/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/ |
H A D | gbdriver.pm | 225 my $seqdata; 303 my $delim = ($seqdata && $seqdata->{NAME} eq 'FEATURES') ? "\n" : ' '; 304 $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? $delim.$data : $data; 314 my $seqdata; 376 my $delim = ($seqdata && $seqdata->{NAME} eq 'FEATURES') ? "\n" : ' '; 377 $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? $delim.$data : $data; 427 my ($self, $seqdata) = @_; 429 delete $seqdata->{DATA}; 442 ((ref($seqdata->{$qual})) ? scalar(@{ $seqdata->{$qual} }) : 1) 449 (exists $seqdata->{$qual}) ? ($seqdata->{$qual}.= $delim.$qualdata || '') : [all …]
|
H A D | swissdriver.pm | 174 if ($seqdata) { 176 $seqdata = (); 181 $seqdata->{NAME} = $ann; 188 ((ref($seqdata->{$qual})) ? scalar(@{ $seqdata->{$qual} }) : 1) 193 $seqdata->{$qual} .= ($seqdata->{$qual}) ? 197 $seqdata->{$qual} = [$seqdata->{$qual}]; 209 $seqdata = (); 218 $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? 228 $seqdata->{DATA} = $data; 231 $seqdata = (); [all …]
|
H A D | embldriver.pm | 244 $hobj->data_handler($seqdata) if $seqdata; 245 $seqdata = (); 247 $seqdata->{NAME} = $ann; 252 ((ref($seqdata->{$qual})) ? scalar(@{ $seqdata->{$qual} }) : 1) 259 $seqdata->{$qual} .= ($seqdata->{$qual}) ? 264 $seqdata->{$qual} = [$seqdata->{$qual}]; 278 $seqdata = (); 290 $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? 303 $seqdata = (); 312 $hobj->data_handler($seqdata) if $seqdata; [all …]
|
/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
H A D | gtf_tracking.cpp | 491 seqdata.umrnas[j]->strand='+'; in fix_umrnas() 532 seqdata.umrnas[j]->strand='+'; in fix_umrnas() 547 seqdata.umrnas[j]->strand='-'; in fix_umrnas() 555 seqdata.mrnas_f.Add(seqdata.umrnas[i]); in fix_umrnas() 557 seqdata.umrnas.Forget(i); in fix_umrnas() 560 seqdata.mrnas_r.Add(seqdata.umrnas[i]); in fix_umrnas() 561 seqdata.umrnas.Forget(i); in fix_umrnas() 573 seqdata.umrnas.Pack(); in fix_umrnas() 682 cluster_mRNAs(seqdata[g]->mrnas_f, seqdata[g]->loci_f, qfidx); in read_mRNAs() 683 cluster_mRNAs(seqdata[g]->mrnas_r, seqdata[g]->loci_r, qfidx); in read_mRNAs() [all …]
|
H A D | cuffcompare.cpp | 1308 compareLoci2R(seqdata.loci_f, seqdata.gstats_f, refdata->loci_f, qfidx); in processLoci() 1309 compareLoci2R(seqdata.loci_r, seqdata.gstats_r, refdata->loci_r, qfidx); in processLoci() 1435 if (seqdata==NULL) { in collectStats() 1445 seqdata->nloci_f.Add(seqdata->loci_f[l]); in collectStats() 1448 seqdata->nloci_r.Add(seqdata->loci_r[l]); in collectStats() 1452 collectQData(stats, seqdata->loci_f); in collectStats() 1453 collectQData(stats, seqdata->loci_r); in collectStats() 1454 collectQU(stats, seqdata->nloci_u); in collectStats() 1462 collectQNOvl(stats, seqdata->loci_f , seqdata->nloci_f); in collectStats() 1463 collectQNOvl(stats, seqdata->loci_r , seqdata->nloci_r); in collectStats() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/ |
