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/** @source ontogetsibs
**
** Find ontology terms by common parent
**
** @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 ontogetsibs **********************************************************
**
** Find ontology terms by common parent
**
******************************************************************************/
int main(int argc, char **argv)
{
/* Variable declarations */
AjPOutfile outfile = NULL;
AjBool obsolete = ajTrue;
AjPObo obo = NULL;
AjPObo oboparent = NULL;
AjPOboall oboall = NULL;
AjPObo obochild = NULL;
AjPOboin oboinparent = NULL;
AjPOboin oboinchild = NULL;
AjPStr oboqryup = NULL;
AjPStr obochildqry = NULL;
AjPStr qrystr = NULL;
AjPTable obotable = NULL;
AjPStrTok handle = NULL;
AjPStr up = NULL;
AjPList uplist = NULL;
ajuint ifound = 0;
ajuint ikeep = 0;
/* ACD processing */
embInit("ontogetsibs", argc, argv);
oboall = ajAcdGetOboall("oboterms");
outfile = ajAcdGetOutobo("outfile");
obsolete = ajAcdGetBoolean("obsolete");
oboinparent = ajOboinNew();
oboparent = ajOboNew();
oboinchild = ajOboinNew();
obochild = ajOboNew();
uplist = ajListNew();
obotable = ajTablestrNew(600);
while(ajOboallNext(oboall, &obo))
{
if(!obsolete && ajOboIsObsolete(obo))
continue;
ifound++;
ajOboGetParents(obo, uplist);
while(ajListstrPop(uplist, &up))
{
ajFmtPrintS(&oboqryup, "%S-id:%S", ajOboGetDb(obo), up);
ajOboinQryS(oboinparent, oboqryup);
while(ajOboinRead(oboinparent, oboparent))
{
if(!obsolete && ajOboIsObsolete(oboparent))
continue;
ajFmtPrintS(&obochildqry, "%S-isa:%S",
ajOboGetDb(obo), oboparent->Id);
ajOboinQryS(oboinchild, obochildqry);
while(ajOboinRead(oboinchild, obochild))
{
if(!ajTableMatchS(obotable, obochild->Id))
{
ajObooutWrite(outfile, obochild);
ajTablePut(obotable, ajStrNewS(obochild->Id),
(void *) 1);
ikeep++;
}
}
}
ajStrDel(&up);
}
}
if(!ifound)
ajErr("No matching terms");
/* Memory clean-up and exit */
ajOboallDel(&oboall);
ajOboinDel(&oboinchild);
ajOboinDel(&oboinparent);
ajOboDel(&obo);
ajOboDel(&obochild);
ajOboDel(&oboparent);
ajStrTokenDel(&handle);
ajStrDel(&qrystr);
ajStrDel(&oboqryup);
ajStrDel(&obochildqry);
ajListFree(&uplist);
ajTablestrFreeKey(&obotable);
ajOutfileClose(&outfile);
embExit();
return 0;
}
/* ==================================================================== */
/* ============================ functions ============================= */
/* ==================================================================== */
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