                              GtUword length, GtUword offset)
Return a new GtRegionMapping object which maps to the given sequence
   rawseq with the corresponding length and offset.
GtRegionMapping*  gt_region_mapping_ref(GtRegionMapping *region_mapping)
Increase the reference count for region_mapping and return it.
int               gt_region_mapping_get_sequence(GtRegionMapping *region_mapping,
                                                char **seq, GtStr *seqid,
                                                GtUword start,
                                                GtUword end,
                                                GtError *err)
Use region_mapping to extract the sequence from start to end of the
   given sequence ID seqid into a buffer written to seq (the caller is
   responsible to free it).
   In the case of an error, -1 is returned and err is set accordingly.
int               gt_region_mapping_get_sequence_length(GtRegionMapping
                                                       *region_mapping,
                                                       GtUword *length,
                                                       GtStr *seqid,
                                                       GtError *err)
Use region_mapping to retrieve the sequence length of the given
   sequence ID seqid and store the result in length.
   In the case of an error, -1 is returned and err is set accordingly.
int               gt_region_mapping_get_description(GtRegionMapping
                                                   *region_mapping,
                                                   GtStr *desc,
                                                   GtStr *seqid,
                                                   GtError *err)
Use region_mapping to get the description of the MD5 sequence ID seqid.
   The description is appended to desc.
   In the case of an error, -1 is returned and err is set accordingly.
const char*       gt_region_mapping_get_md5_fingerprint(GtRegionMapping
                                                       *region_mapping,
                                                       GtStr *seqid,
                                                       const GtRange *range,
                                                       GtUword *offset,
                                                       GtError *err)
Use region_mapping to return the MD5 fingerprint of the sequence with the
   sequence ID seqid and its corresponding range. The offset of the sequence
   is stored in offset.
   In the case of an error, NULL is returned and err is set accordingly.
void              gt_region_mapping_delete(GtRegionMapping *region_mapping)
Delete region_mapping.
Class GtRegionNode
 Implements the GtGenomeNode interface. Region nodes correspond to the
   ##sequence-region lines in GFF3 files.
GtGenomeNode*  gt_region_node_new(GtStr *seqid, GtUword start,
                                               GtUword end)
Create a new GtRegionNode* representing sequence with ID seqid from
   base position start to base position end (1-based).
   start has to be smaller or equal than end.
   The GtRegionNode* stores a new reference to seqid, so make sure you do
   not modify the original seqid afterwards!
GtRegionNode*  gt_region_node_try_cast(GtGenomeNode *gn)
Test whether the given genome node is a region node. If so, a pointer to the region node is returned. If not, NULL is returned. Note that in most cases, one should implement a GtNodeVisitor to handle processing of different GtGenomeNode types.
GtRegionNode*  gt_region_node_cast(GtGenomeNode *gn)
Test whether the given genome node is a region node. If so, a pointer to the region node is returned. If not, an assertion fails.
Class GtScoreMatrix
 GtScoreMatrix represents a matrix of signed integer values, for example
   for scoring alphabet symbols against each other. 
GtScoreMatrix*  gt_score_matrix_new(GtAlphabet *alphabet)
A score matrix is always defined over a given alphabet.
GtScoreMatrix*  gt_score_matrix_clone_empty(const GtScoreMatrix *scorematrix)
Create empty score matrix with same dimension as scorematrix.
GtScoreMatrix*  gt_score_matrix_new_read_protein(const char *path, GtError *err)
Read in a protein score matrix from the given path and return it.
GtScoreMatrix*  gt_score_matrix_new_read(const char *path, GtAlphabet *alphabet,
                                        GtError *err)
Read in score matrix from path over given alphabet and return it.
unsigned int    gt_score_matrix_get_dimension(const GtScoreMatrix *scorematrix)
Return the dimension of scorematrix.
int             gt_score_matrix_get_score(const GtScoreMatrix *scorematrix,
                                         unsigned int idx1, unsigned int idx2)
Return the score value in scorematrix at positions (idx1,idx2).
void            gt_score_matrix_set_score(GtScoreMatrix *scorematrix,
                                         unsigned int idx1, unsigned int idx2,
                                         int score)
Set the score value in scorematrix at positions (idx1,idx2) to
   score.
const int**     gt_score_matrix_get_scores(const GtScoreMatrix *scorematrix)
Return the score values in scorematrix as a two-dimensional array.
void            gt_score_matrix_show(const GtScoreMatrix *scorematrix, FILE *fp)
Print scorematrix to output fp.
void            gt_score_matrix_delete(GtScoreMatrix *scorematrix)
Delete scorematrix.
Class GtScriptWrapperStream
 Implements the GtScriptWrapperStream interface. This stream is
   only used to store pointers to external callbacks, e.g. written in a
   scripting language. This class does not store any state or logic, relying
   on the developer of the external custom stream class to do so.  
GtNodeStream*  gt_script_wrapper_stream_new(GtScriptWrapperStreamNextFunc,
                                           GtScriptWrapperStreamFreeFunc)
Creates a new GtScriptWrapperStream given a next and a free function.
Class GtScriptWrapperVisitor
 Implements the GtNodeVisitor interface. 
GtNodeVisitor*  gt_script_wrapper_visitor_new(
                                         GtScriptWrapperVisitorCommentNodeFunc,
                                         GtScriptWrapperVisitorFeatureNodeFunc,
                                         GtScriptWrapperVisitorRegionNodeFunc,
                                         GtScriptWrapperVisitorSequenceNodeFunc,
                                         GtScriptWrapperVisitorMetaNodeFunc,
                                         GtScriptWrapperVisitorEOFNodeFunc,
                                         GtScriptWrapperVisitorFreeFunc)
Creates a new GtScriptWrapperVisitor for a number of callback functions.
Class GtSelectStream
 Implements the GtNodeStream interface. A GtSelectStream selects certain
   nodes it retrieves from its node source and passes them along. 
GtNodeStream*  gt_select_stream_new(GtNodeStream *in_stream,
                                   GtStr *seqid,
                                   GtStr *source,
                                   const GtRange *contain_range,
                                   const GtRange *overlap_range,
                                   GtStrand strand,
                                   GtStrand targetstrand,
                                   bool has_CDS,
                                   GtUword max_gene_length,
                                   GtUword max_gene_num,
                                   double min_gene_score,
                                   double max_gene_score,
                                   double min_average_splice_site_prob,
                                   GtUword feature_num,
                                   GtStrArray *select_files,
                                   GtStr *select_logic,
                                   GtError *err)
Create a GtSelectStream object which selects genome nodes it retrieves from
   its in_stream and passes them along if they meet the criteria defined by
   the other arguments. All comment nodes are selected.
   If seqid is defined, a genome node must have it to be selected.
   If source is defined, a genome node must have it to be selected.
   If contain_range is defined, a genome node must be contained in it to be
   selected.
   If overlap_range is defined, a genome node must overlap it to be selected.
   If strand is defined, a (top-level) genome node must have it to be
   selected.
   If targetstrand is defined, a feature with a target attribute must have
   exactly one of it and its strand must equal targetstrand.
   If had_cds is true, all top-level features are selected which have a
   child with type CDS.
   If max_gene_length is defined, only genes up to the this length are
   selected.
   If max_gene_num is defined, only so many genes are selected.
   If min_gene_score is defined, only genes with at least this score are
   selected.
   If max_gene_score is defined, only genes with at most this score are
   selected.
   If min_average_splice_site_prob is defined, feature nodes which have
   splice sites must have at least this average splice site score to be
   selected.
   If feature_num is defined, just the feature_numth feature node occurring
   in the in_stream is selected.
   If select_files is defined and has at least one entry, the entries are
   evaluated as Lua scripts containing functions taking GtGenomeNodes that
   are evaluated to boolean values to determine selection. select_logic
   can be "OR" or "AND", defining how the results from the select scripts are
   combined.
   Returns a pointer to a new GtSelectStream or NULL on error (err is set
   accordingly).
void           gt_select_stream_set_drophandler(GtSelectStream *sstr,
                                               GtSelectNodeFunc fp,
                                               void *data)
Sets fp as a handler function to be called for every GtGenomeNode not
   selected by sstr. The void pointer data can be used for arbitrary user
   data.
Class GtSeq
 GtSeq is a container for a sequence plus metadata. 
GtSeq*             gt_seq_new(const char *seq, GtUword seqlen,
                             GtAlphabet *seqalpha)
Create and return a new GtSeq, storing the pointer for seq
   (of length seqlen and with alphabet seqalpha).
GtSeq*             gt_seq_new_own(char *seq, GtUword seqlen,
                                 GtAlphabet *seqalpha)
Like gt_seq_new(), but tkes ownership of seq.
void               gt_seq_set_description(GtSeq *s, const char *desc)
Associates s with description desc, storing its pointer.
void               gt_seq_set_description_own(GtSeq *s, char *desc)
Like gt_seq_set_description(), but takes ownership of desc.
const char*        gt_seq_get_description(GtSeq *s)
Return the description string for s.
const char*        gt_seq_get_orig(const GtSeq *s)
Return the underlying sequence memory for s, not guaranteed to be '\0'
   terminated.
const GtUchar*     gt_seq_get_encoded(GtSeq *s)
Return the sequence for s, encoded using the defined alphabet.
const GtAlphabet*  gt_seq_get_alphabet(const GtSeq*)
Return the alphabet associated with s.
GtUword            gt_seq_length(const GtSeq *s)
Return the length of the sequence in s.
void               gt_seq_delete(GtSeq *s)
Delete s and free all associated memory.
Class GtSeqIterator
void             gt_seq_iterator_set_symbolmap(GtSeqIterator*,
                                              const GtUchar *symbolmap)
Sets a symbol map for the GtSeqIterator.
   If a symbolmap is given, all read in sequences are transformed with it.
   Set to NULL to disable alphabet transformation.
void             gt_seq_iterator_set_sequence_output(GtSeqIterator*, bool)
If set to true, sequences and descriptions are processed (otherwise
   only the descriptions). By default, sequences are processed.
int              gt_seq_iterator_next(GtSeqIterator *seqit,
                                     const GtUchar **sequence,
                                     GtUword *len,
                                     char **description,
                                     GtError *err)
Get next sequence (of length len) and description from seqit.
   Note that seqit retains ownership of the sequence and description.
   Returns 1 if another sequence could be parsed, 0 if all given sequence
   files are exhausted, And -1 if an error occurred (err is set
   accordingly).
const GtUint64*  gt_seq_iterator_getcurrentcounter(GtSeqIterator*,
                                                  GtUint64)
Returns a pointer to the current total number of read characters.
bool             gt_seq_iterator_has_qualities(GtSeqIterator *seqit)
Returns TRUE if seqit supports setting of a quality buffer.
void             gt_seq_iterator_set_quality_buffer(GtSeqIterator *seqit,
                                                   const GtUchar **qualities)
Turns on reporting of sequence qualities to the location
   pointed to by qualities. That pointer will be set to a string containing
   the quality data (which must then be processed into scores).
void             gt_seq_iterator_delete(GtSeqIterator *seqit)
Deletes seqit and frees associated memory.
Class GtSeqIteratorFastQ
GtSeqIterator*  gt_seq_iterator_fastq_new(const GtStrArray *filenametab,
                                         GtError *err)
Create a new GtSeqIteratorFastQ for all sequence files in filenametab.
GtSeqIterator*  gt_seq_iterator_fastq_new_colorspace(const GtStrArray
                                                    *filenametab,
                                                    GtError *err)
Create a new GtSeqIteratorFastQ for all sequence files in filenametab
   containing color space reads.
GtUword   gt_seq_iterator_fastq_get_file_index(GtSeqIteratorFastQ *seqit)
Returns the number of the file in the file name array which seqit is
   currently reading.
void            gt_seq_iterator_fastq_relax_check_of_quality_description(
                                                    GtSeqIteratorFastQ *seqit)
Disable checking if quality description is equal to read description in
   seqit (it should be, but it is not in output of some tools, e.g. Coral).
Class GtSeqIteratorSequenceBuffer
GtSeqIterator*  gt_seq_iterator_sequence_buffer_new(const GtStrArray
                                                   *filenametab,
                                                   GtError *err)
Create a new GtSeqIterator for all sequence files in filenametab.
   All files have to be of the same format, which will be guessed by examining
   the beginning of the first file. If an error occurs, NULL is returned (see
   the err object for details).
Class GtSeqid2FileInfo
 The GtSeqid2FileInfo class represents the state of a sequence source
   statement as given by the -seqfile, -seqfiles, -matchdesc, -usedesc and
   -regionmapping options. 
GtSeqid2FileInfo*  gt_seqid2file_info_new(void)
Create a new GtSeqid2FileInfo object.
void               gt_seqid2file_info_delete(GtSeqid2FileInfo *)
Create a new GtSeqid2FileInfo object.
Class GtSequenceNode
 Implements the GtGenomeNode interface. Sequence nodes correspond to
   singular embedded FASTA sequences in GFF3 files. 
GtGenomeNode*             gt_sequence_node_new(const char *description,
                                              GtStr *sequence)
Create a new GtSequenceNode* representing a FASTA entry with the given
   description and sequence. Takes ownership of sequence.
const char*               gt_sequence_node_get_description(const
                                                          GtSequenceNode
                                                          *sequence_node)
Return the description of sequence_node.
const char*               gt_sequence_node_get_sequence(const GtSequenceNode
                                                       *sequence_node)
Return the sequence of sequence_node.
GtUword                   gt_sequence_node_get_sequence_length(const
                                                              GtSequenceNode
                                                              *sequence_node)
Return the sequence length of sequence_node.
GtSequenceNode*           gt_sequence_node_try_cast(GtGenomeNode *gn)
Test whether the given genome node is a sequence node. If so, a pointer to the sequence node is returned. If not, NULL is returned. Note that in most cases, one should implement a GtNodeVisitor to handle processing of different GtGenomeNode types.
GtSequenceNode*           gt_sequence_node_cast(GtGenomeNode *gn)
Test whether the given genome node is a sequence node. If so, a pointer to the sequence node is returned. If not, an assertion fails.
Class GtSetSourceVisitor
 Implements the GtNodeVisitor interface. Used with the GtVisitorStream
   class, a GtSetSourceVisitor resets the source value for GtFeatureNode
   objects. 
GtNodeVisitor*  gt_set_source_visitor_new(GtStr *newsource)
Create a node visitor object which will reset the source value of all
   GtFeatureNode objects it processes to newsource.
Class GtSortStream
 Implements the GtNodeStream interface. A GtSortStream sorts the
   GtGenomeNode objects it retrieves from its node source. 
GtNodeStream*  gt_sort_stream_new(GtNodeStream *in_stream)
Create a GtSortStream* which sorts the genome nodes it retrieves from
   in_stream and returns them unmodified, but in sorted order.
Class GtSpliceSiteInfoStream
 The GtSpliceSiteInfoStream is a GtNodeStream that gathers splice
   site information from GtFeatureNodes. 
GtNodeStream*  gt_splice_site_info_stream_new(GtNodeStream *in_stream,
                                             GtRegionMapping *region_mapping)
Create a GtSpliceSiteInfoStream, takes ownership of region_mapping.
bool           gt_splice_site_info_stream_show(GtNodeStream *ns, GtFile *outfp)
Prints splice site information gathered in ns to outfp.
bool           gt_splice_site_info_stream_intron_processed(GtNodeStream *ns)
Returns true if an intron has been processed in ns, false otherwise
bool           gt_splice_site_info_stream_show_canonical(GtNodeStream *ns,
                                                        bool show_gc)
Print information for canonical splice sites as stored in ns.
