/* @include ajcod ************************************************************* ** ** AJAX codon functions ** ** @author Copyright (C) 1999 Alan Bleasby ** @version $Revision: 1.27 $ ** @modified Aug 07 ajb 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 AJCOD_H #define AJCOD_H /* ========================================================================= */ /* ============================= include files ============================= */ /* ========================================================================= */ #include "ajdefine.h" #include "ajfile.h" AJ_BEGIN_DECLS /* ========================================================================= */ /* =============================== constants =============================== */ /* ========================================================================= */ /* ========================================================================= */ /* ============================== public data ============================== */ /* ========================================================================= */ /* @data AjPCod *************************************************************** ** ** Ajax codon object. ** ** Holds arrays describing codon usage ** The length is known and held internally. ** ** AjPCod is implemented as a pointer to a C data structure. ** ** @alias AjSCod ** @alias AjOCod ** ** @attr Name [AjPStr] Name of codon file ** @attr Species [AjPStr] Species ** @attr Division [AjPStr] Division (gbbct etc.) ** @attr Release [AjPStr] Database name and release ** @attr Desc [AjPStr] Description ** @attr CdsCount [ajint] Number of coding sequences used ** @attr CodonCount [ajint] Number of individual codons used ** @attr aa [ajint*] Amino acid represented by codon ** @attr num [ajint*] Number of codons ** @attr tcount [double*] Codons per thousand ** @attr fraction [double*] Fraction of amino acids of this type ** @attr back [ajint*] Index of favoured amino acid for back translation ** @attr GeneticCode [ajint] Genetic code NCBI number to match ** amino acids to codons. ** @attr Padding [char[4]] Padding to alignment boundary ** @@ ******************************************************************************/ typedef struct AjSCod { AjPStr Name; AjPStr Species; AjPStr Division; AjPStr Release; AjPStr Desc; ajint CdsCount; ajint CodonCount; ajint *aa; ajint *num; double *tcount; double *fraction; ajint *back; ajint GeneticCode; char Padding[4]; } AjOCod; #define AjPCod AjOCod* /* ========================================================================= */ /* =========================== public functions ============================ */ /* ========================================================================= */ /* ** Prototype definitions */ void ajCodSetCodenum(AjPCod thys, ajint geneticcode); void ajCodSetDescC(AjPCod thys, const char* desc); void ajCodSetDescS(AjPCod thys, const AjPStr desc); void ajCodSetDivisionC(AjPCod thys, const char* division); void ajCodSetDivisionS(AjPCod thys, const AjPStr division); void ajCodSetNameC(AjPCod thys, const char* name); void ajCodSetNameS(AjPCod thys, const AjPStr name); void ajCodSetNumcds(AjPCod thys, ajint numcds); void ajCodSetNumcodons(AjPCod thys, ajint numcodon); void ajCodSetReleaseC(AjPCod thys, const char* release); void ajCodSetReleaseS(AjPCod thys, const AjPStr release); void ajCodSetSpeciesC(AjPCod thys, const char* species); void ajCodSetSpeciesS(AjPCod thys, const AjPStr species); void ajCodBacktranslate(AjPStr *b, const AjPStr a, const AjPCod thys); void ajCodBacktranslateAmbig(AjPStr *b, const AjPStr a, const AjPCod thys); ajint ajCodBase(ajint c); double ajCodCalcCaiCod(const AjPCod thys); double ajCodCalcCaiSeq(const AjPCod cod, const AjPStr str); void ajCodCalcGribskov(AjPCod thys, const AjPStr s); double ajCodCalcNc(const AjPCod thys); void ajCodCalcUsage(AjPCod thys, ajint c); void ajCodClear(AjPCod thys); void ajCodClearData(AjPCod thys); void ajCodComp(ajint *NA, ajint *NC, ajint *NG, ajint *NT, const char *str); void ajCodSetTripletsS(AjPCod thys, const AjPStr s, ajint *c); void ajCodDel(AjPCod *thys); ajint ajCodGetCode(const AjPCod thys); const AjPStr ajCodGetDesc(const AjPCod thys); const char* ajCodGetDescC(const AjPCod thys); const AjPStr ajCodGetDivision(const AjPCod thys); const char* ajCodGetDivisionC(const AjPCod thys); void ajCodExit(void); void ajCodGetCodonlist(const AjPCod cod, AjPList list); const AjPStr ajCodGetName(const AjPCod thys); const char* ajCodGetNameC(const AjPCod thys); ajint ajCodGetNumcds(const AjPCod thys); ajint ajCodGetNumcodon(const AjPCod thys); const AjPStr ajCodGetRelease(const AjPCod thys); const char* ajCodGetReleaseC(const AjPCod thys); const AjPStr ajCodGetSpecies(const AjPCod thys); const char* ajCodGetSpeciesC(const AjPCod thys); ajint ajCodIndex(const AjPStr s); ajint ajCodIndexC(const char *codon); AjPCod ajCodNew(void); AjPCod ajCodNewCodenum(ajint code); AjPCod ajCodNewCod(const AjPCod thys); AjBool ajCodRead(AjPCod thys, const AjPStr fn, const AjPStr format); void ajCodSetBacktranslate(AjPCod thys); char* ajCodTriplet(ajint idx); void ajCodWrite(AjPCod thys, AjPFile outf); void ajCodWriteOut(const AjPCod thys, AjPOutfile outf); AjBool ajCodoutformatFind(const AjPStr name, ajint *iformat); void ajCodPrintFormat(AjPFile outf, AjBool full); /* ** End of prototype definitions */ #ifdef AJ_COMPILE_DEPRECATED_BOOK #endif /* AJ_COMPILE_DEPRECATED_BOOK */ #ifdef AJ_COMPILE_DEPRECATED __deprecated ajint ajCodOutFormat(const AjPStr name); __deprecated AjPCod ajCodDup(const AjPCod thys); __deprecated AjPCod ajCodNewCode(ajint code); __deprecated void ajCodAssCode(AjPCod thys, ajint geneticcode); __deprecated void ajCodAssDesc(AjPCod thys, const AjPStr desc); __deprecated void ajCodAssDescC(AjPCod thys, const char* desc); __deprecated void ajCodAssDivision(AjPCod thys, const AjPStr division); __deprecated void ajCodAssDivisionC(AjPCod thys, const char* division); __deprecated void ajCodAssNumcds(AjPCod thys, ajint numcds); __deprecated void ajCodAssNumcodon(AjPCod thys, ajint numcodon); __deprecated void ajCodAssRelease(AjPCod thys, const AjPStr release); __deprecated void ajCodAssReleaseC(AjPCod thys, const char* release); __deprecated void ajCodAssSpecies(AjPCod thys, const AjPStr species); __deprecated void ajCodAssSpeciesC(AjPCod thys, const char* species); __deprecated void ajCodAssName(AjPCod thys, const AjPStr name); __deprecated void ajCodAssNameC(AjPCod thys, const char* name); __deprecated void ajCodCountTriplets(AjPCod thys, const AjPStr s, ajint *c); __deprecated double ajCodCalcCai(const AjPCod cod, const AjPStr str); __deprecated void ajCodCalculateUsage(AjPCod thys, ajint c); #endif /* AJ_COMPILE_DEPRECATED */ AJ_END_DECLS #endif /* !AJCOD_H */