/* @include ajseq ************************************************************* ** ** AJAX SEQ (sequence) functions ** ** These functions control all aspects of AJAX sequence ** reading and writing and include simple utilities. ** ** @author Copyright (C) 1998 Peter Rice ** @version $Revision: 1.82 $ ** @modified Jun 25 pmr First version ** @modified $Date: 2011/10/18 14:23:40 $ by $Author: rice $ ** @@ ** ** This library is free software; you can redistribute it and/or ** modify it under the terms of the GNU Lesser General Public ** License as published by the Free Software Foundation; either ** version 2.1 of the License, or (at your option) any later version. ** ** This library is distributed in the hope that it will be useful, ** but WITHOUT ANY WARRANTY; without even the implied warranty of ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ** Lesser General Public License for more details. ** ** You should have received a copy of the GNU Lesser General Public ** License along with this library; if not, write to the Free Software ** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, ** MA 02110-1301, USA. ** ******************************************************************************/ #ifndef AJSEQ_H #define AJSEQ_H /* ========================================================================= */ /* ============================= include files ============================= */ /* ========================================================================= */ #include "ajseqdata.h" #include "ajrefseq.h" AJ_BEGIN_DECLS /* ========================================================================= */ /* =============================== constants =============================== */ /* ========================================================================= */ /* ========================================================================= */ /* ============================== public data ============================== */ /* ========================================================================= */ /* @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* /* ========================================================================= */ /* =========================== public functions ============================ */ /* ========================================================================= */ /* ** 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*); AjPSeqRange ajSeqrangeNew(void); AjPSeqRange ajSeqrangeNewRange(const AjPSeqRange range); AjPSeqRange ajSeqrangeNewValues(ajulong pos, ajulong len, const AjPStr qry); void ajSeqrangeDel(AjPSeqRange* Prange); AjBool ajSeqrangeSetQuery(AjPSeqRange range, const AjPStr qry); AjBool ajSeqrangeSetRange(AjPSeqRange range, ajulong pos, ajulong len); 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 ajSeqSetCircular(AjPSeq seq); 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 ajSeqIsCircular(const AjPSeq thys); 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 ajSeqNewRefseq(const AjPRefseq refseq); 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 ajSeqsetClear(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 */ #ifdef AJ_COMPILE_DEPRECATED_BOOK #endif /* AJ_COMPILE_DEPRECATED_BOOK */ #ifdef AJ_COMPILE_DEPRECATED __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 /* AJ_COMPILE_DEPRECATED */ AJ_END_DECLS #endif /* !AJSEQ_H */