Class GtSplitter
 The GtSplitter class defines objects which can split given strings into
   tokens delimited by a given character, allowing for convenient access to
   each token. 
GtSplitter*    gt_splitter_new(void)
Create a new GtSplitter object.
void           gt_splitter_split(GtSplitter *splitter, char *string,
                                GtUword length, char delimiter)
Use splitter to split string of given length into tokens delimited by
   delimiter. Note that string is modified in the splitting process!
void           gt_splitter_split_non_empty(GtSplitter *s, char *string,
                                          GtUword length, char delimiter)
Use splitter to split string of given length into tokens delimited by
   delimiter. Empty tokens will be ignored. Note that string is modified in
   the splitting process!
char**         gt_splitter_get_tokens(GtSplitter *splitter)
Return all tokens split by splitter in an array.
char*          gt_splitter_get_token(GtSplitter *splitter,
                                    GtUword token_num)
Return token with number token_num from splitter.
void           gt_splitter_reset(GtSplitter *splitter)
Reset the splitter.
GtUword        gt_splitter_size(GtSplitter *splitter)
Return the number of tokens in splitter.
void           gt_splitter_delete(GtSplitter *splitter)
Delete the splitter.
Class GtStatStream
 Implements the GtNodeStream interface. A GtStatStream gathers statistics
   about the GtGenomeNode objects it retrieves from its node source and passes
   them along unmodified. 
GtNodeStream*  gt_stat_stream_new(GtNodeStream *in_stream,
                                 bool gene_length_distribution,
                                 bool gene_score_distribution,
                                 bool exon_length_distribution,
                                 bool exon_number_distribution,
                                 bool intron_length_distribution,
                                 bool cds_length_distribution,
                                 bool used_sources)
Create a GtStatStream object which gathers statistics about the
   GtGenomeNode objects it retrieves from its in_stream and returns them
   unmodified. Besides the basic statistics, statistics about the following
   distributions can be gathered, if the corresponding argument equals true:
   gene_length_distribution, gene_score_distribution,
   exon_length_distribution, exon_number_distribution,
   intron_length_distribution, cds_length_distribution.
   If used_sources equals true, it is recorded which source tags have been
   encountered.
void           gt_stat_stream_show_stats(GtStatStream *stat_stream,
                                        GtFile *outfp)
Write the statistics gathered by stat_stream to outfp.
Class GtStr
 Objects of the GtStr class are strings which grow on demand. 
GtStr*   gt_str_new(void)
Return an empty GtStr object.
GtStr*   gt_str_new_cstr(const char *cstr)
Return a new GtStr object whose content is set to cstr.
GtStr*   gt_str_clone(const GtStr *str)
Return a clone of str.
GtStr*   gt_str_ref(GtStr *str)
Increase the reference count for str and return it.
   If str is NULL, NULL is returned without any side effects.
char*    gt_str_get(const GtStr *str)
Return the content of str.  Never returns NULL, and the content is always
   \0-terminated
void     gt_str_set(GtStr *str, const char *cstr)
Set the content of str to cstr.
void     gt_str_append_str(GtStr *dest, const GtStr *src)
Append the string src to dest.
void     gt_str_append_cstr(GtStr *str, const char *cstr)
Append the \0-terminated cstr to str.
void     gt_str_append_cstr_nt(GtStr *str, const char *cstr, GtUword length)
Append the (not necessarily \0-terminated) cstr with given length to
   str.
void     gt_str_append_char(GtStr *str, char c)
Append character c to str.
void     gt_str_append_double(GtStr *str, double d, int precision)
Append double d to str with given precision.
void     gt_str_append_sci_double(GtStr *dest, double d, int precision)
Append double d to str in scientific notation e.g. 0.52e10,
   with given precision.
void     gt_str_append_uword(GtStr *str, GtUword uword)
Append ulong to str.
void     gt_str_append_int(GtStr *str, int intval)
Append intval to str.
void     gt_str_append_uint(GtStr *str, unsigned int uint)
Append uint to str.
void     gt_str_set_length(GtStr *str, GtUword length)
Set length of str to length. length must be smaller or equal than
   gt_str_length(str).
void     gt_str_reset(GtStr *str)
Reset str to length 0.
int      gt_str_cmp(const GtStr *str1, const GtStr *str2)
Compare str1 and str2 and return the result (similar to strcmp(3)).
GtUword  gt_str_length(const GtStr *str)
Return the length of str. If str is NULL, 0 is returned.
void*   gt_str_get_mem(const GtStr *str)
Return the memory pointed to by *str. Never returns NULL, not always '\0' terminated.
void    gt_str_clip_suffix(GtStr *s, char c)
Remove end of s beginning with first occurrence of c
int     gt_str_read_next_line(GtStr *str, FILE *fpin)
Read the next line from file pointer fpin and store the result in str
   (without the terminal newline). If the end of file fpin is reached, EOF
   is returned, otherwise 0. str should be empty, or the next line will be
   concatenated to its content.
int     gt_str_read_next_line_generic(GtStr*, GtFile*)
Read the next line via a GtFile-object, but otherwise behave as
   the previous function.
void    gt_str_delete(GtStr *str)
Decrease the reference count for str or delete it, if this was the last
   reference.
GtStr*  GtStrConstructorFunc(void *str_source, GtUword index)
Function to obtain a GtStr from a str_source, given an index.
Class GtStrArray
 GtStrArray* objects are arrays of string which grow on demand. 
GtStrArray*    gt_str_array_new(void)
Return a new GtStrArray object.
GtStrArray*    gt_str_array_ref(GtStrArray*)
Increases the reference to a GtStrArray.
void           gt_str_array_add_cstr(GtStrArray *str_array, const char *cstr)
Add cstr to str_array. Thereby, an internal copy of cstr is created.
void           gt_str_array_add_cstr_nt(GtStrArray *str_array, const char *cstr,
                                       GtUword length)
Add the non \0-terminated cstr with given length to str_array.
   Thereby, an internal copy of cstr is created.
void           gt_str_array_add(GtStrArray *str_array, const GtStr *str)
Add str to str_array. Thereby, an internal copy of str is created.
const char*    gt_str_array_get(const GtStrArray *str_array,
                               GtUword strnum)
Return pointer to internal string with number strnum of str_array.
   strnum must be smaller than gt_str_array_size(str_array).
void           gt_str_array_set_cstr(GtStrArray *str_array, GtUword strnum,
                                    const char *cstr)
Set the string with number strnum in str_array to cstr.
void           gt_str_array_set(GtStrArray *str_array, GtUword strnum,
                               const GtStr *str)
Set the string with number strnum in str_array to str.
void           gt_str_array_set_size(GtStrArray *str_array, GtUword size)
Set the size of str_array to size. size must be smaller or equal than
   gt_str_array_size(str_array).
void           gt_str_array_reset(GtStrArray *str_array)
Set the size of str_array to 0.
GtUword        gt_str_array_size(const GtStrArray *str_array)
Return the number of strings stored in str_array.
void           gt_str_array_delete(GtStrArray *str_array)
Delete str_array.
Class GtStrCache
 GtStrCache is a string cache. That is, the first time a certain string is
   requested with the method gt_str_cache_get(), a new string object is
   created via str_constructor and then cached and returned.
   Subsequent calls to gt_str_cache_get() for the same string return a
   new reference made from the cached string. 
GtStrCache*  gt_str_cache_new(void *str_source,
                             GtStrConstructorFunc str_constructor,
                             GtUword num_of_strings)
Create a new string cache object for num_of_strings many strings creatable
   from str_source with the function str_constructor.
GtStr*       gt_str_cache_get(GtStrCache *str_cache, GtUword index)
Return a new (i.e., the caller is responsible to free it) GtStr* object
   from str_cache for string with given index. The mechanics of the cache
   are described in detail in the documentation of GtStrCache.
void         gt_str_cache_delete(GtStrCache *str_cache)
Delete str_cache.
Class GtStrand
 This enum type defines the possible strands. The following strands are
   defined: GT_STRAND_FORWARD, GT_STRAND_REVERSE, GT_STRAND_BOTH, and
   GT_STRAND_UNKNOWN. 
#define GT_STRAND_CHARS
Use this string to map strand enum types to their corresponding character.
GtStrand  gt_strand_get(char strand_char)
Map strand_char to the corresponding strand enum type.
   Returns GT_NUM_OF_STRAND_TYPES if strand_char is not a valid one.
Class GtStyle
 Objects of the GtStyle class hold AnnotationSketch style information
   like colors, margins, collapsing options, and others. The class provides
   methods to set values of various types. Each value is organized into
   a section and is identified by a key. That is, a section, key
   pair must uniquely identify a value. 
GtStyle*            gt_style_new(GtError*)
Creates a new GtStyle object.
GtStyle*            gt_style_ref(GtStyle*)
Increments the reference count of the given GtStyle.
void                gt_style_unsafe_mode(GtStyle*)
Enables unsafe mode (``io'' and ``os'' libraries loaded).
void                gt_style_safe_mode(GtStyle*)
Enables safe mode (``io'' and ``os'' libraries not accessible).
bool                gt_style_is_unsafe(GtStyle *sty)
Returns true if sty is in unsafe mode.
GtStyle*            gt_style_clone(const GtStyle*, GtError*)
Creates a independent (``deep'') copy of the given GtStyle object.
int                 gt_style_load_file(GtStyle*, const char *filename, GtError*)
Loads and executes Lua style file with given filename.
   This file must define a global table called style.
int                 gt_style_load_str(GtStyle*, GtStr *instr, GtError*)
Loads and executes Lua style code from the given GtStr instr.
   This code must define a global table called style.
int                 gt_style_to_str(const GtStyle*, GtStr *outstr, GtError*)
Generates Lua code which represents the given GtStyle object and
   writes it into the GtStr object outstr.
void                gt_style_reload(GtStyle*)
Reloads the Lua style file.
void                gt_style_set_color(GtStyle*, const char *section,
                                      const char *key, const GtColor *color)
Sets a color value in the GtStyle for section section and key to a
   certain color.
GtStyleQueryStatus  gt_style_get_color(const GtStyle *style, const char *section,
                                      const char *key, GtColor *result,
                                      GtFeatureNode *fn, GtError *err)
Retrieves a color value from style for key key in section section.
   The color is written to the location pointed to by result. Optionally, a
   feature node pointer fn can be specified for handling in node-specific
   callbacks.
   Because color definitions can be functions, gt_style_get_color() can fail
   at runtime. In this case, this function returns GT_STYLE_QUERY_ERROR and
   err is set accordingly.
   If the color was not specified in style, a grey default color
   is written to result and GT_STYLE_QUERY_NOT_SET is returned so the caller
   can provide a custom default.
   In case of successful retrieval of an existing color, GT_STYLE_QUERY_OK
   is returned.
GtStyleQueryStatus  gt_style_get_color_with_track(const GtStyle *style,
                                                 const char *section,
                                                 const char *key,
                                                 GtColor *result,
                                                 GtFeatureNode *fn,
                                                 const GtStr *track_id,
                                                 GtError *err)
Identical to gt_style_get_color(), except that it also takes a track_id
   which is passed to a potential callback function in the style file.
void                gt_style_set_str(GtStyle*, const char *section,
                                    const char *key, GtStr *value)
Set string with key key in section to value.
GtStyleQueryStatus  gt_style_get_str(const GtStyle *style, const char *section,
                                    const char *key, GtStr *result,
                                    GtFeatureNode *fn, GtError *err)
Retrieves a string value from style for key key in section section.
   The string is written to the GtStr object result, overwriting its prior
   contents. Optionally, a feature node pointer fn can be specified for
   handling in node-specific callbacks.
   Because color definitions can be functions, gt_style_get_str() can fail at
   runtime. In this case, this function returns GT_STYLE_QUERY_ERROR and err
   is set accordingly.
   If the string was not specified in style, result is left untouched and
   GT_STYLE_QUERY_NOT_SET is returned so the caller can handle this case.
   In case of successful retrieval of an existing string, GT_STYLE_QUERY_OK
   is returned.
GtStyleQueryStatus  gt_style_get_str_with_track(const GtStyle *style,
                                               const char *section,
                                               const char *key,
                                               GtStr *result,
                                               GtFeatureNode *fn,
                                               const GtStr *track_id,
                                               GtError *err)
Identical to gt_style_get_str(), except that it also takes a track_id
   which is passed to a potential callback function in the style file.
void                gt_style_set_num(GtStyle*, const char *section,
                                    const char *key, double number)
Set numeric value of key key in section to number.
GtStyleQueryStatus  gt_style_get_num(const GtStyle *style, const char *section,
                                    const char *key, double *result,
                                    GtFeatureNode *fn, GtError *err)
Retrieves a numeric value from style for key key in section section.
   The value is written to the location pointed to by result. Optionally, a
   feature node pointer fn can be specified for handling in node-specific
   callbacks.
   Because the definitions can be functions, gt_style_get_num() can fail at
   runtime. In this case, this function returns GT_STYLE_QUERY_ERROR and err
   is set accordingly.
   If the number was not specified in style, result is left untouched and
   GT_STYLE_QUERY_NOT_SET is returned so the caller can handle this case.
   In case of successful retrieval of an existing number, GT_STYLE_QUERY_OK
   is returned.
GtStyleQueryStatus  gt_style_get_num_with_track(const GtStyle *style,
                                               const char *section,
                                               const char *key,
                                               double *result,
                                               GtFeatureNode *fn,
                                               const GtStr *track_id,
                                               GtError *err)
Identical to gt_style_get_num(), except that it also takes a track_id
   which is passed to a potential callback function in the style file.
void                gt_style_set_bool(GtStyle*, const char *section,
                                     const char *key, bool val)
Set boolean value of key key in section to val.
GtStyleQueryStatus  gt_style_get_bool(const GtStyle *style, const char *section,
                                     const char *key, bool *result,
                                     GtFeatureNode *fn, GtError *err)
Retrieves a boolean value from style for key key in section section.
   The value is written to the location pointed to by result. Optionally, a
   feature node pointer fn can be specified for handling in node-specific
   callbacks.
   Because the definitions can be functions, gt_style_get_bool() can fail at
   runtime. In this case, this function returns GT_STYLE_QUERY_ERROR and err
   is set accordingly.
   If the value was not specified in style, result is left untouched and
   GT_STYLE_QUERY_NOT_SET is returned so the caller can handle this case.
   In case of successful retrieval of an existing boolean, GT_STYLE_QUERY_OK
   is returned.
GtStyleQueryStatus  gt_style_get_bool_with_track(const GtStyle *style,
                                                const char *section,
                                                const char *key,
                                                bool *result,
                                                GtFeatureNode *fn,
                                                const GtStr *track_id,
                                                GtError *err)
Identical to gt_style_get_bool(), except that it also takes a track_id
   which is passed to a potential callback function in the style file.
void                gt_style_unset(GtStyle*, const char *section,
                                  const char *key)
Unset value of key key in section.
void                gt_style_delete(GtStyle *style)
Deletes this style.
