PredictionTranscript *PredictionTranscript_shallowCopy(PredictionTranscript *trans) {
PredictionTranscript *newTranscript = PredictionTranscript_new();
// Exons will come in mem copy so free vector just created in PredictionTranscript_new
Vector_free(newTranscript->exons);
memcpy(newTranscript,trans,sizeof(PredictionTranscript));
return newTranscript;
}
SeqFeature *SeqFeatureFactory_newFeature(ClassType type) {
void *feature;
switch (type) {
case CLASS_BASEALIGNFEATURE:
feature = BaseAlignFeature_new();
break;
case CLASS_DNADNAALIGNFEATURE:
feature = DNAAlignFeature_new();
break;
case CLASS_DNAPEPALIGNFEATURE:
feature = DNAPepAlignFeature_new();
break;
case CLASS_FEATUREPAIR:
feature = FeaturePair_new();
break;
case CLASS_PREDICTIONTRANSCRIPT:
feature = PredictionTranscript_new();
break;
case CLASS_SIMPLEFEATURE:
feature = SimpleFeature_new();
break;
case CLASS_SEQFEATURE:
feature = SeqFeature_new();
break;
case CLASS_EXON:
feature = Exon_new();
break;
case CLASS_TRANSCRIPT:
feature = Transcript_new();
break;
case CLASS_PREDICTIONEXON:
feature = PredictionExon_new();
break;
case CLASS_REPEATFEATURE:
feature = RepeatFeature_new();
break;
case CLASS_INTRONSUPPORTINGEVIDENCE:
fprintf(stderr,"!!!!!! ise new in seqfeaturefactory\n");
feature = IntronSupportingEvidence_new();
break;
default:
fprintf(stderr,"Error: Unknown feature type %s SeqFeatureFactory_newFeature\n",Class_findByType(type)->name);
exit(1);
}
return (SeqFeature *)feature;
}
/*
=head2 _objs_from_sth
Arg [1] : DBI:st $sth
An executed DBI statement handle
Arg [2] : (optional) Bio::EnsEMBL::Mapper $mapper
An mapper to be used to convert contig coordinates
to assembly coordinates.
Arg [3] : (optional) Bio::EnsEMBL::Slice $slice
A slice to map the prediction transcript to.
Example : $p_transcripts = $self->_objs_from_sth($sth);
Description: Creates a list of Prediction transcripts from an executed DBI
statement handle. The columns retrieved via the statement
handle must be in the same order as the columns defined by the
_columns method. If the slice argument is provided then the
the prediction transcripts will be in returned in the coordinate
system of the $slice argument. Otherwise the prediction
transcripts will be returned in the RawContig coordinate system.
Returntype : reference to a list of Bio::EnsEMBL::PredictionTranscripts
Exceptions : none
Caller : superclass generic_fetch
Status : Stable
=cut
*/
Vector *PredictionTranscriptAdaptor_objectsFromStatementHandle(PredictionTranscriptAdaptor *pta,
StatementHandle *sth,
AssemblyMapper *assMapper,
Slice *destSlice) {
SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(pta->dba);
AnalysisAdaptor *aa = DBAdaptor_getAnalysisAdaptor(pta->dba);
Vector *pTranscripts = Vector_new();
IDHash *sliceHash = IDHash_new(IDHASH_SMALL);
long destSliceStart;
long destSliceEnd;
int destSliceStrand;
long destSliceLength;
char * destSliceSrName;
IDType destSliceSrId = 0;
if (destSlice) {
destSliceStart = Slice_getStart(destSlice);
destSliceEnd = Slice_getEnd(destSlice);
destSliceStrand = Slice_getStrand(destSlice);
destSliceLength = Slice_getLength(destSlice);
destSliceSrName = Slice_getSeqRegionName(destSlice);
destSliceSrId = Slice_getSeqRegionId(destSlice);
}
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType predictionTranscriptId = row->getLongLongAt(row,0);
