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;
}
static AjBool assemblyexceptionadaptorFetchAllBySQL(
EnsPAssemblyexceptionadaptor aea,
const AjPStr statement,
AjPList aes)
{
ajint ori = 0;
ajuint identifier = 0;
ajuint erid = 0;
ajuint srid = 0;
ajuint erstart = 0;
ajuint srstart = 0;
ajuint erend = 0;
ajuint srend = 0;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
AjPStr typestr = NULL;
EnsEAssemblyexceptionType type = ensEAssemblyexceptionTypeNULL;
EnsPAssemblyexception ae = NULL;
if(!aea)
return ajFalse;
if(!statement)
return ajFalse;
if(!aes)
return ajFalse;
sqls = ensDatabaseadaptorSqlstatementNew(aea->Adaptor, statement);
sqli = ajSqlrowiterNew(sqls);
while(!ajSqlrowiterDone(sqli))
{
identifier = 0;
srid = 0;
srstart = 0;
srend = 0;
typestr = ajStrNew();
erid = 0;
erstart = 0;
erend = 0;
ori = 0;
type = ensEAssemblyexceptionTypeNULL;
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToUint(sqlr, &identifier);
ajSqlcolumnToUint(sqlr, &srid);
ajSqlcolumnToUint(sqlr, &srstart);
ajSqlcolumnToUint(sqlr, &srend);
ajSqlcolumnToStr(sqlr, &typestr);
ajSqlcolumnToUint(sqlr, &erid);
ajSqlcolumnToUint(sqlr, &erstart);
ajSqlcolumnToUint(sqlr, &erend);
ajSqlcolumnToInt(sqlr, &ori);
/* Set the Assembly Exception type. */
type = ensAssemblyexceptionTypeFromStr(typestr);
if(!type)
ajFatal("assemblyexceptionadaptorFetchAllBySQL "
"got unexpected Assembly Exception type '%S' "
"from database.\n",
typestr);
ae = ensAssemblyexceptionNew(aea,
identifier,
srid,
srstart,
srend,
erid,
erstart,
erend,
ori,
type);
ajListPushAppend(aes, (void *) ae);
ajStrDel(&typestr);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(aea->Adaptor, &sqls);
return ajTrue;
}