Class GtTagValueMap
A very simple tag/value map absolutely optimized for space (i.e., memory consumption) on the cost of time. Basically, each read/write access costs O(n) time, whereas n denotes the accumulated length of all tags and values contained in the map. Tags and values cannot have length 0.
   The implementation as a char* shines through (also to save one additional
   memory allocation), therefore the usage is a little bit different compared
   to other GenomeTools classes.
   See the implementation of gt_tag_value_map_example() for an ussage
   example. 
void  GtTagValueMapIteratorFunc(const char *tag, const char *value,
                                          void *data)
Iterator function used to iterate over tag/value maps. A tag/value pair
   and user data are given as arguments.
GtTagValueMap  gt_tag_value_map_new(const char *tag, const char *value)
Return a new GtTagValueMap object which stores the given tag/value
   pair.
void           gt_tag_value_map_add(GtTagValueMap *tag_value_map,
                                   const char *tag,
                                   const char *value)
Add tag/value pair to tag_value_map. tag_value_map must not contain
   the given tag already!
void           gt_tag_value_map_set(GtTagValueMap *tag_value_map,
                                   const char *tag, const char *value)
Set the given tag in tag_value_map to value.
const char*    gt_tag_value_map_get(const GtTagValueMap tag_value_map,
                                   const char *tag)
Return value corresponding to tag from tag_value_map. If tag_value_map
   does not contain such a value, NULL is returned.
GtUword        gt_tag_value_map_size(const GtTagValueMap tag_value_map)
Return the number of tag-value pairs in tag_value_map.
void           gt_tag_value_map_remove(GtTagValueMap *tag_value_map,
                                      const char *tag)
Removes the given tag from tag_value_map. tag_value_map must contain
   the given tag already! Also, at least one tag-value pair must remain in
   the map.
void           gt_tag_value_map_foreach(const GtTagValueMap tag_value_map,
                                       GtTagValueMapIteratorFunc iterator_func,
                                       void *data)
Apply iterator_func to each tag/value pair contained in tag_value_map and
   pass data along.
int            gt_tag_value_map_example(GtError *err)
Implements an example useage of a tag/value map.
void           gt_tag_value_map_delete(GtTagValueMap tag_value_map)
Delete tag_value_map.
Class GtTextWidthCalculator
 The GtTextWidthCalculator interface answers queries w.r.t.
   text width in a specific drawing backend. This interface is needed to do
   proper line breaking in a GtLayout even if there is no GtCanvas or
   GtGraphics created yet. 
GtTextWidthCalculator*  gt_text_width_calculator_ref(GtTextWidthCalculator*)
Increases the reference count of the GtTextWidthCalculator.
double                  gt_text_width_calculator_get_text_width(
                                                    GtTextWidthCalculator*,
                                                    const char *text,
                                                    GtError *err)
Requests the width of text from the GtTextWidthCalculator.
   If the returned value is negative, an error occurred. Otherwise,
   a positive double value is returned.
void                    gt_text_width_calculator_delete(GtTextWidthCalculator*)
Deletes a GtTextWidthCalculator instance.
Class GtTextWidthCalculatorCairo
 Implements the GtTextWidthCalculator interface with Cairo as the drawing
   backend. If text width is to be calculated with regard to a specific
   transformation etc. which is in effect in a cairo_t and which should be
   used later via a GtCanvasCairoContext, create a
   GtTextWidthCalculatorCairo object and pass it to the GtLayout via
   gt_layout_new_with_twc(). 
GtTextWidthCalculator*  gt_text_width_calculator_cairo_new(cairo_t*, GtStyle*,
                                                          GtError*)
Creates a new GtTextWidthCalculatorCairo object for the given context
   using the text size options given in the GtStyle. If the GtStyle is NULL,
   the current font settings in the cairo_t will be used for all text
   width calculations.
Class GtThread
 The GtThread class represents a handle to a single thread of execution. 
void*  GtThreadFunc(void *data)
A function to be multithreaded.
GtThread*  gt_thread_new(GtThreadFunc function, void *data, GtError *err)
Create a new thread which executes the given function (with data passed
   to it). Returns a GtThread* handle to the newly created thread, if
   successful. Returns NULL and sets err accordingly upon failure.
void       gt_thread_delete(GtThread *thread)
Delete the given thread handle. Does not stop the thread itself!
void       gt_thread_join(GtThread *thread)
Wait for thread to terminate before continuing execution of the current
   thread.
Class GtTimer
 The GtTimer class encapsulates a timer which can be used for run-time
   measurements. 
GtTimer*  gt_timer_new(void)
Return a new GtTimer object.
GtTimer*  gt_timer_new_with_progress_description(const char* description)
Return a new GtTimer object with the first description.
void      gt_timer_start(GtTimer *timer)
Start the time measurement on timer.
void      gt_timer_stop(GtTimer *timer)
Stop the time measurement on timer.
void      gt_timer_show(GtTimer *timer, FILE *fp)
Output the current state of timer in the format
   ""GT_WD".%06lds real "GT_WD"s user "GT_WD"s system" to file
   pointer fp (see gt_timer_show_formatted).
   The timer is then stopped.
void      gt_timer_show_formatted(GtTimer *timer, const char *fmt, FILE *fp)
Output the current state of timer in a user-defined format given by fmt.
   fmt must be a format string for four "GT_WD" numbers, which are filled
   with: elapsed seconds, elapsed microseconds, used usertime in seconds, system
   time in seconds. The output is written to fp. The timer is then stopped.
GtWord  gt_timer_elapsed_usec(GtTimer *t)
return usec of time from start to stop of giben timer. The timer is then stopped.
void      gt_timer_get_formatted(GtTimer *t, const char *fmt, GtStr *str)
Like gt_timer_show_formatted(), but appends the output to str.
void      gt_timer_show_progress(GtTimer *timer, const char *desc, FILE *fp)
Output the current state of timer on fp since the last call of
   gt_timer_show_progress() or the last start of timer, along with the
   current description. The timer is not stopped, but updated with desc to be
   the next description.
void      gt_timer_show_progress_formatted(GtTimer *timer, FILE *fp,
                                          const char *desc, ...)
Like gt_timer_show_progress(), but allows one to format the description in
   a printf()-like fashion.
void      gt_timer_show_progress_va(GtTimer *timer, FILE *fp, const char *desc,
                                   va_list ap)
Like gt_timer_show_progress(), but allows one to format the description in
   a vprintf()-like fashion using a va_list argument ap.
void      gt_timer_show_progress_final(GtTimer *timer, FILE *fp)
Output the overall time measured with timer from start to now on fp.
void      gt_timer_show_cpu_time_by_progress(GtTimer *timer)
Show also user and sys time in output of
   gt_timer_show_progress[_final]().
void      gt_timer_omit_last_stage(GtTimer *timer)
Hide output of last stage time in gt_timer_show_progress_final().
void      gt_timer_delete(GtTimer *timer)
Delete timer.
Class GtTool
 The GtTool class encapsulates a single GenomeTools tool. Can also be
   used in external applications based on libgenometools. 
void*            GtToolArgumentsNew(void)
Callback function. Must return memory to be used as a storage space for tool arguments.
void             GtToolArgumentsDelete(void *tool_arguments)
Callback function. Must free up all memory reserved by the
   GtToolArgumentsNew function in tool_arguments.
GtOptionParser*  GtToolOptionParserNew(void *tool_arguments)
Callback function. Must return a new GtOptionParser filling
   tool_arguments with content.
int              GtToolArgumentsCheck(int rest_argc,
                                                void *tool_arguments,
                                                GtError *err)
Callback function. Checks the validity of tool_arguments when rest_argc
   additional parameters are given to the tool command line.
   Must return zero if checks are successful, and a negative value otherwise.
   In that case err should be set accordingly.
int              GtToolRunner(int argc, const char **argv,
                                        int parsed_args, void *tool_arguments,
                                        GtError*)
Callback function. Acts as a main entry point for the tool logic.
   Parameters argc and argv are similar to a regular main() function.
   The parsed_args parameter gives the number of parameters already parsed
   by the option parser before additional parameters start. Use tool_arguments
   to access options set by the option parser and write errors to err.
   This function should return the error status of the tool (i.e. 0 for
   success). If the return value is not equal to 0, errors written to err
   will be printed on stderr.
GtTool*          GtToolConstructor(void)
Returns a new self-contained GtTool.
GtTool*  gt_tool_new(GtToolArgumentsNew tool_arguments_new,
                    GtToolArgumentsDelete tool_arguments_delete,
                    GtToolOptionParserNew tool_option_parser_new,
                    GtToolArgumentsCheck tool_arguments_check,
                    GtToolRunner tool_runner)
Create a new tool object, with
   a tool argument constructor gt_tool_arguments_new (optional),
   a tool argument destructor gt_tool_arguments_delete (optional).
   a tool option parser constructor gt_tool_option_parser_new (required),
   a tool argument checker gt_tool_arguments_check (optional),
   a tool runner gt_tool_runner (required), and
   tool_arguments_new and tool_arguments_delete imply each other.
   Returns a new GtTool object.
int      gt_tool_run(GtTool*, int argc, const char **argv, GtError *err)
Run the given tool as follows:
   1. Create a tool arguments object, if necessary.
   2. Create a new option parser and pass the tool arguments along.
   3. Parse the options (argc and argv) with the created option parser.
      Return upon error, continue otherwise.
   4. Check the tool arguments, if necessary.
      Return upon error, continue otherwise.
   5. Run the actual tool with the given arguments (the tool arguments object
      is passed along).
   6. Delete the tool arguments object, if one was created.
      Returns -1 and sets err on error, returns 0 otherwise.
void     gt_tool_delete(GtTool*)
Delete the given tool.
Class GtToolbox
 The GtToolbox class groups several tools into one and can be used to
   structure GenomeTools into sensible sets of subtools. 
GtToolbox*  gt_toolbox_new(void)
Return a new empty GtToolbox.
void        gt_toolbox_add_tool(GtToolbox *toolbox, const char *toolname,
                               GtTool *tool)
Add tool with name toolname to toolbox. Takes ownership of tool.
void        gt_toolbox_add_hidden_tool(GtToolbox *toolbox, const char *toolname,
                                      GtTool *tool)
Add (hidden) tool with name toolname to toolbox. Hidden tools are not
   shown in the output of gt_toolbox_show(). Takes ownership of tool.
GtTool*     gt_toolbox_get_tool(GtToolbox *toolbox, const char *toolname)
Get GtTool with name toolname from toolbox. Returns NULL if tool does
   not exist in toolbox.
int         gt_toolbox_show(const char *progname, void *toolbox, GtError*)
Show all tools in toolbox except the hidden ones. Intended to be used
   as an argument to gt_option_parser_set_comment_func().
void        gt_toolbox_delete(GtToolbox *toolbox)
Deletes toolbox.
Class GtTransTable
 The GtTransTable represents a translation table, i.e. a mapping between
   codons and amino acids, as well as associated metadata. 
GtStrArray*    gt_trans_table_get_scheme_descriptions(void)
Returns a GtStrArray of translation scheme descriptions, each of the
   format "%d: %s", where the number is the translation scheme number (usable
   in gt_translator_set_translation_scheme()) and the string is the scheme
   name.
GtTransTable*  gt_trans_table_new(unsigned int scheme, GtError *err)
Returns a translation table as given by scheme which refers to the numbers
   as reported by gt_translator_get_translation_table_descriptions() or the
   list given at the NCBI web site
   http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi.
   Returns NULL if an error occurred, see err for details.
GtTransTable*  gt_trans_table_new_standard(GtError *err)
Returns the standard translation table.
const char*    gt_trans_table_description(const GtTransTable *tt)
Returns the description of tt.
int            gt_trans_table_translate_codon(const GtTransTable *tt,
                                             char c1, char c2, char c3,
                                             char *amino, GtError *err)
Writes the translation for the codon c1,c2,c3 to the position pointed
   to by amino. The current translation scheme set in translator is used.
   Returns a negative value if an error occurred, see err for details.
   Otherwise, 0 is returned.
bool           gt_trans_table_is_start_codon(const GtTransTable *tt,
                                            char c1, char c2, char c3)
Returns TRUE if the codon c1,c2,c3 is a start codon in tt.
bool           gt_trans_table_is_stop_codon(const GtTransTable *tt,
                                           char c1, char c2, char c3)
Returns TRUE if the codon c1,c2,c3 is a stop codon in tt.
void           gt_trans_table_delete(GtTransTable *tt)
Deletes tt.
Class GtTranslator
 The GtTranslator can be used to  produce 3-frame translations of DNA
   sequences via an iterator interface. 
GtTranslator*       gt_translator_new_with_table(GtTransTable *tt,
                                                GtCodonIterator *ci)
Creates a new GtTranslator, starting its translation at the current
   position of ci. The current reading frame is also taken from the state of
   ci. The translation table tt is used.
GtTranslator*       gt_translator_new(GtCodonIterator *ci)
Creates a new GtTranslator, starting its translation at the current
   position of ci. The current reading frame is also taken from the state of
   ci. The standard translation table is used.
void                gt_translator_set_codon_iterator(GtTranslator *translator,
                                                    GtCodonIterator *ci)
Reinitializes translator with the position and frame status as given in
   ci.
void                gt_translator_set_translation_table(GtTranslator *translator,
                                                       GtTransTable *tt)
Selects the translation scheme in translator to the one identified by
   translation table tt.
GtTranslatorStatus  gt_translator_next(GtTranslator *translator,
                                      char *translated,
                                      unsigned int *frame,
                                      GtError *err)
Returns the translation of the next codon. The currently translated
   character is put in translated while the current reading frame is put in
   frame.
   Returns GT_TRANSLATOR_ERROR if an error occurred, see err for details.
   If the end of the sequence region to translate has been reached,
   GT_TRANSLATOR_END is returned.
   Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned.
GtTranslatorStatus  gt_translator_find_startcodon(GtTranslator *translator,
                                                 GtUword *pos,
                                                 GtError *err)
Moves the translator to the beginning of the first codon in dnaseq (of
   length dnalen) which is a start codon according to the selected translation
   scheme in translator.
   The offset is written to the location pointed to by pos.
   Returns GT_TRANSLATOR_ERROR if an error occurred, see err for details.
   If the end of the sequence region to scan has been reached without finding a
   start codon, GT_TRANSLATOR_END is returned.
   Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned.
GtTranslatorStatus  gt_translator_find_stopcodon(GtTranslator *translator,
                                                GtUword *pos,
                                                GtError *err)
Moves the translator to the beginning of the first codon in dnaseq (of
   length dnalen) which is a stop codon according to the selected translation
   scheme in translator.
   The offset is written to the location pointed to by pos.
   Returns GT_TRANSLATOR_ERROR if an error occurred, see err for details.
   If the end of the sequence region to scan has been reached without finding a
   stop codon, GT_TRANSLATOR_END is returned.
   Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned.
GtTranslatorStatus  gt_translator_find_codon(GtTranslator *translator,
                                            GtStrArray *codons,
                                            GtUword *pos,
                                            GtError *err)
Moves the translator to the beginning of the first codon in dnaseq (of
   length dnalen) which belongs to the set of codons specified in codons.
   The offset is written to the location pointed to by pos.
   Returns GT_TRANSLATOR_ERROR if an error occurred, see err for details.
   If the end of the sequence region to scan has been reached without finding
   one of the codons, GT_TRANSLATOR_END is returned.
   Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned.
void                gt_translator_delete(GtTranslator *translator)
Delete translator.
Class GtTypeChecker
 The GtTypeChecker interface, allows one to check the validity of (genome
   feature) types. 
GtTypeChecker*  gt_type_checker_ref(GtTypeChecker *type_checker)
Increase the reference count for type_checker and return it.
const char*     gt_type_checker_description(GtTypeChecker *type_checker)
Return description of type_checker.
bool            gt_type_checker_is_valid(GtTypeChecker *type_checker,
                                        const char *type)
Return true if type is a valid type for the given type_checker, false
   otherwise.
bool            gt_type_checker_is_partof(GtTypeChecker *type_checker,
                                         const char *parent_type,
                                         const char *child_type)
Return true if child_type is partof parent_type, false otherwise.
bool            gt_type_checker_is_a(GtTypeChecker *type_checker,
                                    const char *parent_type,
                                    const char *child_type)
Return true if child_type is a parent_type, false otherwise.
void            gt_type_checker_delete(GtTypeChecker *type_checker)
Decrease the reference count for type_checker or delete it, if this was the
   last reference.
Class GtTypeCheckerOBO
 Implements the GtTypeChecker interface with types from an OBO file. 
GtTypeChecker*  gt_type_checker_obo_new(const char *obo_file_path, GtError *err)
Create a new GtTypeChecker* for OBO file with given obo_file_path.
   If the OBO file cannot be parsed correctly, NULL is returned and err is
   set correspondingly.
Class GtUniqStream
 Implements the GtNodeStream interface. A GtUniqStream filters out
   repeated features it retrieves from its node source. 
GtNodeStream*  gt_uniq_stream_new(GtNodeStream*)
Create a GtUniqStream object which filters out repeated feature node graphs
   it retrieves from the sorted in_stream and return all other nodes.  Two
   feature node graphs are considered to be repeated if they have the same
   depth-first traversal and each corresponding feature node pair is similar
   according to the gt_feature_node_is_similar() method. For such a repeated
   feature node graph the one with the higher score (of the top-level feature)
   is kept. If only one of the feature node graphs has a defined score, this one
   is kept.
Class GtVisitorStream
 Implements the GtNodeStream interface. 
GtNodeStream*  gt_visitor_stream_new(GtNodeStream *in_stream,
                                    GtNodeVisitor *node_visitor)
Create a new GtVisitorStream*, takes ownership of node_visitor.
   This stream applies node_visitor to each node which passes through it.
   Can be used to implement all streams with such a functionality.
Class GtXRFChecker
 The GtXRFChecker interface, allows one to check the validity of
   Dbxref and Ontology_type attributes. 
GtXRFChecker*  gt_xrf_checker_new(const char *file_path, GtError *err)
Create a new GtXRFChecker from the definitions found in file_path.
   Returns NULL on error, and err is set accordingly.
GtXRFChecker*  gt_xrf_checker_ref(GtXRFChecker *xrf_checker)
Increase reference count for xrf_checker
bool           gt_xrf_checker_is_valid(GtXRFChecker *xrf_checker,
                                      const char *value, GtError *err)
Return true if value is valid for the given xrf_checker,
   false otherwise. In case of value being invalid, err is
   set accordingly.
void           gt_xrf_checker_delete(GtXRFChecker *xrf_checker)
Decrease the reference count for xrf_checker or delete it.
Module Array2dim
#define gt_array2dim_malloc(ARRAY2DIM, ROWS, COLUMNS)
Allocates a new 2-dimensional array with dimensions ROWS x COLUMNS and
   assigns a pointer to the newly allocated space to ARRAY2DIM.
   The size of each element is determined automatically from the type of the
   ARRAY2DIM pointer.
#define gt_array2dim_calloc(ARRAY2DIM, ROWS, COLUMNS)
Allocates a new 2-dimensional array with dimensions ROWS x COLUMNS and
   assigns a pointer to the newly allocated space to ARRAY2DIM.
   The allocated space is initialized to be filled with zeroes.
   The size of each element is determined automatically from the type of the
   ARRAY2DIM pointer.
int      gt_array2dim_example(GtError*)
An example for usage of the Array2dim module.
#define gt_array2dim_delete(ARRAY2DIM)
Frees the space allocated for the 2-dimensional array pointed to by
   ARRAY2DIM.
#define gt_array2dim_sparse_calloc(ARRAY2DIM, ROWS, SIZE, ROWINFO)
Allocates a new 2-dimensional sparse array with the given number of ROWS
   and a total SIZE. Each row starts at the corresponding offset given in
   ROWINFO and has the corresponding length. It assigns a pointer to the newly
   allocated space to ARRAY2DIM. The size of each element is determined
   automatically from the type of the ARRAY2DIM pointer.
Module Array3dim
#define gt_array3dim_malloc(ARRAY3DIM, X_SIZE, Y_SIZE, Z_SIZE)
Allocates a new 3-dimensional array with dimensions X_SIZE x Y_SIZE x
   Z_SIZE and assigns a pointer to the newly allocated space to ARRAY3DIM.
   The size of each element is determined automatically from the type of the
   ARRAY3DIM pointer.
#define gt_array3dim_calloc(ARRAY3DIM, X_SIZE, Y_SIZE, Z_SIZE)
Allocates a new 3-dimensional array with dimensions X_SIZE x Y_SIZE and
   assigns a pointer to the newly allocated space to ARRAY3DIM.
   The allocated space is initialized to be filled with zeroes.
   The size of each element is determined automatically from the type of the
   ARRAY3DIM pointer.
int      gt_array3dim_example(GtError*)
An example for usage of the Array3dim module.
#define gt_array3dim_delete(ARRAY3DIM)
Frees the space allocated for the 3-dimensional array pointed to by
   ARRAY3DIM.
Module Arraydef
#define GT_DECLAREARRAYSTRUCT(TYPE)
GT_DECLAREARRAYSTRUCT expands to a corresponding type definition over some given type.
#define GT_INITARRAY(A,TYPE)
GT_INITARRAY initializes an empty array.
#define GT_COPYARRAY(A,B)
GT_COPYARRAY copies an array.
#define GT_CHECKARRAYSPACE_GENERIC(A,TYPE,L,ADD)
GT_CHECKARRAYSPACE checks if the next (L) cells in the array have been allocated. If this is not the case, then the number of cells allocated is incremented by ADD, which must not be smaller than (L). The contents of the previously filled array elements is of course.
#define GT_CHECKARRAYSPACE(A,TYPE,L)
GT_CHECKARRAYSPACE checks if the integer nextfree##T points to an index for which the space is not allocated yet. If this is the case, the number of cells allocated is incremented by L. The contents of the previously filled array elements is of course maintained.
#define GT_CHECKARRAYSPACEMULTI(A,TYPE,L)
The next macro is a variation of GT_CHECKARRAYSPACE, which checks if the next L cells have been allocated. If not, then this is done.
#define GT_GETNEXTFREEINARRAY(P,A,TYPE,L)
This macro checks the space and delivers a pointer P to the next free element in the array.
#define GT_STOREINARRAY(A,TYPE,L,VAL)
This macro checks the space and stores V in the nextfree-component of the array. nextfree is incremented.
#define GT_FREEARRAY(A,TYPE)
This macro frees the space for an array if it is not NULL.
Module Assert
#define gt_assert(expression)
The gt_assert() macro tests the given expression and if it is false, the
   calling process is terminated. A diagnostic message is written to stderr
   and the abort(3) function is called, effectively terminating the program.
   If expression is true, the gt_assert() macro does nothing.
Module Bsearch
void*  gt_bsearch_data(const void *key, const void *base, size_t nmemb,
                      size_t size, GtCompareWithData, void *data)
Similar interface to bsearch(3), except that the GtCompareWithData
   function gets an additional data pointer.
void   gt_bsearch_all(GtArray *members, const void *key, const void *base,
                     size_t nmemb, size_t size, GtCompareWithData, void *data)
Similar interface to gt_bsearch_data(), except that all members which
   compare as equal are stored in the members array. The order in which the
   elements are added is undefined.
void   gt_bsearch_all_mark(GtArray *members, const void *key, const void *base,
                          size_t nmemb, size_t size, GtCompareWithData,
                          void *data, GtBittab*)
Similar interface to gt_bsearch_all(). Additionally, if a bittab is given
   (which must be of size nmemb), the bits corresponding to the found
   elements are marked (i.e., set).
Module BytePopcount
extern const unsigned char  gt_byte_popcount[256]
Lookup table containing the popcount (number of set bits). Entry at i
   equals popcount(i).
Module ByteSelect
extern const unsigned char  gt_byte_select[2048]
Contains 256 * 8 select values, Entry at index 256 * j + i equals the
   position of the (j + 1)-th set bit in byte i. Positions lie in the range
   [0..7]. Returns 8 if byte i contains less than j set bits.
Module ClassAlloc
void*  gt_class_alloc(size_t size)
Allocates space for a class with size size.
void   gt_class_alloc_clean(void)
Frees static memory allocated for classes.
Module Compat
int      gt_mkstemp(char *templ)
Return (read-write) handle of temporary file, with template templ.
GtUword  gt_pagesize(void)
Returns the page size of the current platform.
Module ConsensusSplicedAlignment
GtRange   GtGetGenomicRangeFunc(const void *sa)
Function to obtain the genomic range from spliced alignment sa.
GtStrand  GtGetStrandFunc(const void *sa)
Function to obtain the strand from spliced alignment sa.
void    GtGetExonsFunc(GtArray *exon_ranges, const void *sa)
Function to obtain exon ranges from spliced alignment sa.
void    GtProcessSpliceFormFunc(GtArray *spliced_alignments_in_form,
                                        const void *set_of_sas,
                                        GtUword number_of_sas,
                                        size_t size_of_sa,
                                        void *userdata)
Function to process the generated from the consensus spliced alignment process.
void  gt_consensus_sa(const void *set_of_sas, GtUword number_of_sas,
                     size_t size_of_sa, GtGetGenomicRangeFunc, GtGetStrandFunc,
                     GtGetExonsFunc, GtProcessSpliceFormFunc, void *userdata)
Construct consensus spliced alignments according to: B.J. Haas, A.L. Delcher, S.M. Mount, J.R. Wortman, R.K. Smith Jr, L.I. Hannick, R. Maiti, C.M. Ronning, D.B. Rusch, C.D. Town, S.L. Salzberg, and O. White. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res., 31(19):5654-5666, 2003. following the description on page 972 and 973 of the paper: G. Gremme, V. Brendel, M.E. Sparks, and S. Kurtz. Engineering a Software Tool for Gene Structure Prediction in Higher Organisms. Information and Software Technology, 47(15):965-978, 2005.
Module Countingsort
void           gt_countingsort(void *out, const void *in, size_t elem_size,
                              GtUword size, GtUword max_elemvalue,
                              void *data, GtGetElemvalue get_elemvalue)
Sort the array of elements pointed to by in containing size many elements
   of size elem_size and store the result in the array out of the same size.
   max_elemvalue denotes the maximum value an element can have.
   get_elemvalue should return an integer value for the given element elem.
   Implements the counting sort algorithm.
   For a description see for example page 175 to page 177 of the book:
   T.H. Cormen, C.E. Leiserson and R.L. Rivest. Introduction to Algorithms.
   MIT Press: Cambridge, MA, 1990.
GtUword  gt_countingsort_get_max(const void *in, size_t elem_size,
                                      GtUword size, void *data,
                                      GtGetElemvalue get_elemvalue)
If max_elemvalue is not known, it can be determined with this function.
Module Cstr
char*    gt_cstr_dup(const char *cstr)
Creates a duplicate of string cstr using the GenomeTools memory
   allocator.
char**   gt_cstr_split(const char *cstr, char sep)
Splits the \0-terminated cstr at all positions where sep occurs and
   returns a C string array in which each element is a separate string between
   the occurrences of sep. The string array is terminated by NULL. The caller
   is responsible to free the result.
char*    gt_cstr_dup_nt(const char *cstr, GtUword length)
Creates a duplicate of string cstr using the GenomeTools memory
   allocator. The string needs not be \0-terminated, instead its length must
   be given.
void     gt_cstr_rep(char *cstr, char f, char t)
Replace each occurrence of f in cstr to t.
void     gt_cstr_show(const char *cstr, GtUword length, FILE *outfp)
Outputs the first length characters of the string cstr to file pointer
   outfp.
GtUword  gt_cstr_length_up_to_char(const char *cstr, char c)
Returns the length of the prefix of cstr ending just before c, if cstr
   does not contain c, strlen(cstr) is returned.
char*    gt_cstr_rtrim(char* cstr, char remove)
Removes all occurrences of remove from the right end of cstr.
Module CstrArray
char**   gt_cstr_array_dup(const char **cstr_array)
Return copy of cstr_array.
char**   gt_cstr_array_prefix_first(const char **cstr_array, const char *p)
Use p and a blank as prefix for cstr_array[0] and return the result.
char**   gt_cstr_array_preprend(const char **cstr_array, const char *p)
Use p as prefix for cstr_array[0] and return the result.
void     gt_cstr_array_show(char **cstr_array, FILE *fp)
Print cstr_array to fp, separated b newlines.
void     gt_cstr_array_show_genfile(const char **cstr_array, GtFile *fp)
Print cstr_array to fp, separated b newlines.
GtUword  gt_cstr_array_size(const char **cstr_array)
Return the count of strings in cstr_array. O(n).
void     gt_cstr_array_delete(char **cstr_array)
Delete cstr_array.
Module Deprecated
#define GT_DEPRECATED(msg)
Deprecated functions, typedefs and structs in API headers should be annotated
   with this macro to get warnings when the gcc or clang compiler is used.
   msg should inform about an alternative API.
Module Divmodmul
#define GT_DIV2(N)
Division by 2.
#define GT_DIV4(N)
Division by 4.
#define GT_DIV8(N)
Division by 8.
#define GT_DIV16(N)
Division by 16.
#define GT_DIV32(N)
Division by 32.
#define GT_DIV64(N)
Division by 64.
#define GT_MOD2(N)
Modulo 2.
#define GT_MOD4(N)
Modulo 4.
#define GT_MOD8(N)
Modulo 8.
#define GT_MOD16(N)
Modulo 16.
#define GT_MOD32(N)
Modulo 32.
#define GT_MOD64(N)
Modulo 64.
#define GT_MULT2(N)
Multiplication by 2.
#define GT_MULT4(N)
Multiplication by 4.
#define GT_MULT8(N)
Multiplication by 8.
#define GT_MULT16(N)
Multiplication by 16.
#define GT_MULT32(N)
Multiplication by 32.
#define GT_MULT64(N)
Multiplication by 64.
#define GT_POW2(N)
Power of 2 to the N-th.
#define GT_LOG2(v)
Binary logarithm of v.
Module Endianess
bool  gt_is_little_endian(void)
Returns true if host CPU is little-endian, false otherwise.
Module Ensure
#define gt_ensure(expr)
The ensure macro used for unit tests. If the expression expr evaluates
   to FALSE, the GtError err will be set and had_err will be set to -1.
   These variables are expected to exist when using this macro.
