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Searched refs:seqdata (Results 1 – 25 of 73) sorted by relevance

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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/
H A Dgbdriver.pm225 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 || '') :
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H A Dswissdriver.pm174 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 Dembldriver.pm244 $hobj->data_handler($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;
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/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/
H A Dgtf_tracking.cpp491 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()
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H A Dcuffcompare.cpp1308 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 Dcsamformatter.cpp194 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 Dcsamformatter.hpp24 …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 Daln_writer.cpp185 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/
H A Dseq_edit.cpp53 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 Dseq_edit.cpp53 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 Dcsra_test_mt.cpp147 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 Dcached_sequence.cpp115 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 Dcached_sequence.cpp115 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 DMakefile.unit_test_gene_model.app15 …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 Dtest.sh56 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 DPrimer.pm317 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 Dunit_test_flatfile_parser.cpp60 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 Dncbishrh.rc4 ROOT=/harddisk/seqdata
13 ROOT=/harddisk/seqdata
H A Dncbishrc.rc4 ROOT=/harddisk/seqdata
15 ROOT=/harddisk/seqdata
/dports/biology/ncbi-toolkit/ncbi/config/vms/
H A Dncbishrh.cfg4 ROOT=device:[user.seqdata]
13 ROOT=device:[user.seqdata]
H A Dncbishrc.cfg4 ROOT=device:[user.seqdata]
15 ROOT=device:[user.seqdata]
/dports/audio/qmidiarp/qmidiarp-qmidiarp-0.6.5/src/
H A Dmidiarp_lv2.cpp88 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 Dmidilfo_lv2.cpp91 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 Dtest_csra_loader_mt.cpp196 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 DgetDoSeq.R91 list(fun=.foreachGlobals$seqFun, data=.foreachGlobals$seqdata)

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