| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/streamtest/ |
| H A D | process_seqvector.hpp | 163 EGapType gap_type = eGT_letters; in SeqEntryProcess() local
165 gap_type = eGT_one_dash; in SeqEntryProcess()
167 gap_type = eGT_dashes; in SeqEntryProcess()
169 gap_type = eGT_letters; in SeqEntryProcess()
171 gap_type = eGT_count; in SeqEntryProcess()
176 if ( gap_type != eGT_letters && sv_iter.GetGapSizeForward() > 0 ) { in SeqEntryProcess()
178 if ( gap_type == eGT_one_dash ) { in SeqEntryProcess()
181 } else if ( gap_type == eGT_dashes ) { in SeqEntryProcess()
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| H A D | process_explore.hpp | 222 string gap_type = ""; in DoOneBioseq() local
232 gap_type = sgr->GetGapType(); in DoOneBioseq()
238 …this, &bsx, gaps, num_gaps, &next_gap, &has_gap, &gap_start, &gap_end, &gap_type](CFeatureIndex& s… in DoOneBioseq()
246 … *m_out << "Gap type: " << gap_type << ", from: " << gap_start << ", to: " << gap_end << '\n'; in DoOneBioseq()
251 gap_type = sgr->GetGapType(); in DoOneBioseq()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/readers/ |
| H A D | agp_util.hpp | 188 EGap gap_type; member in CAgpRow
227 static bool GapValidAtObjectEnd(EGap gap_type) in GapValidAtObjectEnd() argument
229 return gap_type==eGapCentromere || gap_type==eGapTelomere || in GapValidAtObjectEnd()
230 gap_type==eGapShort_arm || gap_type==eGapHeterochromatin || in GapValidAtObjectEnd()
231 gap_type==eGapContamination; in GapValidAtObjectEnd()
247 if( gap_type==eGapFragment) return false; in GapEndsScaffold()
253 return GapValidAtObjectEnd(gap_type); in GapValidAtObjectEnd()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/readers/ |
| H A D | agp_util.hpp | 188 EGap gap_type; member in CAgpRow
227 static bool GapValidAtObjectEnd(EGap gap_type) in GapValidAtObjectEnd() argument
229 return gap_type==eGapCentromere || gap_type==eGapTelomere || in GapValidAtObjectEnd()
230 gap_type==eGapShort_arm || gap_type==eGapHeterochromatin || in GapValidAtObjectEnd()
231 gap_type==eGapContamination; in GapValidAtObjectEnd()
247 if( gap_type==eGapFragment) return false; in GapEndsScaffold()
253 return GapValidAtObjectEnd(gap_type); in GapValidAtObjectEnd()
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| H A D | agp_validate_reader.hpp | 267 void x_GetMostFreqGapsText(int gap_type, string& eol_text, string& attrs);
269 …void x_PrintGapCountsLine(XPrintTotalsItem& xprint, int gap_type, const string& label=NcbiEmptyStr…
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/ |
| H A D | unit_test_gap_analysis.cpp | 151 GA::EGapType gap_type = GA::eGapType_All, in AnalyzeSeqEntryTextAsn() argument
163 return gap_analysis.GetGapLengthSummary(gap_type); in AnalyzeSeqEntryTextAsn()
230 const GA::EGapType gap_type; member
242 << GA::s_GapTypeToStr(gap_type_expected_result.gap_type) << ": " in CheckGapTypeExpectedResult()
392 gap_type_expected_results[gap_type_idx].gap_type)); in BOOST_AUTO_TEST_CASE()
456 gap_type_expected_result.gap_type)); in BOOST_AUTO_TEST_CASE()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
| H A D | agp_util.cpp | 689 gap_type=it->second; in ParseGapCols()
703 if( gap_type != eGapClone && in ParseGapCols()
704 gap_type != eGapRepeat && in ParseGapCols()
705 gap_type != eGapFragment && in ParseGapCols()
706 gap_type != eGapScaffold && in ParseGapCols()
731 if( gap_type == eGapClone || gap_type == eGapFragment ) { in ParseGapCols()
743 if( gap_type == eGapScaffold ) { in ParseGapCols()
819 gap_types[gap_type] + "\t" + in ToString()
936 if( gap_type == eGapFragment ) { in SubstOldGap()
939 else if( gap_type == eGapClone ) { in SubstOldGap()
[all …]
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
| H A D | agp_util.cpp | 689 gap_type=it->second; in ParseGapCols()
703 if( gap_type != eGapClone && in ParseGapCols()
704 gap_type != eGapRepeat && in ParseGapCols()
705 gap_type != eGapFragment && in ParseGapCols()