Module FASTA
void  gt_fasta_show_entry(const char *description, const char *sequence,
                         GtUword sequence_length, GtUword width, GtFile *outfp)
Print a fasta entry with optional description and mandatory sequence to
   outfp. If width is != 0 the sequence is formatted accordingly.
void  gt_fasta_show_entry_nt(const char *description, GtUword description_length,
                            const char *sequence, GtUword sequence_length,
                            GtUword width, GtFile *outfp)
Print a fasta entry with optional description and mandatory sequence to
   outfp. If width is != 0 the sequence is formatted accordingly.
   Will print at most sequence_length characters from sequence if no
   '\0'-byte is encountered. description and description_length are handled
   accordingly if present.
void  gt_fasta_show_entry_str(const char *description, const char *sequence,
                             GtUword sequence_length, GtUword width,
                             GtStr *outstr)
Append a fasta entry with optional description and mandatory sequence to
   outstr. If width is != 0 the sequence is formatted accordingly.
void  gt_fasta_show_entry_nt_str(const char *description,
                                GtUword description_length,
                                const char *sequence,
                                GtUword sequence_length,
                                GtUword width,
                                GtStr *outstr)
Print a fasta entry with optional description and mandatory sequence to
   outstr. If width is != 0 the sequence is formatted accordingly.
   Will print at most sequence_length characters from sequence if no
   '\0'-byte is encountered. description and description_length are handled
   accordingly if present.
void  gt_fasta_show_entry_with_suffix(const char *description,
                                     const char *sequence,
                                     GtUword sequence_length,
                                     const char *suffix, GtUword width,
                                     GtFile *outfp)
Print a fasta entry with optional description and suffix plus mandatory
   sequence to outfp. If width is != 0 the sequence is formatted
   accordingly.
void  gt_fasta_show_entry_nt_with_suffix(const char *description,
                                        GtUword description_length,
                                        const char *sequence,
                                        GtUword sequence_length,
                                        const char *suffix,
                                        GtUword width,
                                        GtFile *outfp)
Print a fasta entry with optional description and suffix plus mandatory
   sequence to outfp. If width is != 0 the sequence is formatted
   accordingly.
   Will print at most sequence_length characters from sequence and at most
   description_length characters from description if present.
void  gt_fasta_show_entry_with_suffix_str(const char *description,
                                         const char *sequence,
                                         GtUword sequence_length,
                                         const char *suffix, GtUword width,
                                         GtStr *outstr)
Print a fasta entry with optional description and suffix plus mandatory
   sequence to outstr. If width is != 0 the sequence is formatted
   accordingly.
void  gt_fasta_show_entry_nt_with_suffix_str(const char *description,
                                            GtUword description_length,
                                            const char *sequence,
                                            GtUword sequence_length,
                                            const char *suffix,
                                            GtUword width,
                                            GtStr *outstr)
Print a fasta entry with optional description and suffix plus mandatory
   sequence to outstr. If width is != 0 the sequence is formatted
   accordingly.
   Will print at most sequence_length characters from sequence and at most
   description_length characters from description if present.
Module FileAllocator
void     gt_fa_init(void)
Initialize file allocator. Only needs to be called once per process.
#define gt_fa_fopen(path, mode, err)
Returns a FILE pointer after opening the file at path with mode.
   If an error occurs, NULL is returned and err is set accordingly.
#define gt_fa_xfopen(path, mode)
Returns a FILE pointer after opening the file at path with mode.
   If an error occurs, the program is terminated.
#define gt_fa_fopen_with_suffix(path, suffix, mode, err)
Returns a FILE pointer after opening the file at path with suffix
   suffix and mode mode. If an error occurs, NULL is returned and err
   is set accordingly.
void     gt_fa_fclose(FILE *stream)
Closes the file stream.
void     gt_fa_xfclose(FILE *stream)
Closes the file stream, terminating on error.
void     gt_fa_lock_shared(FILE *stream)
Obtain a shared lock on stream.
void     gt_fa_lock_exclusive(FILE *stream)
Obtain an exclusive lock on stream.
void     gt_fa_unlock(FILE *stream)
Unlock stream.
#define gt_fa_gzopen(path, mode, err)
Returns a FILE pointer after opening the gzipped file at path with mode.
   If an error occurs, NULL is returned and err is set accordingly.
#define gt_fa_xgzopen(path, mode)
Returns a FILE pointer after opening the gzipped file at path with mode.
   If an error occurs, the program is terminated.
void     gt_fa_gzclose(gzFile stream)
Closes the gzipped file stream.
void     gt_fa_xgzclose(gzFile stream)
Closes the gzipped file stream, terminating on error.
#define gt_fa_bzopen(path, mode, err)
Returns a FILE pointer after opening the bzipped file at path with mode.
   If an error occurs, NULL is returned and err is set accordingly.
#define gt_fa_xbzopen(path, mode)
Returns a FILE pointer after opening the bzipped file at path with mode.
   If an error occurs, the program is terminated.
void     gt_fa_bzclose(BZFILE *stream)
Closes the bzipped file stream.
void     gt_fa_xbzclose(BZFILE *stream)
Closes the bzipped file stream, terminating on error.
#define gt_xtmpfp_generic(template_code, flags)
Create a temp file optionally using template analogous to mkstemp(3).
#define gt_xtmpfp(template_code)
Create a temp file optionally using template analogous to mkstemp(3), with default flags.
#define gt_fa_mmap_read(path, len, err)
Map file path with len len into memory for reading and returns a
   pointer to the mapped region. err is set on error.
#define gt_fa_mmap_read_range(path, len, offset, err)
Map file path with len len starting from offset into memory for
   reading and returns a pointer to the mapped region. err is set on
   error.
#define gt_fa_mmap_write(path, len, err)
Map file path with len len into memory for writing and returns a
   pointer to the mapped region. err is set on error.
#define gt_fa_mmap_write_range(path, len, offset, err)
Map file path with len len starting from offset into memory for
   writing and returns a pointer to the mapped region. err is set on
   error.
#define gt_fa_xmmap_read(path, len)
Map file path with len len into memory for reading and returns a
   pointer to the mapped region. Terminates on error.
#define gt_fa_xmmap_read_range(path, len, offset)
Map file path with len len starting from offset into memory for
   reading and returns a pointer to the mapped region. Terminates on
   error.
#define gt_fa_xmmap_write(path, len)
Map file path with len len into memory for writing and returns a
   pointer to the mapped region. Terminates on error.
#define gt_fa_xmmap_write_range(path, len, offset)
Map file path with len len starting from offset into memory for
   writing and returns a pointer to the mapped region. Terminates on
   error.
void     gt_fa_xmunmap(void *addr)
Unmap mmapped file at address addr.
int      gt_fa_check_fptr_leak(void)
Check if all allocated file pointer have been released, prints to stderr.
int      gt_fa_check_mmap_leak(void)
Check if all allocated memory maps have been freed, prints to stderr.
void     gt_fa_enable_global_spacepeak(void)
Enable bookkeeping for global space peak.
GtUword  gt_fa_get_space_peak(void)
Return current global space peak, in bytes.
GtUword  gt_fa_get_space_current(void)
Return current space usage, in bytes.
void     gt_fa_show_space_peak(FILE *fp)
Print statistics about current space peak to fp.
void     gt_fa_clean(void)
Finalize and free static data held by file allocator.
Module Fileutils
const char*  gt_file_suffix(const char *path)
Returns the suffix of path, if there is any. Returns "" otherwise.
   The suffix is the part after and including the last '.' but after the last
   '/' (or '\' on Windows). Except if path ends with ".gz" or ".bz2", then the
   suffix is the part after and including the second last '.'.
bool         gt_file_exists(const char *path)
Returns true if the file with the given path exists, false otherwise.
bool         gt_file_exists_with_suffix(const char *path, const char *suffix)
Returns true if the file with the name composed of the concatenation of
   path and suffix exists, false otherwise.
bool         gt_file_is_newer(const char *a, const char *b)
Returns true if the file with path a has a later modification time than the
   file with path b, false otherwise.
GtUword      gt_file_number_of_lines(const char*)
Returns the number of lines in a file.
void         gt_file_dirname(GtStr *path, const char *file)
Set path to the dirname of file, if it has one, to "" otherwise.
int          gt_file_find_in_path(GtStr *path, const char *file, GtError*)
Find file in $PATH, if it has no dirname; set path to dirname otherwise.
   Sets path to the empty string if file could not be found in $PATH.
int          gt_file_find_in_env(GtStr *path, const char *file, const char *env,
                                GtError*)
Find  file in the ':'-separated directory list (on Windows ';'-separated)
   specified in environment variable $env, if it has no dirname; set path to
   dirname otherwise. Sets path to the empty string if file could not be
   found in $env.
off_t        gt_file_estimate_size(const char *file)
Return the (estimated) size of file. If file is uncompressed, the exact
   size is returned. If file is compressed, an estimation which assumes that
   file contains a DNA sequence is returned.
off_t        gt_files_estimate_total_size(const GtStrArray *filenames)
Return the (estimated) total size of all files given in filenames.
   Uses gt_file_estimate_size().
int          gt_files_guess_if_protein_sequences(const GtStrArray *filenames,
                                                GtError *err)
Guesse if the sequences contained in the files given in filenames are
   protein sequences. Returns 1 if the guess is that the files contain protein
   sequences. Returns 0 if the guess is that the files contain DNA sequences.
   Returns -1 if an error occurs while reading the files (err is set
   accordingly).
int          gt_file_find_exec_in_path(GtStr *path, const char *file,
                                      GtError *err)
Find regular executable file in $PATH, if it has no dirname; set path to
   dirname otherwise. Sets path to the empty string if regular executable
   file could not be found in $PATH.
off_t        gt_file_size(const char *file)
Return the size of file in bytes. file must exist.
off_t        gt_file_size_with_suffix(const char *path, const char *suffix)
Returns the size of the file whose name is composed of the
  concatenation of path and suffix. file must exist.
bool         gt_file_exists_and_is_dir(const char *path)
Returns true if the file with the given path exists and is a directory,
   false otherwise.
void         gt_xfile_cmp(const char *file1, const char *file2)
Compare two files bytewise, fails hard with exit(1) if files differ.
Module FunctionPointer
int   GtCompare(const void *a, const void *b)
Functions of this type return less than 0 if a is smaller than b,
   0 if a is equal to b, and greater 0 if a is larger than b.
   Thereby, the operators smaller, equal, and larger are
   implementation dependent.
   Do not count on these functions to return -1, 0, or 1!
int   GtCompareWithData(const void*, const void*, void *data)
Similar to GtCompare, but with an additional data pointer.
void  GtFree(void*)
The generic free function pointer type.
Module GFF3Escaping
void  gt_gff3_escape(GtStr *escaped_seq, const char *unescaped_seq,
                    GtUword length)
Escape unescaped_seq of given length for GFF3 format and append the
   result to escaped_seq.
int   gt_gff3_unescape(GtStr *unescaped_seq, const char *escaped_seq,
                      GtUword length, GtError *err)
Unescape GFF3 format escaped_seq of given length and append the result to
   unescaped_seq. Returns a value less than zero on error. err is set
   accordingly.
Module GlobalChaining
void  GtChainProc(GtChain *c, GtFragment *frags,
                            GtUword num_of_fragments,
                            GtUword max_gap_width, void *cpinfo)
Function to process a chain. frags is an array of GtFragments,
   of size num_of_fragments. max_gap_width and cpinfo are passed from
   the gt_globalchaining_*() calls.
void  gt_globalchaining_max(GtFragment *fragments,
                           GtUword num_of_fragments,
                           GtUword max_gap_width, GtChainProc,
                           void *cpinfo)
Perform global chaining with overlaps of num_of_fragments many fragments
   in quadratic time w.r.t. num_of_fragments.
   Two fragments can maximally be max_gap_width many bases away.
   For all global chains of maximal score, the GtChainProc function is called.
   Thereby, GtChainProc does not get the ownership of the GtChain.
void  gt_globalchaining_coverage(GtFragment *fragments,
                                GtUword num_of_fragments,
                                GtUword max_gap_width,
                                GtUword seqlen1, double mincoverage,
                                GtChainProc, void *cpinfo)
Perform global chaining with overlaps of num_of_fragments many fragments
   in quadratic time w.r.t. num_of_fragments.
   Two fragments can maximally be max_gap_width many bases away.
   For all non-overlapping global chains with a coverage of more then
   mincoverage of the sequence in dimension 1 (with length seqlen1), the
   GtChainProc function is called. Thereby, GtChainProc does not get the
   ownership of the GtChain.
Module Grep
int  gt_grep(bool *match, const char *pattern, const char *line, GtError*)
Set match to true if pattern matches line, to false otherwise.
int  gt_grep_nt(bool *match, const char *pattern, const char *line, size_t len,
               GtError *err)
Set match to true if pattern matches line up to len, to false
   otherwise.
Module Init
void  gt_lib_init(void)
Initialize this GenomeTools library instance. This has to be called before the library is used!
void  gt_lib_reg_atexit_func(void)
Registers exit function which calls gt_lib_clean() at exit.
int   gt_lib_clean(void)
Frees all static data associated with the library. Returns 0 if no memory map, file pointer, or memory has been leaked and a value != 0 otherwise.
Module Log
void  gt_log_enable(void)
Enable logging.
bool  gt_log_enabled(void)
Returns true if logging is enabled, false otherwise
void   gt_log_log(const char *format, ...)
Prints the log message obtained from format and following parameters according if logging is enabled. The logging output is prefixed with the string "debug: " and finished by a newline.
void   gt_log_vlog(const char *format, va_list)
Prints the log message obtained from format and following parameter according
   to if logging is enabled analog to gt_log_log(). But in contrast to
   gt_log_log() gt_log_vlog() does not accept individual arguments but a single
   va_list argument instead.
FILE*  gt_log_fp(void)
Return logging file pointer.
void   gt_log_set_fp(FILE *fp)
Set logging file pointer to fp.
Module MD5Fingerprint
char*  gt_md5_fingerprint(const char *sequence, GtUword seqlen)
Returns an MD5 fingerprint of sequence with length seqlen transformed to
   upper case letters (with toupper(3)).
   It is the responsibility of the caller to free the returned string.
Module MD5Seqid
bool  gt_md5_seqid_has_prefix(const char *seqid)
Returns true if seqid has the prefix used to denote MD5 sequence IDs,
   false otherwise.
int   gt_md5_seqid_cmp_seqids(const char *id_a, const char *id_b)
Compares \0-terminated seqid strings id_a and id_b (similarly to
   strcmp(3)), but is aware of MD5 prefixes. That is, if both seqids have MD5
   prefixes, only the MD5 prefixes will be compared. If at least one seqid has
   no MD5 prefix, the sequd without the prefix will sort before the other
   one.
Module Mathsupport
double        gt_logsum(double p1, double p2)
Returns the log of the sum of two log probabilities.
bool          gt_double_equals_one(double)
Returns TRUE if the passed double value equals 1.
bool          gt_double_equals_double(double, double)
Returns TRUE if d1 equals d2.
int           gt_double_compare(double d1, double d2)
Compares two doubles with standard comparator semantics.
bool          gt_double_smaller_double(double d1, double d2)
Returns TRUE if d1 is smaller than d2.
bool          gt_double_larger_double(double d1, double d2)
Returns TRUE if d1 is larger than d2.
