#ifdef __cplusplus extern "C" { #endif #ifndef ajseq_h #define ajseq_h #include "ajseqdata.h" #include "ajax.h" /* @data AjPSeqCvt ************************************************************ ** ** Sequence conversion data. Used to convert a sequence to binary. ** ** @new ajSeqCvtNew Creates from a character string of valid bases. ** @new ajSeqCvtNewText Creates from a character string of valid bases. ** @new ajSeqCvtNewZero Creates from a character string of valid bases. ** @new ajSeqCvtNewZeroS Creates from an array of strings of valid bases. ** @new ajSeqCvtNewZeroSS Creates from an array of strings of valid bases. ** @output ajSeqCvtTrace Reports on contents for debugging * ** @alias AjSSeqCvt ** @alias AjOSeqCvt ** ** @attr size [ajint] Number of characters in table, usually ** all possible characters. ** @attr len [ajint] Number of characters defined ** @attr missing [ajint] Index of the missing character value ** @attr nrlabels [ajint] Number of row labels ** @attr bases [AjPStr] The bases which can be converted ** @attr rlabels [AjPStr*] Row labels ** @attr clabels [AjPStr*] Column labels ** @attr table [char*] Binary character value for each character in bases ** @attr nclabels [ajint] Number of column labels ** @attr Padding [char[4]] Padding to alignment boundary ** @@ ******************************************************************************/ typedef struct AjSSeqCvt { ajint size; ajint len; ajint missing; ajint nrlabels; AjPStr bases; AjPStr* rlabels; AjPStr* clabels; char *table; ajint nclabels; char Padding[4]; } AjOSeqCvt; #define AjPSeqCvt AjOSeqCvt* /* ** Prototype definitions */ AjBool ajSeqtestIsAccession (const AjPStr accnum); const AjPStr ajSeqtestIsSeqversion (const AjPStr sv); void ajSeqallDel(AjPSeqall *thys); ajlong ajSeqallGetCount (const AjPSeqall seq); const AjPStr ajSeqallGetFilename(const AjPSeqall thys); const AjPStr ajSeqallGetseqName (const AjPSeqall thys); ajint ajSeqallGetseqBegin (const AjPSeqall seq); ajint ajSeqallGetseqEnd (const AjPSeqall seq); ajint ajSeqallGetseqLen (const AjPSeqall seqall); const AjPStr ajSeqallGetName(const AjPSeqall seq); ajint ajSeqallGetseqRange (const AjPSeqall thys, ajint* begin, ajint* end); ajlong ajSeqallGetTotlength (const AjPSeqall seq); const AjPStr ajSeqallGetUsa (const AjPSeqall thys); AjPSeqall ajSeqallNew (void); void ajSeqallClear (AjPSeqall thys); void ajSeqallClearStats (AjPSeqall thys); AjBool ajSeqallNext (AjPSeqall seqall, AjPSeq* retseq); void ajSeqallSetRange (AjPSeqall seq, ajint ibegin, ajint iend); void ajSeqallSetRangeRev (AjPSeqall seq, ajint ibegin, ajint iend); void ajSeqAddCmt(AjPSeq thys, AjPStr str); void ajSeqAddGene(AjPSeq thys, AjPSeqGene gene); void ajSeqAddKey(AjPSeq thys, AjPStr str); void ajSeqAddRef(AjPSeq thys, AjPSeqRef ref); void ajSeqAddXref(AjPSeq thys, AjPSeqXref xref); void ajSeqAssignAccC(AjPSeq seq, const char* text); void ajSeqAssignAccS(AjPSeq seq, const AjPStr str); void ajSeqAssignDescC(AjPSeq seq, const char* text); void ajSeqAssignDescS(AjPSeq seq, const AjPStr str); void ajSeqAssignEntryC(AjPSeq seq, const char* text); void ajSeqAssignEntryS(AjPSeq seq, const AjPStr str); void ajSeqAssignFileC(AjPSeq seq, const char* text); void ajSeqAssignFileS(AjPSeq seq, const AjPStr str); void ajSeqAssignFullC(AjPSeq seq, const char* text); void ajSeqAssignFullS(AjPSeq