void ensProjectionsegmentDel(EnsPProjectionsegment *Pps)
{
EnsPProjectionsegment pthis = NULL;
if(!Pps)
return;
if(!*Pps)
return;
pthis = *Pps;
pthis->Use--;
if(pthis->Use)
{
*Pps = NULL;
return;
}
ensSliceDel(&pthis->TrgSlice);
AJFREE(pthis);
*Pps = NULL;
return;
}
AjBool ensKaryotypebandadaptorFetchAllByChromosomeBand(
EnsPKaryotypebandadaptor adaptor,
const AjPStr name,
const AjPStr band,
AjPList kblist)
{
char *txtband = NULL;
AjBool value = AJFALSE;
AjPStr constraint = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSlice slice = NULL;
EnsPSliceadaptor sa = NULL;
if(!adaptor)
return ajFalse;
if(!name)
return ajFalse;
if(!band)
return ajFalse;
if(!kblist)
return ajFalse;
dba = ensFeatureadaptorGetDatabaseadaptor(adaptor->Adaptor);
sa = ensRegistryGetSliceadaptor(dba);
ensSliceadaptorFetchByRegion(sa,
(const AjPStr) NULL,
(const AjPStr) NULL,
name,
0,
0,
0,
&slice);
ensDatabaseadaptorEscapeC(dba, &txtband, band);
constraint = ajFmtStr("karyotype.band LIKE '%s%%'", txtband);
ajCharDel(&txtband);
value = ensFeatureadaptorFetchAllBySliceConstraint(adaptor->Adaptor,
slice,
constraint,
(const AjPStr) NULL,
kblist);
ajStrDel(&constraint);
ensSliceDel(&slice);
return value;
}
AjBool ensKaryotypebandadaptorFetchAllByChromosomeName(
EnsPKaryotypebandadaptor adaptor,
const AjPStr name,
AjPList kblist)
{
AjBool value = AJFALSE;
EnsPDatabaseadaptor dba = NULL;
EnsPSlice slice = NULL;
EnsPSliceadaptor sa = NULL;
if(!adaptor)
return ajFalse;
if(!name)
return ajFalse;
if(!kblist)
return ajFalse;
dba = ensFeatureadaptorGetDatabaseadaptor(adaptor->Adaptor);
sa = ensRegistryGetSliceadaptor(dba);
ensSliceadaptorFetchByRegion(sa,
(const AjPStr) NULL,
(const AjPStr) NULL,
name,
0,
0,
0,
&slice);
value = ensFeatureadaptorFetchAllBySlice(adaptor->Adaptor,
slice,
(const AjPStr) NULL,
kblist);
ensSliceDel(&slice);
return value;
}
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;
}