GtUword       gt_rand_max(GtUword maximal_value)
Returns a random number between 0 and maximal_value.
double        gt_rand_max_double(double maximal_value)
Returns a random double between 0.0 and maximal_value.
double        gt_rand_0_to_1(void)
Returns a random double between 0.0 and 1.0.
char          gt_rand_char(void)
Returns a random character from 'a' to 'z'.
unsigned int  gt_determinebitspervalue(GtUword maxvalue)
Retuns the log base 2 of an integer maxvalue in
   O(wordsize) operations
GtUword       gt_power_for_small_exponents(unsigned int base,
                                          unsigned int exponent)
Determine pow(base,exponent) for small values of exponent
GtWord        gt_round_to_long(double x)
Return x rounded to the nearest long integer, similar to
   lrint() which may not be available on older glibc versions.
unsigned int  gt_gcd_uint(unsigned int m, unsigned int n)
Compute the greatest common divisor of two unsigned integers
unsigned int  gt_lcm_uint(unsigned int m, unsigned int n)
Compute the least common multiplier of two unsigned integers
double        gt_log_base(double x, double b)
Compute the logarithm of x to the base b
Module MemoryAllocation
void     gt_ma_init(bool bookkeeping)
Initialize the memory allocator. Only needs to be done once per process.
void     gt_ma_enable_global_spacepeak(void)
Enable bookkeeping for global space peak.
void     gt_ma_disable_global_spacepeak(void)
Disable bookkeeping for global space peak.
GtUword  gt_ma_get_space_peak(void)
Return current global space peak, in bytes.
GtUword  gt_ma_get_space_current(void)
Return current space usage, in bytes.
void     gt_ma_show_space_peak(FILE *fp)
Print statistics about current space peak to fp.
void     gt_ma_show_allocations(FILE *fp)
Print statistics about allocations to fp.
bool     gt_ma_bookkeeping_enabled(void)
Returns TRUE if any bookeeping is enabled.
int      gt_ma_check_space_leak(void)
Check if all allocated memory has been freed, prints result to stderr.
void     gt_ma_clean(void)
Finalize and free static data held by memory allocator.
#define gt_malloc(size)
Allocate uninitialized space for an object whose size is specified by
   size and return it.
   Besides the fact that it never returns NULL analog to malloc(3).
#define gt_calloc(nmemb, size)
Allocate contiguous space for an array of nmemb objects, each of whose size
   is size.  The space is initialized to zero.
   Besides the fact that it never returns NULL analog to calloc(3).
#define gt_realloc(ptr, size)
Change the size of the object pointed to by ptr to size bytes and return
   a pointer to the (possibly moved) object.
   Besides the fact that it never returns NULL analog to realloc(3).
#define gt_free(ptr)
Free the space pointed to by ptr. If ptr equals NULL, no action occurs.
   Analog to free(3).
void           gt_free_func(void *ptr)
Analog to gt_free(), but usable as a function pointer.
Module Msort
void  gt_msort(void *base, size_t nmemb, size_t size, GtCompare compar)
Sorts an array of nmemb elements, each of size size, according to compare
   function compar. Uses the merge sort algorithm, the interface equals
   qsort(3).
void  gt_msort_r(void *base, size_t nmemb, size_t size, void *comparinfo,
                GtCompareWithData compar)
Identical to gt_msort() except that the compare function is of
   GtCompareWithData type accepting comparinfo as arbitrary data.
Module Multithread
int        gt_multithread(GtThreadFunc function, void *data, GtError *err)
Execute function (with data passed to it) in gt_jobs many parallel
   threads, if threading is enabled. Otherwise function is executed gt_jobs
   many times sequentially. gt_jobs is a global unsigned int variable.
Module ORF
void  GtORFProcessor(void *data, GtRange *orf, GtUword framenum,
                               const char *frame, bool ends_with_stop_codon)
Function to handle ORFs produced by gt_determine_ORFs().
void  gt_determine_ORFs(GtORFProcessor orf_processor, void *data,
                       unsigned int framenum, const char *frame,
                       GtUword framelen, bool start_codon,
                       bool final_stop_codon, bool framepos,
                       const char *start_codons)
Determine all ORFs in the given frame of length framelength and frame
   number framenum (0, 1, or 2). If start_codon is true a frame has to
   start with a start codon, otherwise a frame can start everywhere (i.e., at
   the first amino acid or after a stop codon). If final_stop_codon is true
   the last ORF must end with a stop codon, otherwise it can be ``open''. For
   each ORF the orf_processor function is called and data, framenum and
   frame is passed along. If framepos is true, the ORF range is reported in
   the coordinate system of the frame (i.e., the amino acids). Otherwise the
   coordinate system of the original sequence is used (i.e., the nucleotides).
   The correct framenum is needed for the conversion.
Module POSIX
char*  gt_basename(const char *path)
This module implements the function gt_basename() according to the
  specifications in
  http://www.unix-systems.org/onlinepubs/7908799/xsh/basename.html
  and
  http://www.opengroup.org/onlinepubs/009695399/
  gt_basename() is equivalent to the function basename(3) which
  is available on most unix systems, but in different libraries and
  with slightly different functionality.
  gt_basename() takes the pathname pointed to by path and returns a pointer to
  the final component of the pathname, deleting any trailing '/' characters.
  If path consists entirely of the '/' character,  then gt_basename() returns
  a pointer to the string "/".
  On Windows '\' is used instead of '/'.
  If path is a null pointer or points to an empty string, gt_basename()
  returns a pointer to the string ".".
  See the implementation of gt_basename_unit_test() for additional examples.
  The caller is responsible for freeing the received pointer!
Module Parseutils
int  gt_parse_int(int *out, const char *nptr)
Parse integer from nptr and store result in out.
   Returns 0 upon success and -1 upon failure.
int  gt_parse_uint(unsigned int *out, const char *nptr)
Parse unsigned integer from nptr and store result in out.
   Returns 0 upon success and -1 upon failure.
int  gt_parse_long(GtWord *out, const char *nptr)
Parse long from nptr and store result in out.
   Returns 0 upon success and -1 upon failure.
int  gt_parse_word(GtWord *out, const char *nptr)
Parse GtWord from nptr and store result in out.
   Returns 0 upon success and -1 upon failure.
int  gt_parse_ulong(GtUword *out, const char *nptr)
Parse ulong from nptr and store result in out.
   Returns 0 upon success and -1 upon failure. Deprecated, use
   gt_parse_uword() instead.
int  gt_parse_uword(GtUword *out, const char *nptr)
Parse GtUword from nptr and store result in out.
   Returns 0 upon success and -1 upon failure.
int  gt_parse_double(double *out, const char *nptr)
Parse double from nptr and store result in out.
   Returns 0 upon success and -1 upon failure.
int  gt_parse_range(GtRange *rng, const char *start, const char *end,
                   unsigned int line_number, const char *filename, GtError*)
Parse a range given by start and end, writing the result into rng.
   Enforces that start is smaller or equal than end. Give filename and
   line_number for error reporting. Returns 0 upon success and -1 upon
   failure.
int  gt_parse_description_range(const char *description, GtRange *range)
Parse the range description in the given description and store it in
   range. Range descriptions have the folowing format: III:1000001..2000000
   That is, the part between ':' and '..' denotes the range start and the part
   after '..' the end. Returns 0 upon success and -1 upon failure.
int  gt_parse_range_tidy(GtRange *rng, const char *start, const char *end,
                        unsigned int line_number, const char *filename,
                        GtError*)
Like gt_parse_range, but issues a warning if start is larger then end
   and swaps both values. It also issues a warning, if start and/or end is
   not-positive and sets the corresponding value to 1.
Module Qsort
void  gt_qsort_r(void *a, size_t n, size_t es, void *data,
                GtCompareWithData cmp)
Like qsort(3), but allows an additional data pointer passed to the
   GtCompareWithData comparison function cmp.
Module RegularSeqID
void  gt_regular_seqid_save(GtStr *seqid, GtStr *description)
Parse ``regular'' sequence ID from description and save it in seqid.
Module Reverse
int  gt_reverse_complement(char *dna_seq, GtUword seqlen, GtError*)
Reverse dna_seq of length seqlen in place.
Module Safearith
void  (GtOverflowHandlerFunc)(const char *src_file, int src_line,
                                      void *data)
Function called when an integer overflow occurs.
#define gt_safearith_assign(dest, src)
Safely assign src to dest, returns false on success, true otherwise.
#define gt_safearith_add_of(c, a, b)
Safely add a to b and assign the result to c,
   returns false on success, true otherwise.
#define gt_safearith_sub_of(c, a, b)
Safely subtract b from a and assign the result to c,
   returns false on success, true otherwise.
#define gt_safe_assign(dest, src)
Assign src to dest or exit upon overflow.
#define gt_safe_add(c, a, b)
Add a to b and assign the result to c or exit upon overflow.
#define gt_safe_sub(c, a, b)
Subtract b from a and assign the result to c or exit upon overflow.
   Warning: this will result in an overflow if c is signed and a and b are
   unsigned values, as integer promotion will garble the tests.
#define gt_safe_abs(j)
Overflow-safe version of abs().
#define gt_safe_labs(j)
Overflow-safe version of labs().
#define gt_safe_llabs(j)
Overflow-safe version of llabs().
#define gt_safe_mult_u32(i, j)
Overflow-safe multiplication of two unsigned 32-bit integers.
#define gt_safe_mult_u64(i, j)
Overflow-safe multiplication of two unsigned 64-bit integers.
#define gt_safe_mult_ulong(i, j)
Overflow-safe multiplication of two ulong integers.
#define gt_safe_cast2long(j)
Overflow-safe typecast to long.
#define gt_safe_cast2ulong(j)
Overflow-safe typecast to unsigned long.
#define gt_safe_cast2ulong_64(j)
Overflow-safe typecast to ulong64.
Module SeqID2File
void               gt_seqid2file_register_options(GtOptionParser *option_parser,
                                                 GtSeqid2FileInfo *s2fi)
Add the options -seqfile, -seqfiles, -matchdesc, -usedesc and
   -regionmapping to the given option_parser.
void               gt_seqid2file_register_options_ext(GtOptionParser
                                                     *option_parser,
                                                     GtSeqid2FileInfo *s2fi,
                                                     bool mandatory,
                                                     bool debug)
Add the options -seqfile, -seqfiles, -matchdesc, -usedesc and
   -regionmapping to the given option_parser. If mandatory is set,
   either option -seqfile, -seqfiles or -regionmapping is mandatory.
   If debug is set, then the options are marked as development options.
bool               gt_seqid2file_option_used(GtSeqid2FileInfo *s2fi)
Returns TRUE if any of the options -seqfile, -seqfiles, -matchdesc,
   -usedesc or -regionmapping stored in s2fi has been specified and
   given a parameter.
GtRegionMapping*   gt_seqid2file_region_mapping_new(GtSeqid2FileInfo *s2fi,
                                                   GtError *err)
Returns a GtRegionMapping based on the s2fi. NULL will be returned
   on error, and err will be set accordingly.
Module Strcmp
int  gt_strcmp(const char *s1, const char *s2)
Returns 0 if s1 == s2, otherwise the equivalent of strcmp(s1,s2).
   Useful as a performance improvement in some cases (for example, to compare
   symbols).
Module Symbol
const char*  gt_symbol(const char *cstr)
Return a symbol (a canonical representation) for cstr. An advantage of
   symbols is that they can be compared for equality by a simple pointer
   comparison, rather than using strcmp() (as it is done in gt_strcmp()).
   Furthermore, a symbol is stored only once in memory for equal cstrs, but
   keep in mind that this memory can never be freed safely during the lifetime
   of the calling program. Therefore, it should only be used for a small set of
   cstrs.
Module Threads
extern unsigned int  gt_jobs
Number of parallel threads to be used.
Module Tooldriver
int  GtToolFunc(int argc, const char **argv, GtError *err)
The prototype of a tool function.
int  gt_tooldriver(GtToolFunc tool, int argc, char *argv[])
The tool driver module allows one to compile a tool into a separate binary.
   This is mostly useful for stand-alone applications like GenomeThreader.
   The tool driver creates an GtError object, calls tool, and reports errors.
int  gt_toolobjdriver(GtToolConstructor, GtShowVersionFunc version_func,
                     int argc, char *argv[])
Optional version_func to override the default one.
Module Undef
#define GT_UNDEF_BOOL
The undefined bool value.
#define GT_UNDEF_CHAR
The undefined char value.
#define GT_UNDEF_DOUBLE
The undefined double value.
#define GT_UNDEF_FLOAT
The undefined float value.
#define GT_UNDEF_INT
The undefined int value.
#define GT_UNDEF_WORD
The undefined GtWord value.
#define GT_UNDEF_LONG
The undefined long value. deprecated
#define GT_UNDEF_UCHAR
The undefined unsigned char value.
#define GT_UNDEF_UINT
The undefined unsigned int value.
#define GT_UNDEF_UWORD
The undefined GtUword value.
#define GT_UNDEF_ULONG
The undefined unsigned long value. deprecated
Module UnitTest
int  GtUnitTestFunc(GtError*)
A unit test function. It is assumed to return 0 on successful test
   completion, otherwise err should be set accordingly.
int  gt_unit_test_run(void *key, void *value, void *data, GtError *err)
Run unit test. key is expected to be a C string, value a
   GtUnitTestFunc. data is assumed to be a pointer to an int,
   containing the test return code. err should not be touched.
Module Unused
#define GT_UNUSED
Unused function arguments should be annotated with this macro to get rid of compiler warnings.
Module Version
const char*  gt_version_check(unsigned int required_major,
                             unsigned int required_minor,
                             unsigned int required_micro)
Check that the GenomeTools library in use is compatible with the given
   version. Generally you would pass in the constants GT_MAJOR_VERSION,
   GT_MINOR_VERSION, and GT_MICRO_VERSION as the three arguments to this
   function.
   Returns NULL if the GenomeTools library is compatible with the given
   version, or a string describing the version mismatch, if the library is not
   compatible.
const char*  gt_version(void)
Return the version of the GenomeTools library in use as a string.
Module VersionFunc
void  gt_versionfunc(const char *progname)
Prints the GenomeTools version header with progname being the name of the
   tool where it is called from.
void  gt_showshortversion(const char *progname)
Prints the short GenomeTools version header with progname being the name
   of the tool where it is called from.
Module Warning
void  GtWarningHandler(void *data, const char *format, va_list ap)
Handler type used to process warnings.
void  gt_warning(const char *format, ...)
Print a warning according to format and ..., if a handler is set.
void  gt_warning_disable(void)
Disable that warnings are shown. That is, subsequent gt_warning() calls
   have no effect.
void  gt_warning_set_handler(GtWarningHandler warn_handler, void *data)
Set warn_handler to handle all warnings issued with gt_warning().
   The data is passed to warning_handler on each invocation.
void  gt_warning_default_handler(void *data, const char *format, va_list ap)
The default warning handler which prints on stderr.
   "warning: " is prepended and a newline is appended to the message defined by
   format and ap. Does not use data.
GtWarningHandler  gt_warning_get_handler(void)
Return currently used GtWarningHandler.
void*  gt_warning_get_data(void)
Return currently used data which is passed to the currently used
   GtWarningHandler.