IDType seqRegionId = row->getLongLongAt(row,1);
long seqRegionStart = row->getLongAt(row,2);
long seqRegionEnd = row->getLongAt(row,3);
int seqRegionStrand = row->getIntAt(row,4);
IDType analysisId = row->getLongLongAt(row,5);
char *displayLabel = row->getStringAt(row,6);
// get the analysis object
Analysis *analysis = AnalysisAdaptor_fetchByDbID(aa, analysisId);
if (! IDHash_contains(sliceHash, seqRegionId)) {
IDHash_add(sliceHash, seqRegionId, SliceAdaptor_fetchBySeqRegionId(sa, seqRegionId, POS_UNDEF, POS_UNDEF, STRAND_UNDEF));
}
Slice *slice = IDHash_getValue(sliceHash, seqRegionId);
Slice *ptSlice = slice;
char *srName = Slice_getSeqRegionName(slice);
CoordSystem *srCs = Slice_getCoordSystem(slice);
//
// remap the feature coordinates to another coord system
// if a mapper was provided
//
if (assMapper != NULL) {
MapperRangeSet *mrs;
// Slightly suspicious about need for this if statement so left in perl statements for now
if (destSlice != NULL &&
assMapper->objectType == CLASS_CHAINEDASSEMBLYMAPPER) {
mrs = ChainedAssemblyMapper_map(assMapper, srName, seqRegionStart, seqRegionEnd, seqRegionStrand, srCs, 1, destSlice);
} else {
mrs = AssemblyMapper_fastMap(assMapper, srName, seqRegionStart, seqRegionEnd, seqRegionStrand, srCs, NULL);
}
// skip features that map to gaps or coord system boundaries
if (MapperRangeSet_getNumRange(mrs) == 0) {
continue;
}
MapperRange *range = MapperRangeSet_getRangeAt(mrs, 0);
if (range->rangeType == MAPPERRANGE_GAP) {
fprintf(stderr,"Got a mapper gap in gene obj_from_sth - not sure if this is allowed\n");
exit(1);
} else {
MapperCoordinate *mc = (MapperCoordinate *)range;
seqRegionId = mc->id;
seqRegionStart = mc->start;
seqRegionEnd = mc->end;
seqRegionStrand = mc->strand;
}
MapperRangeSet_free(mrs);
if (! IDHash_contains(sliceHash, seqRegionId)) {
IDHash_add(sliceHash, seqRegionId, SliceAdaptor_fetchBySeqRegionId(sa, seqRegionId, POS_UNDEF, POS_UNDEF, STRAND_UNDEF));
}
ptSlice = IDHash_getValue(sliceHash, seqRegionId);
}
//
// If a destination slice was provided convert the coords
// If the dest_slice starts at 1 and is foward strand, nothing needs doing
//
if (destSlice != NULL) {
if (destSliceStart != 1 || destSliceStrand != 1) {
if (destSliceStrand == 1) {
seqRegionStart = seqRegionStart - destSliceStart + 1;
seqRegionEnd = seqRegionEnd - destSliceStart + 1;
} else {
long tmpSeqRegionStart = seqRegionStart;
seqRegionStart = destSliceEnd - seqRegionEnd + 1;
seqRegionEnd = destSliceEnd - tmpSeqRegionStart + 1;
seqRegionStrand = -seqRegionStrand;
}
}
// throw away features off the end of the requested slice
if (seqRegionEnd < 1 || seqRegionStart > destSliceLength || (destSliceSrId != seqRegionId)) {
continue;
}
ptSlice = destSlice;
}
// Finally, create the new PredictionTranscript.
PredictionTranscript *pt = PredictionTranscript_new();
PredictionTranscript_setStart (pt, seqRegionStart);
PredictionTranscript_setEnd (pt, seqRegionEnd);
PredictionTranscript_setStrand (pt, seqRegionStrand);
PredictionTranscript_setSlice (pt, ptSlice);
PredictionTranscript_setAnalysis (pt, analysis);
PredictionTranscript_setAdaptor (pt, (BaseAdaptor *)pta);
PredictionTranscript_setDbID (pt, predictionTranscriptId);
PredictionTranscript_setDisplayLabel(pt, displayLabel);
Vector_addElement(pTranscripts, pt);
}
IDHash_free(sliceHash, NULL);
return pTranscripts;
}