706 gap_type != eGapScaffold && in ParseGapCols()
731 if( gap_type == eGapClone || gap_type == eGapFragment ) { in ParseGapCols()
743 if( gap_type == eGapScaffold ) { in ParseGapCols()
819 gap_types[gap_type] + "\t" + in ToString()
936 if( gap_type == eGapFragment ) { in SubstOldGap()
939 else if( gap_type == eGapClone ) { in SubstOldGap()
[all …]
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/edit/ |
| H A D | gaps_edit.hpp | 57 CGapsEditor(CSeq_gap::EType gap_type,
62 CGapsEditor(CSeq_gap::EType gap_type,
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| H A D | seq_entry_edit.hpp | 177 …bool is_assembly_gap = false, int gap_type = CSeq_gap::eType_unknown, int linkage = -1, int linkag…
183 …bool is_assembly_gap = false, int gap_type = CSeq_gap::eType_unknown, int linkage = -1, int linkag…
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/edit/ |
| H A D | gaps_edit.hpp | 57 CGapsEditor(CSeq_gap::EType gap_type,
62 CGapsEditor(CSeq_gap::EType gap_type,
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| H A D | seq_entry_edit.hpp | 177 …bool is_assembly_gap = false, int gap_type = CSeq_gap::eType_unknown, int linkage = -1, int linkag…
183 …bool is_assembly_gap = false, int gap_type = CSeq_gap::eType_unknown, int linkage = -1, int linkag…
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| /dports/devel/boost-docs/boost_1_72_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
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| /dports/devel/boost-python-libs/boost_1_72_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
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| /dports/databases/percona57-pam-for-mysql/boost_1_59_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
|
| /dports/databases/mysqlwsrep57-server/boost_1_59_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
|
| /dports/databases/percona57-server/boost_1_59_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
|
| /dports/databases/xtrabackup/boost_1_59_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
|
| /dports/databases/percona57-client/boost_1_59_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
|
| /dports/devel/boost-libs/boost_1_72_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
|
| /dports/devel/hyperscan/boost_1_75_0/libs/geometry/test/algorithms/ |
| H A D | maximum_gap.cpp | 88 typedef typename interval_type::difference_type gap_type; in test_one() typedef
90 gap_type gap = bg::maximum_gap(intervals); in test_one()
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/agp_validate/test/ |
| H A D | bad_test.out | 3 ERROR, line skipped: invalid linkage "yes" for gap_type short_arm
36 ERROR, line skipped: invalid linkage "yes" for gap_type contig
42 ERROR, line skipped: invalid linkage "yes" for gap_type centromere
48 ERROR, line skipped: invalid linkage "yes" for gap_type heterochromatin
95 ERROR, line skipped: invalid value for gap_type (column 7)
108 ERROR, line skipped: invalid linkage "yes" for gap_type telomere
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
| H A D | block.cpp | 102 if(gfp->gap_type != NULL) in GapFeatsFree()
103 MemFree(gfp->gap_type); in GapFeatsFree()
396 gap_type(NULL), in _gap_feats()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | gaps_edit.cpp | 216 CGapsEditor::CGapsEditor(CSeq_gap::EType gap_type, const TEvidenceSet& evidences, in CGapsEditor() argument
218 m_gap_type(gap_type), in CGapsEditor()
226 CGapsEditor::CGapsEditor(CSeq_gap::EType gap_type, in CGapsEditor() argument
232 m_gap_type(gap_type), in CGapsEditor()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | gaps_edit.cpp | 216 CGapsEditor::CGapsEditor(CSeq_gap::EType gap_type, const TEvidenceSet& evidences, in CGapsEditor() argument
218 m_gap_type(gap_type), in CGapsEditor()
226 CGapsEditor::CGapsEditor(CSeq_gap::EType gap_type, in CGapsEditor() argument
232 m_gap_type(gap_type), in CGapsEditor()
|