Module XANSI
void    gt_xatexit(void (*function)
Similar to atexit(3), terminates on error.
void    gt_xfclose(FILE*)
Similar to fclose(3), terminates on error.
void    gt_xfflush(FILE*)
Similar to fflush(3), terminates on error.
int     gt_xfgetc(FILE*)
Similar to fgetc(3), terminates on error.
char*   gt_xfgets(char *s, int size, FILE *stream)
Similar to fgets(3), terminates on error.
void    gt_xfgetpos(FILE*, fpos_t*)
Similar to fgetpos(3), terminates on error.
FILE*   gt_xfopen(const char *path, const char *mode)
Similar to fopen(3), terminates on error.
void    gt_xfputc(int, FILE*)
Similar to fputc(3), terminates on error.
void    gt_xfputs(const char*, FILE*)
Similar to fputs(3), terminates on error.
size_t  gt_xfread(void *ptr, size_t size, size_t nmemb, FILE *fp)
Similar to fread(3), terminates on error.
#define gt_xfread_one(ptr, fp)
Shortcut to gt_xfread() which reads a single element of data (of size
   sizeof (*ptr)) from fp and stores the result in ptr.
void    gt_xfseek(FILE*, GtWord offset, int whence)
Similar to fseek(3), terminates on error.
void    gt_xfsetpos(FILE*, const fpos_t*)
Similar to fsetpos(3), terminates on error.
void    gt_xfwrite(const void *ptr, size_t size, size_t nmemb, FILE *fp)
Similar to fwrite(3), terminates on error.
#define gt_xfwrite_one(ptr, fp)
Shortcut to gt_xfwrite() which writes a single element of data (of size
   sizeof (*ptr)) from ptr to fp.
void    gt_xputchar(int)
Similar to putchar(3), terminates on error.
void    gt_xputs(const char*)
Similar to puts(3), terminates on error.
void    gt_xremove(const char*)
Similar to remove(3), terminates on error.
void    gt_xungetc(int, FILE*)
Similar to ungetc(3), terminates on error.
void    gt_xvfprintf(FILE *stream, const char *format, va_list ap)
Similar to vfprintf(3), terminates on error.
int     gt_xvsnprintf(char *str, size_t size, const char *format, va_list ap)
Similar to vsnprintf(3), terminates on error.
Module XPOSIX
void    gt_xclose(int d)
Wrapper around close(), terminating on error.
FILE*   gt_xfdopen(int filedes, const char *mode)
Wrapper around fdopen(), terminating on error.
void    gt_xfstat(int fd, struct stat *sb)
Wrapper around fstat(), terminating on error.
void    gt_xgetrusage(int who, struct rusage *rusage)
Wrapper around getrusage(), terminating on error.
void    gt_xglob(const char *pattern, int flags,
                int (*errfunc)
Wrapper around glob(), terminating on error.
int     gt_xopen(const char *path, int flags, mode_t mode)
Wrapper around open(), terminating on error.
void    gt_xmkdir(const char *path)
Wrapper around mkdir(), terminating on error.
int     gt_xmkstemp(char *temp)
Wrapper around mkstemp(), terminating on error.
void*   gt_xmmap(void *addr, size_t len, int prot, int flags, int fd,
                off_t offset)
Low-level wrapper for the mmap() routine, terminating on error.
void    gt_xmunmap(void *addr, size_t len)
Generic unmapping routine, terminating on error.
void    gt_xraise(int sig)
Wrapper around raise(), terminating on error.
void    gt_xstat(const char *path, struct stat *sb)
Wrapper around stat(), terminating on error.
time_t  gt_xtime(time_t *tloc)
Wrapper around time(), terminating on error.
void    gt_xunlink(const char *path)
Wrapper around unlink(), terminating on error.
void    gt_xwrite(int d, const void *buf, size_t nbytes)
Wrapper around write(), terminating on error.
Module Yarandom
unsigned int  gt_ya_random(void)
Return a random number.
unsigned int  gt_ya_rand_init(unsigned int)
Initialize random number generator using given seed.
void          gt_ya_rand_clean(void)
Clean up static data for random number generator.
#define GT_RAND_MAX
Maximum random number (2147483647)
#define random()
Return random number up to RAND_MAX.
Index
GT_CHECKARRAYSPACEGT_CHECKARRAYSPACEMULTIGT_CHECKARRAYSPACE_GENERICGT_COPYARRAYGT_DECLAREARRAYSTRUCTGT_DEPRECATEDGT_DIV16GT_DIV2GT_DIV32GT_DIV4GT_DIV64GT_DIV8GT_FREEARRAYGT_GETNEXTFREEINARRAYGT_INITARRAYGT_LOG2GT_MOD16GT_MOD2GT_MOD32GT_MOD4GT_MOD64GT_MOD8GT_MULT16GT_MULT2GT_MULT32GT_MULT4GT_MULT64GT_MULT8GT_OPTION_PARSER_TERMINAL_WIDTHGT_PHASE_CHARSGT_POW2GT_RAND_MAXGT_STOREINARRAYGT_STRAND_CHARSGT_UNDEF_BOOLGT_UNDEF_CHARGT_UNDEF_DOUBLEGT_UNDEF_FLOATGT_UNDEF_INTGT_UNDEF_LONGGT_UNDEF_UCHARGT_UNDEF_UINTGT_UNDEF_ULONGGT_UNDEF_UWORDGT_UNDEF_WORDGT_UNUSEDGtChainProcGtCompareGtCompareWithDataGtDiscDistriIterFuncGtFastaReaderProcDescriptionGtFastaReaderProcSequenceLengthGtFastaReaderProcSequencePartGtFeatureNodeAttributeIterFuncGtFreeGtGetExonsFuncGtGetGenomicRangeFuncGtGetSeqFuncGtGetSeqLenFuncGtGetStrandFuncGtHashmapVisitFuncGtNodeStreamFreeFuncGtNodeStreamNextFuncGtORFProcessorGtProcessSpliceFormFuncGtStrConstructorFuncGtTagValueMapIteratorFuncGtThreadFuncGtToolArgumentsCheckGtToolArgumentsDeleteGtToolArgumentsNewGtToolConstructorGtToolFuncGtToolOptionParserNewGtToolRunnerGtTrackOrderingFuncGtTrackSelectorFuncGtUnitTestFuncGtWarningHandlergt_add_introns_stream_newgt_alphabet_add_mappinggt_alphabet_add_wildcardgt_alphabet_bits_per_symbolgt_alphabet_charactersgt_alphabet_clonegt_alphabet_decodegt_alphabet_decode_seq_to_cstrgt_alphabet_decode_seq_to_fpgt_alphabet_decode_seq_to_strgt_alphabet_deletegt_alphabet_echo_pretty_symbolgt_alphabet_encodegt_alphabet_encode_seqgt_alphabet_equalsgt_alphabet_guessgt_alphabet_is_dnagt_alphabet_is_proteingt_alphabet_new_dnagt_alphabet_new_emptygt_alphabet_new_from_filegt_alphabet_new_from_file_no_suffixgt_alphabet_new_from_sequencegt_alphabet_new_from_stringgt_alphabet_new_proteingt_alphabet_num_of_charsgt_alphabet_outputgt_alphabet_pretty_symbolgt_alphabet_refgt_alphabet_sizegt_alphabet_symbolmapgt_alphabet_to_filegt_alphabet_to_strgt_alphabet_valid_inputgt_alphabet_wildcard_showgt_anno_db_gfflike_newgt_anno_db_schema_deletegt_anno_db_schema_get_feature_indexgt_array2dim_callocgt_array2dim_deletegt_array2dim_examplegt_array2dim_mallocgt_array2dim_sparse_callocgt_array3dim_callocgt_array3dim_deletegt_array3dim_examplegt_array3dim_mallocgt_array_addgt_array_add_arraygt_array_add_elemgt_array_clonegt_array_cmpgt_array_deletegt_array_elem_sizegt_array_getgt_array_get_firstgt_array_get_lastgt_array_get_spacegt_array_in_stream_newgt_array_newgt_array_out_stream_all_newgt_array_out_stream_newgt_array_popgt_array_prepend_arraygt_array_refgt_array_remgt_array_rem_spangt_array_resetgt_array_reversegt_array_set_sizegt_array_sizegt_array_sortgt_array_sort_stablegt_array_sort_stable_with_datagt_array_sort_with_datagt_assertgt_basenamegt_bed_in_stream_newgt_bed_in_stream_set_block_typegt_bed_in_stream_set_feature_typegt_bed_in_stream_set_thick_feature_typegt_bioseq_deletegt_bioseq_delete_indicesgt_bioseq_filenamegt_bioseq_get_alphabetgt_bioseq_get_chargt_bioseq_get_descriptiongt_bioseq_get_encoded_chargt_bioseq_get_encoded_sequencegt_bioseq_get_encoded_sequence_rangegt_bioseq_get_md5_fingerprintgt_bioseq_get_seqgt_bioseq_get_seq_rangegt_bioseq_get_sequencegt_bioseq_get_sequence_lengthgt_bioseq_get_sequence_rangegt_bioseq_get_total_lengthgt_bioseq_md5_to_indexgt_bioseq_newgt_bioseq_new_recreategt_bioseq_new_strgt_bioseq_number_of_sequencesgt_bioseq_seq_has_wildcardsgt_bioseq_show_as_fastagt_bioseq_show_gc_contentgt_bioseq_show_seqlengthdistrigt_bioseq_show_sequence_as_fastagt_bioseq_show_statgt_bittab_andgt_bittab_and_equalgt_bittab_bit_is_setgt_bittab_cmpgt_bittab_complementgt_bittab_count_set_bitsgt_bittab_deletegt_bittab_equalgt_bittab_get_all_bitnumsgt_bittab_get_first_bitnumgt_bittab_get_last_bitnumgt_bittab_get_next_bitnumgt_bittab_nandgt_bittab_newgt_bittab_orgt_bittab_or_equalgt_bittab_set_bitgt_bittab_shift_left_equalgt_bittab_shift_right_equalgt_bittab_showgt_bittab_sizegt_bittab_unsetgt_bittab_unset_bitgt_block_caption_is_visiblegt_block_clonegt_block_deletegt_block_get_captiongt_block_get_rangegt_block_get_range_ptrgt_block_get_sizegt_block_get_strandgt_block_get_top_level_featuregt_block_get_typegt_block_has_only_one_fullsize_elementgt_block_mergegt_block_newgt_block_new_from_nodegt_block_refgt_block_set_captiongt_block_set_caption_visibilitygt_block_set_strandgt_bool_matrix_deletegt_bool_matrix_getgt_bool_matrix_get_first_columngt_bool_matrix_get_last_columngt_bool_matrix_get_next_columngt_bool_matrix_newgt_bool_matrix_setgt_bsearch_allgt_bsearch_all_markgt_bsearch_datagt_buffer_stream_dequeuegt_buffer_stream_newgt_byte_popcount[256]gt_byte_select[2048]gt_callocgt_canvas_cairo_context_newgt_canvas_cairo_file_newgt_canvas_cairo_file_to_filegt_canvas_cairo_file_to_streamgt_canvas_deletegt_canvas_get_heightgt_cds_stream_newgt_cds_visitor_newgt_cds_visitor_set_region_mappinggt_check_boundaries_visitor_newgt_class_allocgt_class_alloc_cleangt_codon_iterator_current_positiongt_codon_iterator_deletegt_codon_iterator_encseq_newgt_codon_iterator_encseq_new_with_readmodegt_codon_iterator_lengthgt_codon_iterator_nextgt_codon_iterator_rewindgt_codon_iterator_simple_newgt_color_deletegt_color_equalsgt_color_newgt_color_setgt_comment_node_castgt_comment_node_get_commentgt_comment_node_newgt_comment_node_try_castgt_consensus_sagt_countingsortgt_countingsort_get_maxgt_csa_stream_newgt_cstr_array_deletegt_cstr_array_dupgt_cstr_array_prefix_firstgt_cstr_array_preprendgt_cstr_array_showgt_cstr_array_show_genfilegt_cstr_array_sizegt_cstr_dupgt_cstr_dup_ntgt_cstr_length_up_to_chargt_cstr_repgt_cstr_rtrimgt_cstr_showgt_cstr_splitgt_cstr_table_addgt_cstr_table_deletegt_cstr_table_getgt_cstr_table_get_allgt_cstr_table_newgt_cstr_table_removegt_cstr_table_resetgt_custom_track_deletegt_custom_track_gc_content_newgt_custom_track_refgt_custom_track_script_wrapper_newgt_determine_ORFsgt_determinebitspervaluegt_diagram_add_custom_trackgt_diagram_deletegt_diagram_get_rangegt_diagram_newgt_diagram_new_from_arraygt_diagram_reset_track_selector_funcgt_diagram_set_track_selector_funcgt_disc_distri_addgt_disc_distri_add_multigt_disc_distri_foreachgt_disc_distri_foreach_in_reverse_ordergt_disc_distri_getgt_disc_distri_newgt_disc_distri_showgt_dlist_addgt_dlist_deletegt_dlist_examplegt_dlist_findgt_dlist_firstgt_dlist_lastgt_dlist_newgt_dlist_new_with_datagt_dlist_removegt_dlist_sizegt_dlistelem_get_datagt_dlistelem_nextgt_dlistelem_previousgt_double_comparegt_double_equals_doublegt_double_equals_onegt_double_larger_doublegt_double_smaller_doublegt_dup_feature_stream_newgt_encseq_alphabetgt_encseq_builder_add_cstrgt_encseq_builder_add_encodedgt_encseq_builder_add_encoded_owngt_encseq_builder_add_multiple_encodedgt_encseq_builder_add_strgt_encseq_builder_buildgt_encseq_builder_create_des_tabgt_encseq_builder_create_esq_tabgt_encseq_builder_create_sds_tabgt_encseq_builder_create_ssp_tabgt_encseq_builder_deletegt_encseq_builder_disable_description_supportgt_encseq_builder_disable_multiseq_supportgt_encseq_builder_do_not_create_des_tabgt_encseq_builder_do_not_create_esq_tabgt_encseq_builder_do_not_create_sds_tabgt_encseq_builder_do_not_create_ssp_tabgt_encseq_builder_enable_description_supportgt_encseq_builder_enable_multiseq_supportgt_encseq_builder_newgt_encseq_builder_resetgt_encseq_builder_set_loggergt_encseq_create_reader_with_readmodegt_encseq_deletegt_encseq_descriptiongt_encseq_effective_filelengthgt_encseq_encoder_are_descs_clippedgt_encseq_encoder_clip_descgt_encseq_encoder_create_des_tabgt_encseq_encoder_create_md5_tabgt_encseq_encoder_create_sds_tabgt_encseq_encoder_create_ssp_tabgt_encseq_encoder_deletegt_encseq_encoder_des_tab_requestedgt_encseq_encoder_disable_description_supportgt_encseq_encoder_disable_lossless_supportgt_encseq_encoder_disable_md5_supportgt_encseq_encoder_disable_multiseq_supportgt_encseq_encoder_do_not_create_des_tabgt_encseq_encoder_do_not_create_md5_tabgt_encseq_encoder_do_not_create_sds_tabgt_encseq_encoder_do_not_create_ssp_tabgt_encseq_encoder_enable_description_supportgt_encseq_encoder_enable_dustgt_encseq_encoder_enable_lossless_supportgt_encseq_encoder_enable_md5_supportgt_encseq_encoder_enable_multiseq_supportgt_encseq_encoder_encodegt_encseq_encoder_get_timergt_encseq_encoder_is_input_dnagt_encseq_encoder_is_input_proteingt_encseq_encoder_md5_tab_requestedgt_encseq_encoder_newgt_encseq_encoder_representationgt_encseq_encoder_sds_tab_requestedgt_encseq_encoder_set_input_dnagt_encseq_encoder_set_input_proteingt_encseq_encoder_set_loggergt_encseq_encoder_set_timergt_encseq_encoder_ssp_tab_requestedgt_encseq_encoder_symbolmap_filegt_encseq_encoder_use_representationgt_encseq_encoder_use_symbolmap_filegt_encseq_extract_decodedgt_encseq_extract_encodedgt_encseq_filenamesgt_encseq_filenumgt_encseq_filenum_first_seqnumgt_encseq_filestartposgt_encseq_get_decoded_chargt_encseq_get_encoded_chargt_encseq_has_description_supportgt_encseq_has_md5_supportgt_encseq_has_multiseq_supportgt_encseq_indexnamegt_encseq_is_64_bitgt_encseq_is_mirroredgt_encseq_loader_deletegt_encseq_loader_des_tab_requiredgt_encseq_loader_disable_autosupportgt_encseq_loader_do_not_mirrorgt_encseq_loader_do_not_require_des_tabgt_encseq_loader_do_not_require_sds_tabgt_encseq_loader_do_not_require_ssp_tabgt_encseq_loader_drop_description_supportgt_encseq_loader_drop_lossless_supportgt_encseq_loader_drop_md5_supportgt_encseq_loader_drop_multiseq_supportgt_encseq_loader_enable_autosupportgt_encseq_loader_loadgt_encseq_loader_mirrorgt_encseq_loader_newgt_encseq_loader_require_des_tabgt_encseq_loader_require_description_supportgt_encseq_loader_require_lossless_supportgt_encseq_loader_require_md5_supportgt_encseq_loader_require_multiseq_supportgt_encseq_loader_require_sds_tabgt_encseq_loader_require_ssp_tabgt_encseq_loader_sds_tab_requiredgt_encseq_loader_set_loggergt_encseq_loader_ssp_tab_requiredgt_encseq_max_seq_lengthgt_encseq_min_seq_lengthgt_encseq_mirrorgt_encseq_num_of_filesgt_encseq_num_of_sequencesgt_encseq_position_is_separatorgt_encseq_position_is_wildcardgt_encseq_reader_deletegt_encseq_reader_next_decoded_chargt_encseq_reader_next_encoded_chargt_encseq_reader_reinit_with_readmodegt_encseq_refgt_encseq_seqlengthgt_encseq_seqnumgt_encseq_seqstartposgt_encseq_total_lengthgt_encseq_unmirrorgt_encseq_versiongt_ensuregt_eof_node_newgt_eof_node_try_castgt_error_checkgt_error_deletegt_error_getgt_error_get_prognamegt_error_is_setgt_error_newgt_error_setgt_error_set_nonvariadicgt_error_set_prognamegt_error_unsetgt_error_vsetgt_extract_feature_stream_newgt_fa_bzclosegt_fa_bzopengt_fa_check_fptr_leakgt_fa_check_mmap_leakgt_fa_cleangt_fa_enable_global_spacepeakgt_fa_fclosegt_fa_fopengt_fa_fopen_with_suffixgt_fa_get_space_currentgt_fa_get_space_peakgt_fa_gzclosegt_fa_gzopengt_fa_initgt_fa_lock_exclusivegt_fa_lock_sharedgt_fa_mmap_readgt_fa_mmap_read_rangegt_fa_mmap_writegt_fa_mmap_write_rangegt_fa_show_space_peakgt_fa_unlockgt_fa_xbzclosegt_fa_xbzopengt_fa_xfclosegt_fa_xfopengt_fa_xgzclosegt_fa_xgzopengt_fa_xmmap_readgt_fa_xmmap_read_rangegt_fa_xmmap_writegt_fa_xmmap_write_rangegt_fa_xmunmapgt_fasta_reader_deletegt_fasta_reader_rungt_fasta_show_entrygt_fasta_show_entry_ntgt_fasta_show_entry_nt_strgt_fasta_show_entry_nt_with_suffixgt_fasta_show_entry_nt_with_suffix_strgt_fasta_show_entry_strgt_fasta_show_entry_with_suffixgt_fasta_show_entry_with_suffix_strgt_feature_in_stream_newgt_feature_in_stream_use_orig_rangesgt_feature_index_add_feature_nodegt_feature_index_add_gff3filegt_feature_index_add_region_nodegt_feature_index_deletegt_feature_index_get_features_for_rangegt_feature_index_get_features_for_seqidgt_feature_index_get_first_seqidgt_feature_index_get_orig_range_for_seqidgt_feature_index_get_range_for_seqidgt_feature_index_get_seqidsgt_feature_index_gfflike_get_all_featuresgt_feature_index_has_seqidgt_feature_index_memory_get_node_by_ptrgt_feature_index_memory_newgt_feature_index_remove_nodegt_feature_index_savegt_feature_node_add_attributegt_feature_node_add_childgt_feature_node_castgt_feature_node_contains_markedgt_feature_node_foreach_attributegt_feature_node_get_attributegt_feature_node_get_attribute_listgt_feature_node_get_multi_representativegt_feature_node_get_phasegt_feature_node_get_scoregt_feature_node_get_sourcegt_feature_node_get_strandgt_feature_node_get_typegt_feature_node_has_sourcegt_feature_node_has_typegt_feature_node_is_markedgt_feature_node_is_multigt_feature_node_is_pseudogt_feature_node_is_similargt_feature_node_iterator_deletegt_feature_node_iterator_newgt_feature_node_iterator_new_directgt_feature_node_iterator_nextgt_feature_node_make_multi_representativegt_feature_node_markgt_feature_node_newgt_feature_node_new_pseudogt_feature_node_new_pseudo_templategt_feature_node_new_standard_genegt_feature_node_number_of_childrengt_feature_node_number_of_children_of_typegt_feature_node_remove_attributegt_feature_node_remove_leafgt_feature_node_score_is_definedgt_feature_node_set_attributegt_feature_node_set_multi_representativegt_feature_node_set_phasegt_feature_node_set_scoregt_feature_node_set_sourcegt_feature_node_set_strandgt_feature_node_set_typegt_feature_node_try_castgt_feature_node_unmarkgt_feature_node_unset_multigt_feature_node_unset_scoregt_feature_out_stream_newgt_feature_stream_newgt_file_basename_lengthgt_file_deletegt_file_delete_without_handlegt_file_dirnamegt_file_estimate_sizegt_file_existsgt_file_exists_and_is_dirgt_file_exists_with_suffixgt_file_find_exec_in_pathgt_file_find_in_envgt_file_find_in_pathgt_file_is_newergt_file_modegt_file_mode_determinegt_file_mode_suffixgt_file_newgt_file_new_from_fileptrgt_file_number_of_linesgt_file_opengt_file_refgt_file_sizegt_file_size_with_suffixgt_file_suffixgt_file_unget_chargt_file_xfgetcgt_file_xfputcgt_file_xfputsgt_file_xopengt_file_xopen_file_modegt_file_xprintfgt_file_xreadgt_file_xrewindgt_file_xwritegt_files_estimate_total_sizegt_files_guess_if_protein_sequencesgt_freegt_free_funcgt_gcd_uintgt_genome_node_acceptgt_genome_node_add_user_datagt_genome_node_cmpgt_genome_node_deletegt_genome_node_get_endgt_genome_node_get_filenamegt_genome_node_get_lengthgt_genome_node_get_line_numbergt_genome_node_get_rangegt_genome_node_get_seqidgt_genome_node_get_startgt_genome_node_get_user_datagt_genome_node_refgt_genome_node_release_user_datagt_genome_node_set_rangegt_genome_nodes_showgt_genome_nodes_sortgt_genome_nodes_sort_stablegt_gff3_escapegt_gff3_in_stream_check_id_attributesgt_gff3_in_stream_enable_strict_modegt_gff3_in_stream_enable_tidy_modegt_gff3_in_stream_get_used_typesgt_gff3_in_stream_new_sortedgt_gff3_in_stream_new_unsortedgt_gff3_in_stream_set_type_checkergt_gff3_in_stream_show_progress_bargt_gff3_out_stream_newgt_gff3_out_stream_retain_id_attributesgt_gff3_out_stream_set_fasta_widthgt_gff3_parser_check_id_attributesgt_gff3_parser_check_region_boundariesgt_gff3_parser_deletegt_gff3_parser_do_not_check_region_boundariesgt_gff3_parser_enable_tidy_modegt_gff3_parser_newgt_gff3_parser_parse_genome_nodesgt_gff3_parser_resetgt_gff3_parser_set_offsetgt_gff3_parser_set_type_checkergt_gff3_parser_set_xrf_checkergt_gff3_unescapegt_gff3_visitor_newgt_gff3_visitor_retain_id_attributesgt_gff3_visitor_set_fasta_widthgt_globalchaining_coveragegt_globalchaining_maxgt_graphics_cairo_draw_curve_datagt_graphics_cairo_newgt_graphics_cairo_new_from_contextgt_graphics_deletegt_graphics_draw_arrowheadgt_graphics_draw_boxgt_graphics_draw_caretgt_graphics_draw_colored_textgt_graphics_draw_curve_datagt_graphics_draw_dashesgt_graphics_draw_horizontal_linegt_graphics_draw_linegt_graphics_draw_rectanglegt_graphics_draw_textgt_graphics_draw_text_centeredgt_graphics_draw_text_clipgt_graphics_draw_text_leftgt_graphics_draw_text_rightgt_graphics_draw_vertical_linegt_graphics_get_image_heightgt_graphics_get_image_widthgt_graphics_get_text_heightgt_graphics_get_text_widthgt_graphics_get_xmarginsgt_graphics_get_ymarginsgt_graphics_save_to_filegt_graphics_save_to_streamgt_graphics_set_background_colorgt_graphics_set_fontgt_graphics_set_marginsgt_grepgt_grep_ntgt_gtf_in_stream_newgt_gtf_out_stream_newgt_hashmap_addgt_hashmap_deletegt_hashmap_foreachgt_hashmap_foreach_in_key_ordergt_hashmap_foreach_orderedgt_hashmap_getgt_hashmap_get_keygt_hashmap_newgt_hashmap_new_no_magt_hashmap_refgt_hashmap_removegt_hashmap_resetgt_id_to_md5_stream_newgt_image_info_deletegt_image_info_get_heightgt_image_info_get_rec_mapgt_image_info_newgt_image_info_num_of_rec_mapsgt_inter_feature_stream_newgt_interval_tree_deletegt_interval_tree_find_all_overlappinggt_interval_tree_find_first_overlappinggt_interval_tree_insertgt_interval_tree_iterate_overlappinggt_interval_tree_newgt_interval_tree_node_get_datagt_interval_tree_node_newgt_interval_tree_removegt_interval_tree_sizegt_interval_tree_traversegt_is_little_endiangt_jobsgt_layout_deletegt_layout_get_heightgt_layout_newgt_layout_new_with_twcgt_layout_set_track_ordering_funcgt_layout_sketchgt_lcm_uintgt_lib_cleangt_lib_initgt_lib_reg_atexit_funcgt_log_basegt_log_enablegt_log_enabledgt_log_fpgt_log_loggt_log_set_fpgt_log_vloggt_logger_deletegt_logger_disablegt_logger_enablegt_logger_enabledgt_logger_loggt_logger_log_forcegt_logger_log_vagt_logger_log_va_forcegt_logger_newgt_logger_set_targetgt_logger_targetgt_logsumgt_ma_bookkeeping_enabledgt_ma_check_space_leakgt_ma_cleangt_ma_disable_global_spacepeakgt_ma_enable_global_spacepeakgt_ma_get_space_currentgt_ma_get_space_peakgt_ma_initgt_ma_show_allocationsgt_ma_show_space_peakgt_mallocgt_match_blast_get_align_lengthgt_match_blast_get_bitscoregt_match_blast_get_evaluegt_match_blast_get_gapopengt_match_blast_get_mismatchesgt_match_blast_get_similaritygt_match_blast_newgt_match_blast_new_extendedgt_match_blast_set_align_lengthgt_match_blast_set_bitscoregt_match_blast_set_evaluegt_match_blast_set_gapopengt_match_blast_set_mismatchesgt_match_blast_set_similaritygt_match_deletegt_match_get_directiongt_match_get_range_seq1gt_match_get_range_seq2gt_match_get_seqid1gt_match_get_seqid2gt_match_iterator_deletegt_match_iterator_nextgt_match_last_get_scoregt_match_last_get_seqno1gt_match_last_get_seqno2gt_match_last_newgt_match_open_get_weightgt_match_open_newgt_match_open_set_weightgt_match_set_range_seq1gt_match_set_range_seq2gt_match_set_seqid1gt_match_set_seqid1_ntgt_match_set_seqid2gt_match_set_seqid2_ntgt_match_sw_get_alignment_lengthgt_match_sw_get_edistgt_match_sw_get_seqno1gt_match_sw_get_seqno2gt_match_sw_newgt_match_visitor_deletegt_match_visitor_visit_match_blastgt_match_visitor_visit_match_opengt_md5_encoder_add_blockgt_md5_encoder_deletegt_md5_encoder_finishgt_md5_encoder_newgt_md5_encoder_resetgt_md5_fingerprintgt_md5_seqid_cmp_seqidsgt_md5_seqid_has_prefixgt_md5_tab_deletegt_md5_tab_disable_file_lockinggt_md5_tab_getgt_md5_tab_mapgt_md5_tab_newgt_md5_tab_new_from_cache_filegt_md5_tab_refgt_md5_tab_sizegt_md5_to_id_stream_newgt_merge_feature_stream_newgt_merge_stream_newgt_meta_node_castgt_meta_node_get_datagt_meta_node_get_directivegt_meta_node_newgt_meta_node_try_castgt_mkstempgt_msortgt_msort_rgt_multithreadgt_mutex_deletegt_mutex_lockgt_mutex_newgt_mutex_unlockgt_node_stream_castgt_node_stream_class_newgt_node_stream_creategt_node_stream_deletegt_node_stream_is_sortedgt_node_stream_nextgt_node_stream_pullgt_node_stream_refgt_node_visitor_deletegt_node_visitor_visit_comment_nodegt_node_visitor_visit_feature_nodegt_node_visitor_visit_meta_nodegt_node_visitor_visit_region_nodegt_node_visitor_visit_sequence_nodegt_option_argument_is_optionalgt_option_deletegt_option_excludegt_option_get_namegt_option_hide_defaultgt_option_implygt_option_imply_either_2gt_option_imply_either_3gt_option_is_development_optiongt_option_is_extended_optiongt_option_is_mandatorygt_option_is_mandatory_eithergt_option_is_mandatory_either_3gt_option_is_mandatory_either_4gt_option_is_setgt_option_new_boolgt_option_new_choicegt_option_new_debuggt_option_new_doublegt_option_new_double_mingt_option_new_double_min_maxgt_option_new_filenamegt_option_new_filename_arraygt_option_new_intgt_option_new_int_maxgt_option_new_int_mingt_option_new_int_min_maxgt_option_new_longgt_option_new_probabilitygt_option_new_rangegt_option_new_range_min_maxgt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