H A D | csamformatter.cpp | 194 void CSamFormatter::PrintCorrectedIupac( ostream& o, const char * seqdata, int seqlength, const TTr… in PrintCorrectedIupac() argument 197 const char * a = seqdata; const char * A = seqdata + seqlength - 1; in PrintCorrectedIupac() 198 CIupacnaBase status = CIupacnaBase( CColorTwoBase( seqdata ) ); in PrintCorrectedIupac() 201 status = CIupacnaBase( status, CColorTwoBase( seqdata[i] ) ); in PrintCorrectedIupac() 203 seqdata += seqlength - 1; in PrintCorrectedIupac() 213 …+i < seqlength) status = CIupacnaBase( CNcbi8naBase( *target ), CColorTwoBase( seqdata += inc ) ); in PrintCorrectedIupac() 218 … if( ++i < seqlength) status = CIupacnaBase( status, CColorTwoBase( seqdata += inc ) ); in PrintCorrectedIupac() 224 … if( ++i < seqlength) status = CIupacnaBase( status, CColorTwoBase( seqdata += inc ) ); in PrintCorrectedIupac() 230 … if( ++i < seqlength) status = CIupacnaBase( status, CColorTwoBase( seqdata += inc ) ); in PrintCorrectedIupac() 243 cerr << DISPLAY( seqdata - a ) << DISPLAY( A - a ) << DISPLAY( inc ) << "\n"; in PrintCorrectedIupac()
|
H A D | csamformatter.hpp | 24 …void PrintCorrectedIupac( ostream& o, const char * seqdata, int seqlength, const TTrSequence& tr, …
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
H A D | aln_writer.cpp | 185 string seqdata; in WriteAlignDenseSeg() local 193 seqdata += GetSegString(seq_plus, coding, strand, start, len); in WriteAlignDenseSeg() 198 WriteContiguous(defline, seqdata); in WriteAlignDenseSeg() 503 string seqdata; in WriteSparseAlign() local 509 WriteContiguous(">" + GetBestId(first_id), seqdata); in WriteSparseAlign() 530 string seqdata; in WriteSparseAlign() local 536 seqdata += GetSegString(seq_plus, coding, strands[seg], start, len); in WriteSparseAlign() 539 WriteContiguous(">" + GetBestId(second_id), seqdata); in WriteSparseAlign() 546 void CAlnWriter::WriteContiguous(const string& defline, const string& seqdata) in WriteContiguous() argument 557 while (pos < seqdata.size()) { in WriteContiguous() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
H A D | seq_edit.cpp | 53 string seqdata; in BEGIN_SCOPE() local 54 seq_vec.GetSeqData(0, seq_inst.GetLength(), seqdata); in BEGIN_SCOPE() 56 Ref(new CSeq_data(seqdata, seq_vec.GetCoding())); in BEGIN_SCOPE()
|
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
H A D | seq_edit.cpp | 53 string seqdata; in BEGIN_SCOPE() local 54 seq_vec.GetSeqData(0, seq_inst.GetLength(), seqdata); in BEGIN_SCOPE() 56 Ref(new CSeq_data(seqdata, seq_vec.GetCoding())); in BEGIN_SCOPE()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/test/ |
H A D | csra_test_mt.cpp | 147 const string& seqdata = inst.GetSeq_data().GetIupacna().Get(); in s_Check() local 148 _ASSERT(seqdata.size() == inst.GetLength()); in s_Check() 149 ITERATE ( string, i, seqdata ) { in s_Check() 157 const string& seqdata = inst.GetSeq_data().GetIupacna().Get(); in s_AsFASTA() local 158 return seq.GetId().front()->AsFastaString()+' '+seqdata; in s_AsFASTA()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/blastdb/ |
H A D | cached_sequence.cpp | 115 CRef<CSeq_data> seqdata = m_BlastDb.GetSequence(m_OID, 0, m_Length); in x_AddFullSeq_data() local 116 _ASSERT(seqdata.NotEmpty()); in x_AddFullSeq_data() 117 m_TSE->SetSeq().SetInst().SetSeq_data(*seqdata); in x_AddFullSeq_data() 185 CRef<CSeq_data> seqdata = blastdb.GetSequence(oid, begin, end); in CreateSeqDataChunk() local 188 retval->SetSeq_data(*seqdata); in CreateSeqDataChunk()