seq, const AjPStr str); void ajSeqAssignGiC(AjPSeq seq, const char* text); void ajSeqAssignGiS(AjPSeq seq, const AjPStr str); void ajSeqAssignNameC(AjPSeq seq, const char* txt); void ajSeqAssignNameS(AjPSeq seq, const AjPStr str); void ajSeqAssignQualLen(AjPSeq seq, const float* qual, ajuint len); void ajSeqAssignSeqC(AjPSeq seq, const char* text); void ajSeqAssignSeqLenC(AjPSeq seq, const char* txt, ajuint len); void ajSeqAssignSeqS(AjPSeq seq, const AjPStr str); void ajSeqAssignSvC(AjPSeq seq, const char* text); void ajSeqAssignSvS(AjPSeq seq, const AjPStr str); void ajSeqAssignUfoC(AjPSeq seq, const char* text); void ajSeqAssignUfoS(AjPSeq seq, const AjPStr str); void ajSeqAssignUsaC(AjPSeq seq, const char* text); void ajSeqAssignUsaS(AjPSeq seq, const AjPStr str); ajuint ajSeqGetBegin (const AjPSeq seq); const float* ajSeqGetQual(const AjPSeq seq); const char* ajSeqGetSeqC (const AjPSeq thys); const AjPStr ajSeqGetSeqS(const AjPSeq seq); char* ajSeqGetSeqCopyC (const AjPSeq seq); AjPStr ajSeqGetSeqCopyS(const AjPSeq seq); ajint ajSeqCalcCheckgcg (const AjPSeq thys); void ajSeqClear (AjPSeq thys); void ajSeqComplement (AjPSeq thys); void ajSeqstrComplement (AjPStr* thys); AjBool ajSeqstrConvertNum(const AjPStr seq, const AjPSeqCvt cvt, AjPStr* Pnumseq); AjPFeattable ajSeqGetFeatCopy (const AjPSeq thys); void ajSeqCalcCount (const AjPSeq thys, ajint *b); ajuint ajSeqstrCountGaps(const AjPStr str); void ajSeqcvtDel (AjPSeqCvt* thys); ajint ajSeqcvtGetCodeK (const AjPSeqCvt thys, char ch); ajint ajSeqcvtGetCodeS (const AjPSeqCvt thys, const AjPStr ch); ajint ajSeqcvtGetCodeAsymS (const AjPSeqCvt cvt, const AjPStr str); ajint ajSeqcvtGetCodeAsymrowS (const AjPSeqCvt cvt, const AjPStr str); ajuint ajSeqcvtGetLen (const AjPSeqCvt thys); AjPSeqCvt ajSeqcvtNewC (const char* bases); AjPSeqCvt ajSeqcvtNewNumberC (const char* bases); AjPSeqCvt ajSeqcvtNewEndC (const char* bases); AjPSeqCvt ajSeqcvtNewStr (const AjPPStr bases, ajint n); AjPSeqCvt ajSeqcvtNewStrAsym (const AjPPStr bases, ajint n, const AjPPStr rbases, ajint rn); void ajSeqcvtTrace (const AjPSeqCvt cvt); AjPSeqDate ajSeqdateNew(void); AjPSeqDate ajSeqdateNewDate(const AjPSeqDate date); AjBool ajSeqdateSetCreateS(AjPSeqDate date, const AjPStr datestr); AjBool ajSeqdateSetModifyS(AjPSeqDate date, const AjPStr datestr); AjBool ajSeqdateSetModseqS(AjPSeqDate date, const AjPStr datestr); void ajSeqdateClear(AjPSeqDate date); void ajSeqdateDel(AjPSeqDate*); AjPSeqDesc ajSeqdescNew(void); AjPSeqDesc ajSeqdescNewDesc(const AjPSeqDesc); void ajSeqdescClear(AjPSeqDesc desc); void ajSeqdescDel(AjPSeqDesc*); AjBool ajSeqdesclistClone(const AjPList src, AjPList dest); AjPSeqSubdesc ajSeqsubdescNew(void); AjPSeqSubdesc ajSeqsubdescNewSubdesc(const AjPSeqSubdesc); void ajSeqsubdescClear(AjPSeqSubdesc desc); void ajSeqsubdescDel(AjPSeqSubdesc*); AjBool ajSeqsubdesclistClone(const AjPList src, AjPList dest); AjPSeqGene ajSeqgeneNew(void); AjPSeqGene ajSeqgeneNewGene(const AjPSeqGene gene); AjPSeqGene ajSeqgeneNewName(const AjPStr str); void ajSeqgeneDel(AjPSeqGene*); AjPSeqRef ajSeqrefNew(void); AjPSeqRef ajSeqrefNewRef(const AjPSeqRef); void ajSeqrefDel(AjPSeqRef*); AjPSeqXref ajSeqxrefNew(void); AjPSeqXref ajSeqxrefNewDbC(const AjPStr id, const char* db, ajuint reftype); AjPSeqXref ajSeqxrefNewDbS(const AjPStr id, const AjPStr db, ajuint