#include "EXTERN.h" #include "perl.h" #include "XSUB.h" #include "ppport.h" #include "emboss_perl.h" #include "bio_emboss_config.h" MODULE = Bio::Emboss_seq PACKAGE = Bio::Emboss PROTOTYPES: ENABLE # code from ajseq.c: automatically generated AjPSeq ajSeqNew () OUTPUT: RETVAL AjPSeq ajSeqNewNameC (txt, name) const char* txt const char* name OUTPUT: RETVAL AjPSeq ajSeqNewNameS (str, name) const AjPStr str const AjPStr name OUTPUT: RETVAL AjPSeq ajSeqNewRangeC (txt, offset, offend, rev) const char* txt ajint offset ajint offend AjBool rev OUTPUT: RETVAL AjPSeq ajSeqNewRangeS (str, offset, offend, rev) const AjPStr str ajint offset ajint offend AjBool rev OUTPUT: RETVAL AjPSeq ajSeqNewRes (size) size_t size OUTPUT: RETVAL AjPSeq ajSeqNewSeq (seq) const AjPSeq seq OUTPUT: RETVAL void ajSeqAssignAccC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignAccS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignDescC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignDescS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignEntryC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignEntryS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignFileC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignFileS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignFullC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignFullS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignGiC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignGiS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignNameC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignNameS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignSeqC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignSeqLenC (seq, txt, len) AjPSeq seq const char* txt ajint len void ajSeqAssignSeqS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignSvC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignSvS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignUfoC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignUfoS (seq, str) AjPSeq seq const AjPStr str void ajSeqAssignUsaC (seq, txt) AjPSeq seq const char* txt void ajSeqAssignUsaS (seq, str) AjPSeq seq const AjPStr str void ajSeqSetOffsets (seq, offset, origlen) AjPSeq seq ajint offset ajint origlen void ajSeqSetRange (seq, pos1, pos2) AjPSeq seq ajint pos1 ajint pos2 void ajSeqSetRangeRev (seq, pos1, pos2) AjPSeq seq ajint pos1 ajint pos2 void ajSeqComplement (seq) AjPSeq seq void ajSeqFmtLower (seq) AjPSeq seq void ajSeqFmtUpper (seq) AjPSeq seq void ajSeqReverseDo (seq) AjPSeq seq void ajSeqReverseForce (seq) AjPSeq seq void ajSeqReverseOnly (seq) AjPSeq seq const char* ajSeqGetAccC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetAccS (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetBegin (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetBeginTrue (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetDescC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetDescS (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetEnd (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetEndTrue (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetEntryC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetEntryS (seq) const AjPSeq seq OUTPUT: RETVAL const AjPFeattable ajSeqGetFeat (seq) const AjPSeq seq OUTPUT: RETVAL AjPFeattable ajSeqGetFeatCopy (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetGiC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetGiS (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetLen (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetLenTrue (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetNameC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetNameS (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetOffend (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetOffset (seq) const AjPSeq seq OUTPUT: RETVAL ajuint ajSeqGetRange (seq, begin, end) const AjPSeq seq ajint& begin ajint& end OUTPUT: RETVAL begin end AjBool ajSeqGetRev (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetSeqC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetSeqS (seq) const AjPSeq seq OUTPUT: RETVAL char* ajSeqGetSeqCopyC (seq) const AjPSeq seq OUTPUT: RETVAL AjPStr ajSeqGetSeqCopyS (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetSvC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetSvS (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetTaxC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetTaxS (seq) const AjPSeq seq OUTPUT: RETVAL const char* ajSeqGetUsaC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetUsaS (seq) const AjPSeq seq OUTPUT: RETVAL AjBool ajSeqIsNuc (seq) const AjPSeq seq OUTPUT: RETVAL AjBool ajSeqIsProt (seq) const AjPSeq seq OUTPUT: RETVAL AjBool ajSeqIsReversedTrue (seq) const AjPSeq seq OUTPUT: RETVAL AjBool ajSeqIsReversed (seq) const AjPSeq seq OUTPUT: RETVAL AjBool ajSeqIsTrimmed (seq) const AjPSeq seq OUTPUT: RETVAL ajint ajSeqCalcCheckgcg (seq) const AjPSeq seq OUTPUT: RETVAL void ajSeqCalcCount (seq, b) const AjPSeq seq ajint& b OUTPUT: b float ajSeqCalcMolwt (seq) const AjPSeq seq OUTPUT: RETVAL ajint ajSeqCalcTrueposMin (seq, imin, ipos) const AjPSeq seq ajint imin ajint ipos OUTPUT: RETVAL ajint ajSeqCalcTruepos (seq, ipos) const AjPSeq seq ajint ipos OUTPUT: RETVAL void ajSeqExit () AjPSeqall ajSeqallNew () OUTPUT: RETVAL void ajSeqallDel (Pseq) AjPSeqall& Pseq OUTPUT: Pseq void ajSeqallSetRange (seq, pos1, pos2) AjPSeqall seq ajint pos1 ajint pos2 void ajSeqallSetRangeRev (seq, pos1, pos2) AjPSeqall seq ajint pos1 ajint pos2 const AjPStr ajSeqallGetFilename (seq) const AjPSeqall seq OUTPUT: RETVAL const AjPStr ajSeqallGetName (seq) const AjPSeqall seq OUTPUT: RETVAL const AjPStr ajSeqallGetUsa (seq) const AjPSeqall seq OUTPUT: RETVAL AjPSeqset ajSeqsetNew () OUTPUT: RETVAL void ajSeqsetDel (Pseq) AjPSeqset& Pseq OUTPUT: Pseq void ajSeqsetDelarray (PPseq) AjPSeqset*& PPseq OUTPUT: PPseq const AjPStr ajSeqsetGetFilename (seq) const AjPSeqset seq OUTPUT: RETVAL const AjPStr ajSeqsetGetFormat (seq) const AjPSeqset seq OUTPUT: RETVAL ajint ajSeqsetGetRange (seq, begin, end) const AjPSeqset seq ajint& begin ajint& end OUTPUT: RETVAL begin end const AjPStr ajSeqsetGetUsa (seq) const AjPSeqset seq OUTPUT: RETVAL ajint ajSeqsetFill (seq) AjPSeqset seq OUTPUT: RETVAL void ajSeqsetReverse (seq) AjPSeqset seq void ajSeqsetSetRange (seq, pos1, pos2) AjPSeqset seq ajint pos1 ajint pos2 void ajSeqsetTrim (seq) AjPSeqset seq AjBool ajSeqsetIsDna (seq) const AjPSeqset seq OUTPUT: RETVAL AjBool ajSeqsetIsNuc (seq) const AjPSeqset seq OUTPUT: RETVAL AjBool ajSeqsetIsProt (seq) const AjPSeqset seq OUTPUT: RETVAL AjBool ajSeqsetIsRna (seq) const AjPSeqset seq OUTPUT: RETVAL void ajSeqDel (Pseq) AjPSeq& Pseq OUTPUT: Pseq void ajSeqClear (seq) AjPSeq seq void ajSeqallClear (seq) AjPSeqall seq void ajSeqTrace (seq) const AjPSeq seq ajint ajSeqcvtGetCodeAsymS (cvt, str) const AjPSeqCvt cvt const AjPStr str OUTPUT: RETVAL void ajSeqTrim (seq) AjPSeq seq void