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/** @source edamdef
**
** Find EDAM ontology terms by identifier
**
** @author Copyright (C) 2010 Jon Ison / EMBOSS
** @version 1 First version</replaceable>
** @modified July 2010 Jon Ison First version</replaceable>
** @@
**
** This program is free software; you can redistribute it and/or
** modify it under the terms of the GNU General Public License
** as published by the Free Software Foundation; either version 2
** of the License, or (at your option) any later version.
**
** This program 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 General Public License for more details.
**
** You should have received a copy of the GNU General Public License
** along with this program; if not, write to the Free Software
** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
********************************************************************/
/* ==================================================================== */
/* ========================== include files =========================== */
/* ==================================================================== */
#include "emboss.h"
/* Inclusion of system and local header files goes here */
/* ==================================================================== */
/* ============================ constants ============================= */
/* ==================================================================== */
/* #define and enum statements go here */
/* ==================================================================== */
/* ======================== global variables ========================== */
/* ==================================================================== */
/* Global variables definitions go here */
/* ==================================================================== */
/* ============================== data ================================ */
/* ==================================================================== */
/* Definition of datatypes go here */
/* ==================================================================== */
/* ==================== function prototypes =========================== */
/* ==================================================================== */
/* Function prototypes for public (external) functions go here */
/* @prog edamdef **************************************************************
**
** Find EDAM ontology 'data' (identifier) terms by keyword
**
******************************************************************************/
int main(int argc, char **argv)
{
/* Variable declarations */
AjPStr query;
AjPStr *namespace = NULL;
AjPOutfile outfile = NULL;
AjBool subclasses = ajTrue;
AjBool obsolete = ajFalse;
AjPObo obo = NULL;
AjPObo obotest = NULL;
AjPOboin oboin = NULL;
AjPList obolist = NULL;
AjPStr oboqry = NULL;
AjPStr qrystr = NULL;
AjPTable foundtable = NULL;
AjPTable nstable = NULL;
const AjPStr name = NULL;
AjPStrTok handle = NULL;
ajint i;
ajuint ifound = 0;
ajuint ikeep = 0;
/* ACD processing */
embInit("edamdef", argc, argv);
query = ajAcdGetString("query");
namespace = ajAcdGetList("namespace");
outfile = ajAcdGetOutobo("outfile");
subclasses = ajAcdGetBoolean("subclasses");
obsolete = ajAcdGetBoolean("obsolete");
/* Application logic */
/* Check EDAM ontology (edam.obo) is installed indexed.
Loop through queryable fields
:Return list of EDAM ids with fields matching keyword(s)
Merge lists of matching entries
Write output file */
oboin = ajOboinNew();
obo = ajOboNew();
obolist = ajListNew();
foundtable = ajTablestrNew(600);
nstable = ajTablestrNew(6);
for(i=0; namespace[i]; i++)
{
ajTablePut(nstable, namespace[i], (void*) 1);
}
handle = ajStrTokenNewC(query, ",");
while(ajStrTokenNextParse(handle, &qrystr))
{
ajFmtPrintS(&oboqry, "edam-des:%S", qrystr);
ajOboinQryS(oboin, oboqry);
while(ajOboinRead(oboin, obo))
{
if(!obsolete && ajOboIsObsolete(obo))
continue;
ajListPushAppend(obolist, ajOboNewObo(obo));
if(subclasses)
ajOboGetTree(obo, obolist);
ajDebug("%S '%S' %Lu\n",
qrystr, obo->Id, ajListGetLength(obolist));
while(ajListGetLength(obolist))
{
ajListPop(obolist, (void**) &obotest);
if(!obsolete && ajOboIsObsolete(obotest))
{
ajOboDel(&obotest);
continue;
}
ifound++;
name = ajOboGetNamespace(obotest);
if(ajTableMatchS(nstable, name))
{
if(!ajTableMatchS(foundtable, obotest->Id))
{
ajObooutWrite(outfile, obotest);
ajTablePut(foundtable, ajStrNewS(obotest->Id),
(void *) 1);
ikeep++;
}
}
ajOboDel(&obotest);
}
}
}
if(!ifound)
ajErr("No matching terms");
else if(!ikeep)
ajErr("No terms in requested namespace");
/* Memory clean-up and exit */
ajOboDel(&obo);
ajOboinDel(&oboin);
ajListFree(&obolist);
ajStrTokenDel(&handle);
ajStrDel(&query);
ajStrDel(&qrystr);
ajStrDel(&oboqry);
ajTablestrFreeKey(&foundtable);
ajTableFree(&nstable);
for(i=0; namespace[i]; i++)
ajStrDel(&namespace[i]);
AJFREE(namespace);
ajOutfileClose(&outfile);
embExit();
return 0;
}
/* ==================================================================== */
/* ============================ functions ============================= */
/* ==================================================================== */
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