reftype); AjPSeqXref ajSeqxrefNewRef(const AjPSeqXref); void ajSeqxrefDel(AjPSeqXref*); AjBool ajSeqdescAppendName(AjPSeqDesc desc, const AjPStr str); AjBool ajSeqdescSetName(AjPSeqDesc desc, const AjPStr str); AjBool ajSeqsubdescAppendName(AjPSeqSubdesc desc, const AjPStr str); AjBool ajSeqsubdescSetName(AjPSeqSubdesc desc, const AjPStr str); AjBool ajSeqgeneAppendName(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgeneAppendSynonyms(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgeneAppendOrf(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgeneAppendOln(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgeneSetName(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgeneSetSynonyms(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgeneSetOrf(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgeneSetOln(AjPSeqGene gene, const AjPStr str); AjBool ajSeqgenelistClone(const AjPList src, AjPList dest); AjBool ajSeqrefAppendAuthors(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefAppendComment(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefAppendGroupname(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefAppendLocation(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefAppendPosition(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefAppendTitle(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefAppendXref(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefFmtAuthorsEmbl(const AjPSeqRef ref, AjPStr* Pdest); AjBool ajSeqrefFmtAuthorsGb(const AjPSeqRef ref, AjPStr* Pdest); AjBool ajSeqrefFmtLocationEmbl(const AjPSeqRef ref, AjPStr* Pdest); AjBool ajSeqrefFmtLocationGb(const AjPSeqRef ref, AjPStr* Pdest); AjBool ajSeqrefFmtTitleGb(const AjPSeqRef ref, AjPStr* Pdest); AjBool ajSeqreflistClone(const AjPList src, AjPList dest); ajuint ajSeqreflistGetXrefs(const AjPList src, AjPList *Plist); AjBool ajSeqrefSetAuthors(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefSetComment(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefSetGroupname(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefSetLocation(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefSetLoctype(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefSetnumNumber(AjPSeqRef ref, ajuint num); AjBool ajSeqrefSetPosition(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefSetTitle(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefSetXref(AjPSeqRef ref, const AjPStr str); AjBool ajSeqrefStandard(AjPSeqRef ref); AjBool ajSeqxreflistClone(const AjPList src, AjPList dest); AjBool ajSeqxreflistSort(AjPList list); void ajSeqSetName(AjPSeq thys, const AjPStr setname); void ajSeqSetNameMulti(AjPSeq thys, const AjPStr setname); void ajSeqDel (AjPSeq* pthis); void ajSeqDelarray(AjPSeq **PPseq); ajuint ajSeqGetEnd (const AjPSeq seq); void ajSeqExit(void); void ajSeqGapFill (AjPSeq seq, ajuint len); ajuint ajSeqCountGaps(const AjPSeq seq); void ajSeqGapStandard (AjPSeq thys, char gapch); const char* ajSeqGetAccC (const AjPSeq thys); const AjPStr ajSeqGetAccS (const AjPSeq thys); const char* ajSeqGetDbC (const AjPSeq thys); const AjPStr ajSeqGetDbS (const AjPSeq thys); const char* ajSeqGetDescC (const AjPSeq thys); const AjPStr ajSeqGetDescS (const AjPSeq thys); const char* ajSeqGetEntryC (const AjPSeq thys); const AjPStr ajSeqGetEntryS (const AjPSeq