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/** @source ontocount
**
** Get number of ontology term(s) matching a query
**
** @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 ontocount ************************************************************
**
** Count ontology term(s) matching a query
**
******************************************************************************/
int main(int argc, char **argv)
{
/* Variable declarations */
AjPOboall oboall = NULL;
AjBool subclasses = ajFalse;
AjBool obsolete = ajFalse;
AjPFile outf = NULL;
AjPObo obo = NULL;
AjPObo obotest = NULL;
AjPList obolist = ajListNew();
AjPTable foundtable = NULL;
ajuint ifound = 0;
ajuint ikeep = 0;
/* ACD processing */
embInit("ontocount", argc, argv);
oboall = ajAcdGetOboall("oboterms");
outf = ajAcdGetOutfile("outfile");
subclasses = ajAcdGetBoolean("subclasses");
obsolete = ajAcdGetBoolean("obsolete");
foundtable = ajTablestrNew(600);
while(ajOboallNext(oboall, &obo))
{
ajListPushAppend(obolist, ajOboNewObo(obo));
if(subclasses)
ajOboGetTree(obo, obolist);
while(ajListGetLength(obolist))
{
ajListPop(obolist, (void**) &obotest);
if(!obsolete && ajOboIsObsolete(obotest))
{
ajOboDel(&obotest);
continue;
}
ifound++;
if(!ajTableMatchS(foundtable, obotest->Id))
{
ajTablePut(foundtable, ajStrNewS(obotest->Id),
(void *) 1);
ikeep++;
}
ajOboDel(&obotest);
}
}
ajFmtPrintF(outf, "%u\n", ikeep);
/* Memory clean-up and exit */
ajListFree(&obolist);
ajOboallDel(&oboall);
ajOboDel(&obo);
ajFileClose(&outf);
ajTablestrFreeKey(&foundtable);
embExit();
return 0;
}
/* ==================================================================== */
/* ============================ functions ============================= */
/* ==================================================================== */
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