|
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/data_loaders/blastdb/ |
H A D | cached_sequence.cpp | 115 CRef<CSeq_data> seqdata = m_BlastDb.GetSequence(m_OID, 0, m_Length); in x_AddFullSeq_data() local 116 _ASSERT(seqdata.NotEmpty()); in x_AddFullSeq_data() 117 m_TSE->SetSeq().SetInst().SetSeq_data(*seqdata); in x_AddFullSeq_data() 185 CRef<CSeq_data> seqdata = blastdb.GetSequence(oid, begin, end); in CreateSeqDataChunk() local 188 retval->SetSeq_data(*seqdata); in CreateSeqDataChunk()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/ |
H A D | Makefile.unit_test_gene_model.app | 15 …e_model -data-in alignments.asn -data-expected annotations.asn -seqdata-expected seqdata.asn -comb… 16 CHECK_COPY = alignments.asn annotations.asn seqdata.asn combined_annot.asn combined_with_omission.a…
|
/dports/misc/thrill/thrill-12c5b59bca66df93b66628b3829027bd0f110dd9/extlib/libs3/libs3/test/ |
H A D | test.sh | 56 rm -f seqdata 57 seq 1 10000 > seqdata 59 $S3_COMMAND put $TEST_BUCKET/testkey filename=seqdata noStatus=1 67 diff seqdata testkey 69 rm -f seqdata testkey
|
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/ |
H A D | Primer.pm | 317 my $seqdata = Bio::Tools::SeqStats->count_monomers($seqobj); 318 my $gc=$$seqdata{'G'} + $$seqdata{'C'};
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/unit_test/ |
H A D | unit_test_flatfile_parser.cpp | 60 string seqdata { "AATTGGGGCCAAAATTGGCCAAATTGGCCATGC" }; in s_BuildRawBioseq() local 61 pEntry->SetSeq().SetInst().SetSeq_data().SetIupacna().Set(seqdata); in s_BuildRawBioseq() 62 pEntry->SetSeq().SetInst().SetLength(seqdata.size()); in s_BuildRawBioseq()
|
/dports/biology/ncbi-toolkit/ncbi/config/unix/ |
H A D | ncbishrh.rc | 4 ROOT=/harddisk/seqdata 13 ROOT=/harddisk/seqdata
|
H A D | ncbishrc.rc | 4 ROOT=/harddisk/seqdata 15 ROOT=/harddisk/seqdata
|
/dports/biology/ncbi-toolkit/ncbi/config/vms/ |
H A D | ncbishrh.cfg | 4 ROOT=device:[user.seqdata] 13 ROOT=device:[user.seqdata]
|
H A D | ncbishrc.cfg | 4 ROOT=device:[user.seqdata] 15 ROOT=device:[user.seqdata]
|
/dports/audio/qmidiarp/qmidiarp-qmidiarp-0.6.5/src/ |
H A D | midiarp_lv2.cpp | 88 void MidiArpLV2::connect_port ( uint32_t port, void *seqdata ) 92 inEventBuffer = (LV2_Atom_Sequence*)seqdata; 95 outEventBuffer = (const LV2_Atom_Sequence*)seqdata; 98 val[port - 2] = (float *) seqdata;
|
H A D | midilfo_lv2.cpp | 91 void MidiLfoLV2::connect_port ( uint32_t port, void *seqdata ) 95 inEventBuffer = (LV2_Atom_Sequence*)seqdata; 98 outEventBuffer = (const LV2_Atom_Sequence*)seqdata; 101 val[port - 2] = (float *) seqdata;
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/test/ |
H A D | test_csra_loader_mt.cpp | 196 const string& seqdata = inst.GetSeq_data().GetIupacna().Get(); in s_Check() local 197 _ASSERT(seqdata.size() == inst.GetLength()); in s_Check() 198 ITERATE ( string, i, seqdata ) { in s_Check()
|
/dports/devel/R-cran-foreach/foreach/R/ |
H A D | getDoSeq.R | 91 list(fun=.foreachGlobals$seqFun, data=.foreachGlobals$seqdata)
|