thys); const AjPFeattable ajSeqGetFeat (const AjPSeq thys); const char* ajSeqGetGiC (const AjPSeq thys); const AjPStr ajSeqGetGiS (const AjPSeq thys); const char* ajSeqGetNameC (const AjPSeq thys); const AjPStr ajSeqGetNameS (const AjPSeq thys); ajuint ajSeqGetOffend(const AjPSeq seq); ajuint ajSeqGetOffset(const AjPSeq seq); ajuint ajSeqGetRange (const AjPSeq thys, ajint* begin, ajint* end); AjBool ajSeqGetRev (const AjPSeq thys); const char* ajSeqGetSvC (const AjPSeq thys); const AjPStr ajSeqGetSvS (const AjPSeq thys); const char* ajSeqGetTaxC (const AjPSeq thys); const AjPStr ajSeqGetTaxS (const AjPSeq thys); ajuint ajSeqGetTaxid(const AjPSeq seq); const char* ajSeqGetUsaC (const AjPSeq thys); const AjPStr ajSeqGetUsaS (const AjPSeq thys); ajuint ajSeqGetXrefs (const AjPSeq thys, AjPList list); AjBool ajSeqIsNuc (const AjPSeq thys); AjBool ajSeqIsProt (const AjPSeq thys); ajuint ajSeqGetLen (const AjPSeq seq); ajuint ajSeqGetLenTrimmed (const AjPSeq seq); ajuint ajSeqGetLenUngapped (const AjPSeq seq); const char* ajSeqclsGetEmbl(const AjPStr cls); AjBool ajSeqclsSetEmbl(AjPStr *cls, const AjPStr clsembl); AjBool ajSeqclsSetGb(AjPStr *cls, const AjPStr clsembl); const char* ajSeqdivGetEmbl(const AjPStr divi); const char* ajSeqdivGetGb(const AjPStr divi); AjBool ajSeqdivSetEmbl(AjPStr *Pdivi, const AjPStr divembl); AjBool ajSeqdivSetGb(AjPStr *Pdivi, const AjPStr divembl); const char* ajSeqmolGetEmbl(const AjPStr mol); const char* ajSeqmolGetGb(const AjPStr mol); AjBool ajSeqmolSetEmbl(AjPStr *mol, const AjPStr molembl); AjBool ajSeqmolSetGb(AjPStr *mol, const AjPStr molgb); void ajSeqSetUnique(AjPSeq seq); float ajSeqCalcMolwt (const AjPSeq seq); float ajSeqstrCalcMolwt (const AjPStr seq); AjPSeq ajSeqNew (void); AjPSeq ajSeqNewNameC(const char* txt, const char* name); AjPSeq ajSeqNewNameS(const AjPStr str, const AjPStr name); AjPSeq ajSeqNewRes (size_t size); AjPSeq ajSeqNewSeq (const AjPSeq seq); AjPSeq ajSeqNewRangeC(const char* txt, ajint offset, ajint offend, AjBool rev); AjPSeq ajSeqNewRangeS(const AjPStr str, ajint offset, ajint offend, AjBool rev); AjBool ajSeqConvertNum (const AjPSeq thys, const AjPSeqCvt cvt, AjPStr *numseq); AjBool ajSeqIsReversedTrue(const AjPSeq seq); AjBool ajSeqIsReversed (const AjPSeq thys); AjBool ajSeqIsSpeciesBsubtilis(const AjPSeq seq); AjBool ajSeqIsSpeciesHuman(const AjPSeq seq); AjBool ajSeqIsSpeciesMouse(const AjPSeq seq); AjBool ajSeqIsSpeciesYeast(const AjPSeq seq); AjBool ajSeqIsTaxon(const AjPSeq seq, ajuint taxid); AjBool ajSeqIsTrimmed (const AjPSeq thys); void ajSeqReverseDo (AjPSeq thys); void ajSeqReverseForce (AjPSeq thys); void ajSeqstrReverse (AjPStr* thys); void ajSeqReverseOnly (AjPSeq thys); ajuint ajSeqsetGetBegin (const AjPSeqset seq); void ajSeqsetDel(AjPSeqset *thys); void ajSeqsetDelarray(AjPSeqset **thys); ajuint ajSeqsetGetEnd (const AjPSeqset seq); ajint ajSeqsetFill (AjPSeqset seq); const AjPStr ajSeqsetGetFormat (const AjPSeqset thys); const char* ajSeqsetGetNameC (const AjPSeqset thys); const AjPStr ajSeqsetGetNameS (const AjPSeqset thys); ajint ajSeqsetGetOffend(const AjPSeqset seq); ajint ajSeqsetGetOffset(const AjPSeqset seq); ajint ajSeqsetGetRange (const AjPSeqset thys, ajint* begin, ajint* end); const AjPSeq ajSeqsetGetseqSeq (const AjPSeqset thys, ajuint i); const char* ajSeqsetGetseqSeqC (const