EnsPIntron ensIntronNewExons(EnsPExon exon1, EnsPExon exon2)
{
ajint strand = 0;
ajuint start = 0;
ajuint end = 0;
AjPStr seqname1 = NULL;
AjPStr seqname2 = NULL;
EnsPFeature feature = NULL;
EnsPFeature feature1 = NULL;
EnsPFeature feature2 = NULL;
EnsPIntron intron = NULL;
EnsPSlice slice1 = NULL;
EnsPSlice slice2 = NULL;
/*
ajDebug("ensIntronNew\n"
" exon1 %p\n"
" exon2 %p\n",
exon1,
exon2);
ensExonTrace(exon1, 1);
ensExonTrace(exon2, 1);
*/
if(!exon1)
return NULL;
if(!exon2)
return NULL;
feature1 = ensExonGetFeature(exon1);
feature2 = ensExonGetFeature(exon2);
slice1 = ensFeatureGetSlice(feature1);
slice2 = ensFeatureGetSlice(feature2);
seqname1 = ensFeatureGetSequenceName(feature1);
seqname2 = ensFeatureGetSequenceName(feature2);
/* Both Exons have to be on the same Slice or sequence. */
if(slice1 && slice2 && (!ensSliceMatch(slice1, slice2)))
{
ajDebug("ensIntronNewExons got Exons on different Slices.\n");
return NULL;
}
else if(seqname1 && seqname2 && (!ajStrMatchCaseS(seqname1, seqname2)))
{
ajDebug("ensIntronNewExons got Exons on different sequence names.\n");
return NULL;
}
else
{
ajDebug("ensIntronNewExons got Exons on Slice and sequence names.\n");
return NULL;
}
if(ensFeatureGetStrand(feature1) != ensFeatureGetStrand(feature2))
{
ajDebug("ensIntronNewExons got Exons on different strands.\n");
return NULL;
}
if(ensFeatureGetStrand(feature1) >= 0)
{
start = ensFeatureGetEnd(feature1) + 1;
end = ensFeatureGetStart(feature2) - 1;
}
else
{
start = ensFeatureGetEnd(feature2) + 1;
end = ensFeatureGetStart(feature1) - 1;
}
if(start > (end + 1))
{
ajDebug("ensIntronNewExons requires that the start coordinate %u "
"is less than the end coordinate %u + 1 ", start, end);
return NULL;
}
strand = ensFeatureGetStrand(feature1);
if(slice1)
feature = ensFeatureNewS((EnsPAnalysis) NULL,
slice1,
start,
end,
strand);
if(seqname1)
feature = ensFeatureNewN((EnsPAnalysis) NULL,
seqname1,
start,
end,
strand);
if(feature)
{
AJNEW0(intron);
intron->Feature = feature;
intron->PreviousExon = ensExonNewRef(exon1);
intron->NextExon = ensExonNewRef(exon2);
intron->Use = 1;
}
else
ajDebug("ensIntronNewExons could not create an Ensembl Feature.\n");
return intron;
}
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;
}
