Searched refs:sublocs (Results 1 – 12 of 12) sorted by relevance
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Location/ |
H A D | Split.pm | 176 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; [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/ |
H A D | Generic.pm | 333 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; [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
H A D | gtf_writer.cpp | 323 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() [all …]
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H A D | gff3_writer.cpp | 1556 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() [all …]
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H A D | bed_writer.cpp | 613 const list<CRef<CSeq_interval> >& sublocs = pPackedInt->GetPacked_int().Get(); in xWriteFeature() local 615 for (it = sublocs.begin(); it != sublocs.end(); ++it ) { in xWriteFeature()
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H A D | gff_writer.cpp | 1419 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()
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Factory/ |
H A D | FTLocationFactory.pm | 163 my (@sublocs) = (split(q(,),$beg), $mid, split(q(,),$end)); 169 while (@sublocs) { 170 my $subloc = shift @sublocs; 176 my $sub = shift @sublocs;
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/dports/biology/p5-Bio-Coordinate/Bio-Coordinate-1.007001/t/ |
H A D | GeneCoordinateMapper.t | 449 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; [all …]
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H A D | CoordinateMapper.t | 477 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 $sublocs[1]->end, 12;
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/ |
H A D | PrimarySeq.pm | 401 my @sublocs = ($order == -1) ? reverse $loc->each_Location(): $loc->each_Location; 402 foreach my $subloc (@sublocs) {
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/ |
H A D | genbank.t | 161 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;
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H A D | Handler.t | 159 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;
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