AjPSeqset thys, ajuint i); const AjPStr ajSeqsetGetseqSeqS (const AjPSeqset thys, ajuint i); AjPSeq* ajSeqsetGetSeqarray(const AjPSeqset thys); ajint ajSeqsetGetTotlength(const AjPSeqset seq); const AjPStr ajSeqsetGetUsa (const AjPSeqset thys); const AjPStr ajSeqsetGetFilename(const AjPSeqset thys); AjBool ajSeqsetIsDna (const AjPSeqset thys); AjBool ajSeqsetIsNuc (const AjPSeqset thys); AjBool ajSeqsetIsProt (const AjPSeqset thys); AjBool ajSeqsetIsRna (const AjPSeqset thys); ajuint ajSeqsetGetLen (const AjPSeqset seq); const char* ajSeqsetGetseqAccC (const AjPSeqset seq, ajuint i); const AjPStr ajSeqsetGetseqAccS (const AjPSeqset seq, ajuint i); const char* ajSeqsetGetseqNameC (const AjPSeqset seq, ajuint i); const AjPStr ajSeqsetGetseqNameS (const AjPSeqset seq, ajuint i); AjPSeqset ajSeqsetNew (void); void ajSeqSetOffsets(AjPSeq seq, ajint ioff, ajint ioriglen); void ajSeqSetRange (AjPSeq seq, ajint ibegin, ajint iend); void ajSeqSetRangeRev (AjPSeq seq, ajint ibegin, ajint iend); void ajSeqsetReverse (AjPSeqset thys); void ajSeqsetSetRange (AjPSeqset seq, ajint ibegin, ajint iend); ajuint ajSeqsetGetSize (const AjPSeqset seq); void ajSeqsetFmtLower (AjPSeqset seq); void ajSeqsetFmtUpper (AjPSeqset seq); float ajSeqsetGetTotweight (const AjPSeqset seq); void ajSeqsetSortLen(AjPSeqset seq); void ajSeqsetTrim(AjPSeqset thys); float ajSeqsetGetseqWeight (const AjPSeqset seq, ajuint i) ; void ajSeqFmtLower (AjPSeq thys); void ajSeqFmtUpper (AjPSeq thys); void ajSeqTagRev(AjPSeq seq); void ajSeqTrace (const AjPSeq seq); void ajSeqTraceTitle (const AjPSeq seq, const char* title); void ajSeqTrim(AjPSeq thys); ajuint ajSeqGetBeginTrue (const AjPSeq seq); ajuint ajSeqGetEndTrue (const AjPSeq seq); ajuint ajSeqGetLenTrue (const AjPSeq seq); ajint ajSeqCalcTruepos (const AjPSeq thys, ajint ipos); ajint ajSeqCalcTrueposMin (const AjPSeq thys, ajint imin, ajint ipos); /* ** End of prototype definitions */ /* ** These prototypes do not have any corresponding .c code so cannot ** go into the block above, otherwise the VC compilation will fail */ const char* ajSeqdivGetDdbj(const AjPStr divi); AjBool ajSeqdivSetDdbj(AjPStr *Pdivi, const AjPStr divembl); const char* ajSeqmolGetDdbj(const AjPStr mol); AjBool ajSeqmolSetDdbj(AjPStr *mol, const AjPStr molddbj); /* End of prototypes without C code */ __deprecated ajint ajSeqallBegin(const AjPSeqall seq); __deprecated ajint ajSeqallEnd(const AjPSeqall seq); __deprecated ajint ajSeqallGetRange(const AjPSeqall seq, ajint* begin, ajint* end); __deprecated void ajSeqsetToLower(AjPSeqset seqset); __deprecated void ajSeqsetToUpper(AjPSeqset seqset); __deprecated AjPSeq ajSeqNewC (const char* seq, const char* name); __deprecated AjPSeq ajSeqNewStr (const AjPStr str); __deprecated AjPSeq ajSeqNewRange(const AjPStr seq, ajint offset, ajint offend, AjBool rev); __deprecated AjPSeq ajSeqNewRangeCI(const char* seq, ajint len, ajint offset, ajint offend, AjBool rev); __deprecated AjPSeq ajSeqNewL (size_t size); __deprecated AjPSeq ajSeqNewS (const AjPSeq seq); __deprecated void ajSeqAssAcc (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssAccC (AjPSeq thys, const char* text); __deprecated void ajSeqAssDesc (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssDescC (AjPSeq thys, const char* text); __deprecated void ajSeqAssEntry (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssEntryC (AjPSeq thys, const char* text); __deprecated void ajSeqAssFile (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssFileC(AjPSeq thys, const char* text); __deprecated void ajSeqAssFull (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssFullC (AjPSeq thys, const char* text); __deprecated void ajSeqAssGi (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssGiC (AjPSeq thys, const char* text); __deprecated void ajSeqAssName (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssNameC (AjPSeq thys, const char* text); __deprecated void ajSeqAssSeq(AjPSeq seq, const AjPStr str); __deprecated void ajSeqAssSeqC (AjPSeq thys, const char* text); __deprecated void ajSeqAssSeqCI (AjPSeq thys, const char* text, ajint ilen); __deprecated void ajSeqAssSvC (AjPSeq thys, const char* text); __deprecated void ajSeqAssSv (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssUfo (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssUfoC (AjPSeq thys, const char* text); __deprecated void ajSeqAssUsa (AjPSeq thys, const AjPStr str); __deprecated void ajSeqAssUsaC (AjPSeq thys, const char* text); __deprecated void ajSeqSetRangeDir (AjPSeq seq, ajint ibegin, ajint iend, AjBool rev); __deprecated void ajSeqReplace (AjPSeq thys, const AjPStr seq); __deprecated void ajSeqReplaceC (AjPSeq thys, const char* seq); __deprecated void ajSeqMakeUsa (AjPSeq thys, const AjPSeqin seqin); __deprecated void ajSeqMakeUsaS(const AjPSeq thys, const AjPSeqin seqin, AjPStr* usa); __deprecated void ajSeqCompOnly (AjPSeq thys); __deprecated void ajSeqToLower (AjPSeq thys); __deprecated void ajSeqToUpper (AjPSeq thys); __deprecated void ajSeqRevOnly (AjPSeq thys); __deprecated AjBool ajSeqReverse (AjPSeq thys); __deprecated const AjPStr ajSeqGetAcc (const AjPSeq thys); __deprecated ajint ajSeqBegin (const AjPSeq seq); __deprecated ajint ajSeqTrueBegin (const AjPSeq seq); __deprecated const AjPStr ajSeqGetDesc (const AjPSeq thys); __deprecated ajint ajSeqEnd (const AjPSeq seq); __deprecated ajint ajSeqTrueEnd (const AjPSeq seq); __deprecated const AjPStr ajSeqGetEntry (const AjPSeq thys); __deprecated AjPFeattable ajSeqCopyFeat (const AjPSeq thys); __deprecated const AjPStr ajSeqGetGi (const AjPSeq thys); __deprecated ajint ajSeqLen (const AjPSeq seq); __deprecated ajint ajSeqTrueLen (const AjPSeq seq); __deprecated const char* ajSeqName (const AjPSeq seq); __deprecated const AjPStr ajSeqGetName (const AjPSeq thys); __deprecated ajint ajSeqOffend (const AjPSeq seq); __deprecated ajint ajSeqOffset (const AjPSeq seq); __deprecated AjBool ajSeqGetReverse (const AjPSeq thys); __deprecated AjBool ajSeqGetReversed (const AjPSeq thys); __deprecated const AjPStr ajSeqStr (const AjPSeq thys); __deprecated const char* ajSeqChar (const AjPSeq thys); __deprecated AjPStr ajSeqStrCopy (const AjPSeq thys); __deprecated char* ajSeqCharCopy (const AjPSeq seq); __deprecated char* ajSeqCharCopyL (const AjPSeq seq, size_t size); __deprecated const AjPStr ajSeqGetSv (const AjPSeq thys); __deprecated const AjPStr ajSeqGetTax (const AjPSeq thys); __deprecated const AjPStr ajSeqGetUsa (const AjPSeq thys); __deprecated AjBool ajSeqRev (const AjPSeq thys); __deprecated ajint ajSeqCheckGcg (const AjPSeq thys); __deprecated void ajSeqCount (const AjPSeq thys, ajint *b); __deprecated ajint ajSeqPos (const AjPSeq thys, ajint ipos); __deprecated ajint ajSeqPosI (const AjPSeq thys, ajint imin, ajint ipos); __deprecated ajint ajSeqPosII (ajint ilen, ajint imin, ajint ipos); __deprecated ajint ajSeqTruePos (const AjPSeq thys, ajint ipos); __deprecated ajint ajSeqTruePosI (const AjPSeq thys, ajint imin, ajint ipos); __deprecated ajint ajSeqTruePosII (ajint ilen, ajint imin, ajint ipos); __deprecated void ajSeqallReverse (AjPSeqall thys); __deprecated void ajSeqallToLower (AjPSeqall seqall); __deprecated void ajSeqallToUpper (AjPSeqall seqall); __deprecated void ajSeqReverseStr (AjPStr* thys); __deprecated void ajSeqCompOnlyStr (AjPStr* thys); __deprecated float ajSeqMW (const AjPStr seq); __deprecated ajuint ajSeqCrc(const AjPStr seq ); __deprecated void ajSeqCvtDel (AjPSeqCvt* thys); __deprecated ajint ajSeqCvtK (const AjPSeqCvt thys, char ch); __deprecated ajint ajSeqCvtKS (const AjPSeqCvt thys, const AjPStr ch); __deprecated ajint ajSeqCvtKSRow (const AjPSeqCvt thys, const AjPStr ch); __deprecated ajint ajSeqCvtKSColumn (const AjPSeqCvt thys, const AjPStr ch); __deprecated ajint ajSeqCvtLen (const AjPSeqCvt thys); __deprecated AjPSeqCvt ajSeqCvtNew (const char* bases); __deprecated AjPSeqCvt ajSeqCvtNewText (const char* bases); __deprecated AjPSeqCvt ajSeqCvtNewZero (const char* bases); __deprecated AjPSeqCvt ajSeqCvtNewZeroS (const AjPPStr bases, ajint n); __deprecated AjPSeqCvt ajSeqCvtNewZeroSS (const AjPPStr bases, ajint n, const AjPPStr rbases, ajint rn); __deprecated void ajSeqCvtTrace (const AjPSeqCvt cvt); __deprecated AjBool ajIsAccession (const AjPStr accnum); __deprecated const AjPStr ajIsSeqversion (const AjPStr sv); __deprecated ajint ajSeqallLen (const AjPSeqall seqall); __deprecated const AjPStr ajSeqallGetNameSeq (const AjPSeqall thys); __deprecated void ajSeqComplementOnly(AjPSeq pthis); __deprecated void ajSeqstrComplementOnly (AjPStr* thys); __deprecated ajuint ajSeqCalcCrc(const AjPSeq seq ); __deprecated void ajSeqDefName(AjPSeq thys, const AjPStr setname, AjBool multi); __deprecated ajint ajSeqFill (AjPSeq seq, ajint len); __deprecated ajint ajSeqGapCount (const AjPSeq thys); __deprecated ajint ajSeqGapCountS (const AjPStr str); __deprecated void ajSeqGapStandardS(AjPStr thys, char gapch); __deprecated void ajSeqMod (AjPSeq thys); __deprecated AjBool ajSeqNum (const AjPSeq thys, const AjPSeqCvt cvt, AjPStr *numseq); __deprecated AjBool ajSeqNumS (const AjPStr thys, const AjPSeqCvt cvt, AjPStr *numseq); __deprecated ajint ajSeqsetBegin (const AjPSeqset seq); __deprecated ajint ajSeqsetEnd (const AjPSeqset seq); __deprecated const AjPStr ajSeqsetGetName (const AjPSeqset thys); __deprecated const AjPSeq ajSeqsetGetSeq (const AjPSeqset thys, ajint i); __deprecated AjPSeq* ajSeqsetGetSeqArray(const AjPSeqset thys); __deprecated ajint ajSeqsetLen (const AjPSeqset seq); __deprecated const AjPStr ajSeqsetName (const AjPSeqset seq, ajint i); __deprecated const AjPStr ajSeqsetAcc (const AjPSeqset seq, ajint i); __deprecated const char* ajSeqsetSeq (const AjPSeqset seq, ajint i); __deprecated ajint ajSeqsetSize (const AjPSeqset seq); __deprecated float ajSeqsetTotweight (const AjPSeqset seq); __deprecated float ajSeqsetWeight (const AjPSeqset seq, ajint i) ; __deprecated void ajSeqTraceT (const AjPSeq seq, const char* title); #endif #ifdef __cplusplus } #endif