/* @include ajacd ************************************************************* ** ** These functions control all aspects of AJAX command definition ** syntax, command line handling and prompting of the user. ** ** The only major functions visible to callers are the initialisation ** function ajAcdInit and a series of retrieval functions ajGetAcdObject ** for each defined object type (integer, sequence, and so on). ** ** Future extensions are planned, including the ability to write out ** the ACD internal structures in a number of other interface formats. ** ** @author Copyright (C) 1998 Peter Rice ** @version $Revision: 1.16 $ ** @modified Jun 25 pmr First version ** @modified May 06 2004 Jon Ison Minor mods. ** @modified $Date: 2011/12/19 16:30:31 $ 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 AJACD_H #define AJACD_H /* ========================================================================= */ /* ============================= include files ============================= */ /* ========================================================================= */ #include "ajdefine.h" #include "ajstr.h" #include "ajlist.h" #include "ajarr.h" #include "ajrange.h" #include "ajalign.h" #include "ajcod.h" #include "ajgraph.h" #include "ajpat.h" #include "ajphylo.h" #include "ajreg.h" #include "ajreport.h" #include "ajassemdata.h" #include "ajfeatdata.h" #include "ajobodata.h" #include "ajrefseqdata.h" #include "ajresourcedata.h" #include "ajseqdata.h" #include "ajtaxdata.h" #include "ajtextdata.h" #include "ajurldata.h" #include "ajvardata.h" AJ_BEGIN_DECLS /* ========================================================================= */ /* =============================== constants =============================== */ /* ========================================================================= */ /* ========================================================================= */ /* ============================== public data ============================== */ /* ========================================================================= */ /* ========================================================================= */ /* =========================== public functions ============================ */ /* ========================================================================= */ /* ** Prototype definitions */ void ajAcdExit (AjBool single); AjPAlign ajAcdGetAlign (const char *token); AjPFloat ajAcdGetArray (const char *token); AjPAssemload ajAcdGetAssembly (const char *token); AjBool ajAcdGetBoolean (const char *token); AjPCod ajAcdGetCodon (const char *token); AjPFile ajAcdGetCpdb (const char *token); AjPFile ajAcdGetDatafile (const char *token); AjPDir ajAcdGetDirectory (const char *token); AjPStr ajAcdGetDirectoryName (const char *token); AjPList ajAcdGetDirlist (const char *token); AjPPhyloState* ajAcdGetDiscretestates (const char *token); AjPPhyloState ajAcdGetDiscretestatesSingle (const char *token); AjPPhyloDist* ajAcdGetDistances (const char *token); AjPPhyloDist ajAcdGetDistancesSingle (const char *token); double ajAcdGetFloatDouble (const char *token); AjPFeattable ajAcdGetFeatures (const char *token); AjPFeattaball ajAcdGetFeaturesall (const char *token); AjPFeattabOut ajAcdGetFeatout (const char *token); AjPList ajAcdGetFilelist (const char *token); float ajAcdGetFloat (const char *token); AjPPhyloFreq ajAcdGetFrequencies (const char *token); AjPGraph ajAcdGetGraph (const char *token); AjPGraph ajAcdGetGraphxy (const char *token); AjPFile ajAcdGetInfile (const char *token); ajint ajAcdGetInt (const char *token); ajlong ajAcdGetIntLong (const char *token); AjPStr* ajAcdGetList (const char *token); AjPStr ajAcdGetListSingle(const char *token); AjPMatrix ajAcdGetMatrix (const char *token); AjPMatrixf ajAcdGetMatrixf (const char *token); AjPObo ajAcdGetObo(const char *token); AjPOboall ajAcdGetOboall(const char *token); AjPOutfile ajAcdGetOutassembly(const char *token); AjPOutfile ajAcdGetOutcodon(const char *token); AjPOutfile ajAcdGetOutcpdb(const char *token); AjPOutfile ajAcdGetOutdata(const char *token); AjPDirout ajAcdGetOutdir (const char *token); AjPStr ajAcdGetOutdirName (const char *token); AjPOutfile ajAcdGetOutdiscrete(const char *token); AjPOutfile ajAcdGetOutdistance(const char *token); AjPFile ajAcdGetOutfile (const char *token); AjPStr ajAcdGetOutfileName (const char *token); AjPOutfile ajAcdGetOutfreq(const char *token); AjPOutfile ajAcdGetOutmatrix(const char *token); AjPOutfile ajAcdGetOutmatrixf(const char *token); AjPOutfile ajAcdGetOutobo(const char *token); AjPOutfile ajAcdGetOutproperties(const char *token); AjPOutfile ajAcdGetOutrefseq(const char *token); AjPOutfile ajAcdGetOutresource(const char *token); AjPOutfile ajAcdGetOutscop(const char *token); AjPOutfile ajAcdGetOuttaxon(const char *token); AjPOutfile ajAcdGetOuttext(const char *token); AjPOutfile ajAcdGetOuttree(const char *token); AjPOutfile ajAcdGetOuturl(const char *token); AjPOutfile ajAcdGetOutvariation(const char *token); AjPPatlistSeq ajAcdGetPattern (const char *token); AjPPhyloProp ajAcdGetProperties (const char *token); AjPRange ajAcdGetRange (const char *token); AjPRefseq ajAcdGetRefseq (const char *token); AjPPatlistRegex ajAcdGetRegexp (const char *token); AjPRegexp ajAcdGetRegexpSingle (const char *token); AjPReport ajAcdGetReport (const char *token); AjPResource ajAcdGetResource(const char *token); AjPResourceall ajAcdGetResourceall(const char *token); AjPFile ajAcdGetScop (const char *token); AjPStr* ajAcdGetSelect (const char *token); AjPStr ajAcdGetSelectSingle (const char *token); AjPSeq ajAcdGetSeq (const char *token); AjPSeqall ajAcdGetSeqall (const char *token); AjPSeqout ajAcdGetSeqout (const char *token); AjPSeqout ajAcdGetSeqoutall (const char *token); AjPSeqout ajAcdGetSeqoutset (const char *token); AjPSeqset ajAcdGetSeqset (const char *token); AjPSeqset* ajAcdGetSeqsetall (const char *token); AjPSeqset ajAcdGetSeqsetallSingle (const char *token); AjPStr ajAcdGetString (const char *token); AjPTax ajAcdGetTaxon(const char *token); AjPTaxall ajAcdGetTaxonall(const char *token); AjPText ajAcdGetText(const char *token); AjPTextall ajAcdGetTextall(const char *token); AjBool ajAcdGetToggle (const char *token); AjPPhyloTree* ajAcdGetTree (const char *token); AjPPhyloTree ajAcdGetTreeSingle (const char *token); AjPUrl ajAcdGetUrl(const char *token); AjPUrlall ajAcdGetUrlall(const char *token); AjPVarload ajAcdGetVariation(const char *token); const AjPStr ajAcdGetValue (const char* token); const AjPStr ajAcdGetValueDefault (const char* token); void ajAcdInit(const char *pgm, ajint argc, char * const argv[]); void ajAcdInitPV(const char *pgm, ajint argc, char * const argv[], const char *package, const char *packversion); AjBool ajAcdIsUserdefinedC(const char* token); AjBool ajAcdIsUserdefinedS(const AjPStr); const AjPStr ajAcdGetpathC(const char *token); const AjPStr ajAcdGetpathS(const AjPStr); void ajAcdPrintAppl(AjPFile outf, AjBool full); void ajAcdPrintQual(AjPFile outf, AjBool full); void ajAcdPrintType (AjPFile outf, AjBool full); AjBool ajAcdSetControl (const char* optionName); void ajAcdUnused(void); AjBool ajAcdedamParse(const AjPStr relation, AjPStr* id, AjPStr* namespace, AjPStr* name); const char* ajAcdtypeGetGroup(const AjPStr type); /* ** End of prototype definitions */ #ifdef AJ_COMPILE_DEPRECATED_BOOK #endif #ifdef AJ_COMPILE_DEPRECATED __deprecated AjBool ajAcdIsUserdefined(const char* token); __deprecated AjBool ajAcdDebug (void); __deprecated AjBool ajAcdDebugIsSet (void); __deprecated AjBool ajAcdFilter (void); __deprecated AjPPhyloState ajAcdGetDiscretestatesI (const char *token, ajint num); __deprecated AjPStr ajAcdGetListI (const char *token, ajint num); __deprecated AjPStr ajAcdGetSelectI (const char *token, ajint num); __deprecated AjPSeqset ajAcdGetSeqsetallI (const char *token, ajint num); __deprecated AjPPhyloTree ajAcdGetTreeI (const char *token, ajint num); __deprecated const AjPStr ajAcdValue (const char* token); __deprecated AjBool ajAcdStdout (void); __deprecated AjBool ajAcdGetBool (const char *token); __deprecated AjPFeattable ajAcdGetFeat (const char *token); __deprecated void ajAcdGraphicsInit(const char *pgm, ajint argc, char * const argv[]); __deprecated void ajAcdGraphicsInitPV(const char *pgm, ajint argc,char * const argv[], const char *package, const char *packversion); __deprecated void ajGraphicsInit(const char *pgm, ajint argc, char * const argv[]); __deprecated void ajGraphicsInitPV(const char *pgm, ajint argc,char * const argv[], const char *package, const char *packversion); #endif AJ_END_DECLS #endif /* !AJACD_H */