ajSeqGapStandard (seq, gapchar) AjPSeq seq char gapchar OUTPUT: seq void ajSeqstrReverse (Pseq) AjPStr& Pseq OUTPUT: Pseq float ajSeqstrCalcMolwt (seq) const AjPStr seq OUTPUT: RETVAL void ajSeqSetName (seq, setname) AjPSeq seq const AjPStr setname OUTPUT: seq void ajSeqSetNameMulti (seq, setname) AjPSeq seq const AjPStr setname OUTPUT: seq void ajSeqSetUnique (seq) AjPSeq seq void ajSeqGapFill (seq, len) AjPSeq seq ajuint len AjBool ajSeqConvertNum (seq, cvt, Pnumseq) const AjPSeq seq const AjPSeqCvt cvt AjPStr& Pnumseq OUTPUT: RETVAL Pnumseq ajuint ajSeqCountGaps (seq) const AjPSeq seq OUTPUT: RETVAL void ajSeqTraceTitle (seq, title) const AjPSeq seq const char* title ajint ajSeqallGetseqBegin (seq) const AjPSeqall seq OUTPUT: RETVAL ajint ajSeqallGetseqEnd (seq) const AjPSeqall seq OUTPUT: RETVAL ajint ajSeqallGetseqLen (seq) const AjPSeqall seq OUTPUT: RETVAL const AjPStr ajSeqallGetseqName (seq) const AjPSeqall seq OUTPUT: RETVAL ajint ajSeqallGetseqRange (seq, begin, end) const AjPSeqall seq ajint& begin ajint& end OUTPUT: RETVAL begin end ajint ajSeqsetGetOffend (seq) const AjPSeqset seq OUTPUT: RETVAL ajint ajSeqsetGetOffset (seq) const AjPSeqset seq OUTPUT: RETVAL void ajSeqsetFmtLower (seq) AjPSeqset seq void ajSeqsetFmtUpper (seq) AjPSeqset seq ajuint ajSeqsetGetBegin (seq) const AjPSeqset seq OUTPUT: RETVAL ajuint ajSeqsetGetEnd (seq) const AjPSeqset seq OUTPUT: RETVAL ajuint ajSeqsetGetLen (seq) const AjPSeqset seq OUTPUT: RETVAL const char* ajSeqsetGetNameC (seq) const AjPSeqset seq OUTPUT: RETVAL const AjPStr ajSeqsetGetNameS (seq) const AjPSeqset seq OUTPUT: RETVAL AjPSeq* ajSeqsetGetSeqarray (seq) const AjPSeqset seq OUTPUT: RETVAL ajuint ajSeqsetGetSize (seq) const AjPSeqset seq OUTPUT: RETVAL float ajSeqsetGetTotweight (seq) const AjPSeqset seq OUTPUT: RETVAL const char* ajSeqsetGetseqAccC (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL const AjPStr ajSeqsetGetseqAccS (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL const char* ajSeqsetGetseqNameC (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL const AjPStr ajSeqsetGetseqNameS (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL const AjPSeq ajSeqsetGetseqSeq (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL const char* ajSeqsetGetseqSeqC (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL const AjPStr ajSeqsetGetseqSeqS (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL float ajSeqsetGetseqWeight (seq, i) const AjPSeqset seq ajuint i OUTPUT: RETVAL AjBool ajSeqstrConvertNum (seq, cvt, Pnumseq) const AjPStr seq const AjPSeqCvt cvt AjPStr& Pnumseq OUTPUT: RETVAL Pnumseq void ajSeqcvtTrace (cvt) const AjPSeqCvt cvt AjPSeqCvt ajSeqcvtNewC (bases) const char* bases OUTPUT: RETVAL AjPSeqCvt ajSeqcvtNewEndC (bases) const char* bases OUTPUT: RETVAL AjPSeqCvt ajSeqcvtNewNumberC (bases) const char* bases OUTPUT: RETVAL AjPSeqCvt ajSeqcvtNewStr (basearray, numbases) AjPPStr basearray ajint numbases OUTPUT: RETVAL AjPSeqCvt ajSeqcvtNewStrAsym (basearray, numbases, matchbases, nummatch) AjPPStr basearray ajint numbases AjPPStr matchbases ajint nummatch OUTPUT: RETVAL void ajSeqcvtDel (Pcvt) AjPSeqCvt& Pcvt OUTPUT: Pcvt ajint ajSeqcvtGetCodeK (cvt, ch) const AjPSeqCvt cvt char ch OUTPUT: RETVAL ajint ajSeqcvtGetCodeS (cvt, str) const AjPSeqCvt cvt const AjPStr str OUTPUT: RETVAL ajuint ajSeqcvtGetLen (cvt) const AjPSeqCvt cvt OUTPUT: RETVAL AjBool ajSeqtestIsAccession (str) const AjPStr str OUTPUT: RETVAL const AjPStr ajSeqtestIsSeqversion (str) const