void ensKaryotypebandDel(EnsPKaryotypeband *Pkb)
{
EnsPKaryotypeband pthis = NULL;
if(!Pkb)
return;
if(!*Pkb)
return;
pthis = *Pkb;
pthis->Use--;
if(pthis->Use)
{
*Pkb = NULL;
return;
}
ensFeatureDel(&pthis->Feature);
ajStrDel(&pthis->Name);
ajStrDel(&pthis->Stain);
AJFREE(pthis);
*Pkb = NULL;
return;
}
AjBool ensKaryotypebandSetFeature(EnsPKaryotypeband kb, EnsPFeature feature)
{
if(!kb)
return ajFalse;
ensFeatureDel(&kb->Feature);
kb->Feature = ensFeatureNewRef(feature);
return ajTrue;
}
void ensIntronDel(EnsPIntron *Pintron)
{
EnsPIntron pthis = NULL;
if(!Pintron)
return;
if(!*Pintron)
return;
pthis = *Pintron;
/*
ajDebug("ensIntronDel\n"
" *Pintron %p\n",
*Pintron);
ensIntronTrace(*Pintron, 1);
*/
pthis->Use--;
if(pthis->Use)
{
*Pintron = NULL;
return;
}
ensFeatureDel(&pthis->Feature);
ensExonDel(&pthis->PreviousExon);
ensExonDel(&pthis->NextExon);
AJFREE(pthis);
*Pintron = NULL;
return;
}
static AjBool karyotypeBandadaptorFetchAllBySQL(EnsPDatabaseadaptor dba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList kblist)
{
ajuint identifier = 0;
ajuint srid = 0;
ajuint srstart = 0;
ajuint srend = 0;
AjPStr name = NULL;
AjPStr stain = NULL;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
EnsPCoordsystemadaptor csa = NULL;
EnsPFeature feature = NULL;
EnsPKaryotypeband kb = NULL;
EnsPKaryotypebandadaptor kba = NULL;
EnsPSlice srslice = NULL;
EnsPSliceadaptor sa = NULL;
if(!dba)
return ajFalse;
if(!statement)
return ajFalse;
(void) am;
(void) slice;
if(!kblist)
return ajFalse;
csa = ensRegistryGetCoordsystemadaptor(dba);
/*
** AJB: The variable kba, set below, is not used elsewhere
** in the function. Needs fixing appropriately.
*/
kba = ensRegistryGetKaryotypebandadaptor(dba);
sa = ensRegistryGetSliceadaptor(dba);
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while(!ajSqlrowiterDone(sqli))
{
identifier = 0;
srid = 0;
srstart = 0;
srend = 0;
name = ajStrNew();
stain = ajStrNew();
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToUint(sqlr, &identifier);
ajSqlcolumnToUint(sqlr, &srid);
ajSqlcolumnToUint(sqlr, &srstart);
ajSqlcolumnToUint(sqlr, &srend);
ajSqlcolumnToStr(sqlr, &name);
ajSqlcolumnToStr(sqlr, &stain);
/* Need to get the internal Ensembl Sequence Region identifier. */
srid = ensCoordsystemadaptorGetInternalSeqregionIdentifier(csa, srid);
/*
** FIXME: karyotype.seq_region_start and karyotype.seq_region_end are
** defined as signed in the tables.sql file.
** All other features use unsigned start and end coordinates.
*/
ensSliceadaptorFetchBySeqregionIdentifier(sa, srid, 0, 0, 0, &srslice);
feature = ensFeatureNewS((EnsPAnalysis) NULL,
srslice,
srstart,
srend,
1);
kb = ensKaryotypebandNew(identifier, feature, name, stain);
ajListPushAppend(kblist, (void *) kb);
ensFeatureDel(&feature);
ensSliceDel(&srslice);
ajStrDel(&name);
ajStrDel(&stain);
}
ajSqlrowiterDel(&sqli);
ajSqlstatementDel(&sqls);
return ajTrue;
}
