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Searched refs:sublocs (Results 1 – 12 of 12) sorted by relevance

/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Location/
H A DSplit.pm176 return @sublocs if( ($order == 0) || (! @sublocs) );
182 while((! defined($seqid)) && ($i <= $#sublocs)) {
183 $seqid = $sublocs[$i++]->seq_id();
191 grep { $_->seq_id() eq $seqid; } @sublocs :
192 @sublocs);
405 my @sublocs;
413 push @sublocs, $loc;
712 my @sublocs = $self->sub_Location(0);
713 my $start = $sublocs[0]->start;
714 my $end = $sublocs[-1]->end;
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/
H A DGeneric.pm333 my @sublocs = $self->location->sub_Location;
338 for (my $i = 1; $i < scalar @sublocs; $i++) {
339 $a_end = $sublocs[$i-1]->end;
340 $a_strand = $sublocs[$i-1]->strand;
341 $b_start = $sublocs[$i]->start;
342 $b_strand = $sublocs[$i]->strand;
386 my @sublocs = $self->location->sub_Location;
392 $a_end = $sublocs[$i-1]->end;
393 $a_strand = $sublocs[$i-1]->strand;
394 $b_start = $sublocs[$i]->start;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/
H A Dgtf_writer.cpp323 bool needsPartNumbers = (sublocs.size() > 1); in xAssignFeaturesGene()
325 for ( auto it = sublocs.begin(); it != sublocs.end(); it++ ) { in xAssignFeaturesGene()
372 TSeqPos lastFrom = sublocs.front()->GetFrom(); in xAssignFeaturesTranscript()
373 TSeqPos lastTo = sublocs.front()->GetTo(); in xAssignFeaturesTranscript()
374 auto it = sublocs.begin(); in xAssignFeaturesTranscript()
460 bool needsPartNumbers = xIntervalsNeedPartNumbers(sublocs); in xAssignFeaturesCds()
462 for ( auto it = sublocs.begin(); it != sublocs.end(); it++ ) { in xAssignFeaturesCds()
480 pRecord->SetCdsPhase(sublocs, strand); in xAssignFeaturesCds()
510 auto currentIt = sublocs.begin(); in xAssignFeaturesCds()
559 auto currentIt = sublocs.rbegin(); in xAssignFeaturesCds()
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H A Dgff3_writer.cpp1556 for ( auto it = sublocs.begin(); it != sublocs.end(); ++it ) { in xWriteFeatureTrna()
2257 if (sublocs.size() > 1) { in xAssignFeature()
2258 for ( it = sublocs.begin(); it != sublocs.end(); ++it ) { in xAssignFeature()
2268 if (it_floor != sublocs.end() && it_ceil != sublocs.end()) { in xAssignFeature()
2272 if ( it_ceil != sublocs.end() && it_floor != sublocs.end() ) { in xAssignFeature()
2608 for ( it = sublocs.begin(); it != sublocs.end(); ++it ) { in xWriteFeatureCds()
2682 for ( it = sublocs.begin(); it != sublocs.end(); ++it ) { in xWriteFeatureRna()
2742 for (auto it = sublocs.begin(); it != sublocs.end(); ++it ) { in xWriteFeatureCDJVSegment()
2840 for ( auto it = sublocs.begin(); it != sublocs.end(); ++it ) { in xWriteFeatureProtein()
2868 if (sublocs.size() == 1) { in xWriteFeatureRecords()
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H A Dbed_writer.cpp613 const list<CRef<CSeq_interval> >& sublocs = pPackedInt->GetPacked_int().Get(); in xWriteFeature() local
615 for (it = sublocs.begin(); it != sublocs.end(); ++it ) { in xWriteFeature()
H A Dgff_writer.cpp1419 const list<CRef<CSeq_interval>>& sublocs) in xIntervalsNeedPartNumbers() argument
1422 _ASSERT(sublocs.size()); in xIntervalsNeedPartNumbers()
1423 if (sublocs.size() == 1) { // most common in xIntervalsNeedPartNumbers()
1427 const auto& front = *sublocs.front(); in xIntervalsNeedPartNumbers()
1430 for (auto itComp = sublocs.begin()++; itComp != sublocs.end(); itComp++) { in xIntervalsNeedPartNumbers()
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Factory/
H A DFTLocationFactory.pm163 my (@sublocs) = (split(q(,),$beg), $mid, split(q(,),$end));
169 while (@sublocs) {
170 my $subloc = shift @sublocs;
176 my $sub = shift @sublocs;
/dports/biology/p5-Bio-Coordinate/Bio-Coordinate-1.007001/t/
H A DGeneCoordinateMapper.t449 is @sublocs, 2;
451 #print Dumper \@sublocs;
452 is $sublocs[0]->start, 2;
453 is $sublocs[0]->end, 3;
454 is $sublocs[1]->start, 10;
455 is $sublocs[1]->end, 12;
489 is @sublocs, 2;
491 is $sublocs[0]->start, 6;
492 is $sublocs[0]->end, 9;
493 is $sublocs[1]->start, 15;
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H A DCoordinateMapper.t477 ok my @sublocs = $res->each_Location(1);
478 is @sublocs, 2;
480 #print Dumper \@sublocs;
481 is $sublocs[0]->start, 2;
482 is $sublocs[0]->end, 3;
483 is $sublocs[1]->start, 10;
484 is $sublocs[1]->end, 12;
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/
H A DPrimarySeq.pm401 my @sublocs = ($order == -1) ? reverse $loc->each_Location(): $loc->each_Location;
402 foreach my $subloc (@sublocs) {
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/
H A Dgenbank.t161 my @sublocs = $location->sub_Location;
162 is(@sublocs, 29);
236 @sublocs = $location->sub_Location;
238 is(@sublocs, 2);
239 my $loc = shift @sublocs;
244 $loc = shift @sublocs;
H A DHandler.t159 my @sublocs = $location->sub_Location();
160 is(@sublocs, 29);
233 @sublocs = $location->sub_Location();
235 is(@sublocs, 2);
236 my $loc = shift @sublocs;
241 $loc = shift @sublocs;