AjPStr str OUTPUT: RETVAL ajuint ajSeqstrCountGaps (seq) const AjPStr seq OUTPUT: RETVAL void ajSeqstrComplement (Pseq) AjPStr& Pseq OUTPUT: Pseq const char* ajSeqGetDbC (seq) const AjPSeq seq OUTPUT: RETVAL const AjPStr ajSeqGetDbS (seq) const AjPSeq seq OUTPUT: RETVAL AjPSeqDate ajSeqdateNew () OUTPUT: RETVAL AjPSeqDate ajSeqdateNewDate (date) const AjPSeqDate date OUTPUT: RETVAL void ajSeqdateDel (Pdate) AjPSeqDate& Pdate OUTPUT: Pdate AjBool ajSeqdateSetCreateS (date, datestr) AjPSeqDate date const AjPStr datestr OUTPUT: RETVAL date AjBool ajSeqdateSetModifyS (date, datestr) AjPSeqDate date const AjPStr datestr OUTPUT: RETVAL date AjBool ajSeqdateSetModseqS (date, datestr) AjPSeqDate date const AjPStr datestr OUTPUT: RETVAL date AjPSeqRef ajSeqrefNew () OUTPUT: RETVAL AjPSeqRef ajSeqrefNewRef (ref) const AjPSeqRef ref OUTPUT: RETVAL void ajSeqrefDel (Pref) AjPSeqRef& Pref OUTPUT: Pref AjBool ajSeqrefAppendAuthors (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefAppendComment (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefAppendGroupname (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefAppendLocation (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefAppendPosition (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefAppendTitle (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefAppendXref (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefFmtAuthorsEmbl (ref, Pdest) const AjPSeqRef ref AjPStr& Pdest OUTPUT: RETVAL Pdest AjBool ajSeqrefFmtAuthorsGb (ref, Pdest) const AjPSeqRef ref AjPStr& Pdest OUTPUT: RETVAL Pdest AjBool ajSeqrefFmtLocationEmbl (ref, Pdest) const AjPSeqRef ref AjPStr& Pdest OUTPUT: RETVAL Pdest AjBool ajSeqrefFmtLocationGb (ref, Pdest) const AjPSeqRef ref AjPStr& Pdest OUTPUT: RETVAL Pdest AjBool ajSeqrefFmtTitleGb (ref, Pdest) const AjPSeqRef ref AjPStr& Pdest OUTPUT: RETVAL Pdest AjBool ajSeqrefSetAuthors (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetComment (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetGroupname (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetLocation (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetLoctype (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetPosition (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetTitle (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetXref (ref, str) AjPSeqRef ref const AjPStr str OUTPUT: RETVAL AjBool ajSeqrefSetnumNumber (ref, num) AjPSeqRef ref ajuint num OUTPUT: RETVAL AjBool ajSeqrefStandard (ref) AjPSeqRef ref OUTPUT: RETVAL AjBool ajSeqreflistClone (src, dest) const AjPList src AjPList dest OUTPUT: RETVAL dest AjBool ajSeqclsSetEmbl (Pcls, clsembl) AjPStr& Pcls const AjPStr clsembl OUTPUT: RETVAL Pcls AjBool ajSeqclsSetGb (Pcls, clsgb) AjPStr& Pcls const AjPStr clsgb OUTPUT: RETVAL Pcls const char* ajSeqclsGetEmbl (cls) const AjPStr cls OUTPUT: RETVAL AjBool ajSeqdivSetEmbl (Pdivi, divembl) AjPStr& Pdivi const AjPStr divembl OUTPUT: RETVAL Pdivi AjBool ajSeqdivSetGb (Pdivi, divgb) AjPStr& Pdivi const AjPStr divgb OUTPUT: RETVAL Pdivi const char* ajSeqdivGetEmbl (divi) const AjPStr divi OUTPUT: RETVAL const char* ajSeqdivGetGb (divi) const AjPStr divi OUTPUT: RETVAL AjBool ajSeqmolSetEmbl (Pmol, molembl) AjPStr& Pmol const AjPStr molembl OUTPUT: RETVAL Pmol AjBool ajSeqmolSetGb (Pmol, molgb) AjPStr& Pmol const AjPStr molgb OUTPUT: RETVAL Pmol const char* ajSeqmolGetEmbl (mol) const AjPStr mol OUTPUT: RETVAL const char* ajSeqmolGetGb (mol) const AjPStr mol OUTPUT: RETVAL