Home
last modified time | relevance | path

Searched refs:m_IsProtein (Results 1 – 25 of 26) sorted by relevance

12

/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/blastinput/
H A Dblast_args.hpp920 bool IsProtein() const { return m_IsProtein; } in IsProtein()
935 m_IsProtein = search_db->IsProtein(); in SetSearchDatabase()
944 m_IsProtein = is_protein; in SetSubjects()
975 bool m_IsProtein; /**< Is the database/subject(s) protein? */ member in CBlastDatabaseArgs
989 CIgBlastArgs(bool is_protein) : m_IsProtein(is_protein) {}; in CIgBlastArgs()
1010 bool m_IsProtein; member in CIgBlastArgs
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blastinput/
H A Dblast_args.hpp920 bool IsProtein() const { return m_IsProtein; } in IsProtein()
935 m_IsProtein = search_db->IsProtein(); in SetSearchDatabase()
944 m_IsProtein = is_protein; in SetSubjects()
975 bool m_IsProtein; /**< Is the database/subject(s) protein? */ member in CBlastDatabaseArgs
989 CIgBlastArgs(bool is_protein) : m_IsProtein(is_protein) {}; in CIgBlastArgs()
1010 bool m_IsProtein; member in CIgBlastArgs
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dseqsrc_mock.cpp53 m_IsProtein = x_SelectRandomlyBetween(TRUE, FALSE); in CRandomlyFailMockBlastSeqSrc()
98 return m_IsProtein; in GetIsProt()
H A Dseqsrc_mock.hpp133 Boolean m_IsProtein; member in CRandomlyFailMockBlastSeqSrc
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dseqsrc_mock.cpp53 m_IsProtein = x_SelectRandomlyBetween(TRUE, FALSE); in CRandomlyFailMockBlastSeqSrc()
98 return m_IsProtein; in GetIsProt()
H A Dseqsrc_mock.hpp133 Boolean m_IsProtein; member in CRandomlyFailMockBlastSeqSrc
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/
H A Dbuild_db.cpp841 m_IsProtein == !!(info & CSeq_id::fAcc_nuc)) { in AddSequences()
850 if(bs->IsAa() != m_IsProtein ){ in AddSequences()
958 if ((! ambiguities.empty()) && m_IsProtein) { in AddSequences()
1066 : m_IsProtein (is_protein), in CBuildDatabase()
1124 : m_IsProtein (is_protein), in CBuildDatabase()
1226 m_IsProtein in SetSourceDb()
1377 m_IsProtein, in AddFasta()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/
H A Dbuild_db.cpp841 m_IsProtein == !!(info & CSeq_id::fAcc_nuc)) { in AddSequences()
850 if(bs->IsAa() != m_IsProtein ){ in AddSequences()
958 if ((! ambiguities.empty()) && m_IsProtein) { in AddSequences()
1066 : m_IsProtein (is_protein), in CBuildDatabase()
1124 : m_IsProtein (is_protein), in CBuildDatabase()
1226 m_IsProtein in SetSourceDb()
1377 m_IsProtein, in AddFasta()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dseqsrc_seqdb.cpp575 : m_DbName(db), m_IsProtein(is_prot), in CSeqDbSrcNewArgs()
583 char GetDbType() const { return m_IsProtein ? 'p' : 'n'; } in GetDbType()
595 bool m_IsProtein; ///< Is this database protein? member in CSeqDbSrcNewArgs
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dseqsrc_seqdb.cpp575 : m_DbName(db), m_IsProtein(is_prot), in CSeqDbSrcNewArgs()
583 char GetDbType() const { return m_IsProtein ? 'p' : 'n'; } in GetDbType()
595 bool m_IsProtein; ///< Is this database protein? member in CSeqDbSrcNewArgs
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/
H A Dblast_args.cpp1557 int num_genes = (m_IsProtein) ? 1 : 3; in SetArgumentDescriptions()
1591 if (!m_IsProtein) { in SetArgumentDescriptions()
1666 if (! m_IsProtein) { in SetArgumentDescriptions()
1675 if (! m_IsProtein) { in SetArgumentDescriptions()
1736 if (!m_IsProtein) { in ExtractAlgorithmOptions()
1751 _ASSERT(m_IsProtein == m_IgOptions->m_IsProtein); in ExtractAlgorithmOptions()
1801 if (m_IgOptions->m_IsProtein) { in ExtractAlgorithmOptions()
1808 int num_genes = (m_IsProtein) ? 1: 3; in ExtractAlgorithmOptions()
1832 m_IgOptions->m_IsProtein, in ExtractAlgorithmOptions()
2096 m_IsProtein(true), in CBlastDatabaseArgs()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/
H A Dblast_args.cpp1557 int num_genes = (m_IsProtein) ? 1 : 3; in SetArgumentDescriptions()
1591 if (!m_IsProtein) { in SetArgumentDescriptions()
1666 if (! m_IsProtein) { in SetArgumentDescriptions()
1675 if (! m_IsProtein) { in SetArgumentDescriptions()
1736 if (!m_IsProtein) { in ExtractAlgorithmOptions()
1751 _ASSERT(m_IsProtein == m_IgOptions->m_IsProtein); in ExtractAlgorithmOptions()
1801 if (m_IgOptions->m_IsProtein) { in ExtractAlgorithmOptions()
1808 int num_genes = (m_IsProtein) ? 1: 3; in ExtractAlgorithmOptions()
1832 m_IgOptions->m_IsProtein, in ExtractAlgorithmOptions()
2096 m_IsProtein(true), in CBlastDatabaseArgs()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/igblast/
H A Digblast.cpp88 const string suffix = (ig_opt->m_IsProtein) ? ".pdm." : ".ndm."; in CIgAnnotationInfo()
115 if (ig_opt->m_IsProtein) return; in CIgAnnotationInfo()
333 ::Create((m_IgOptions->m_IsProtein)? eBlastp: eBlastn)); in Run()
354 if (m_IgOptions->m_IsProtein) { in Run()
376 ::Create((m_IgOptions->m_IsProtein)? eBlastp: eBlastn)); in Run()
379 int num_genes = (m_IgOptions->m_IsProtein) ? 1 : 3; in Run()
499 if (m_IgOptions->m_IsProtein) { in x_SetupVSearch()
1444 CSeqDB::ESeqType db_type = (m_IgOptions->m_IsProtein)? in x_AnnotateDomain()
1519 CBl2Seq bl2seq(q_loc, s_loc, (m_IgOptions->m_IsProtein)? eBlastp: eBlastn); in x_AnnotateDomain()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/igblast/
H A Digblast.cpp88 const string suffix = (ig_opt->m_IsProtein) ? ".pdm." : ".ndm."; in CIgAnnotationInfo()
115 if (ig_opt->m_IsProtein) return; in CIgAnnotationInfo()
333 ::Create((m_IgOptions->m_IsProtein)? eBlastp: eBlastn)); in Run()
354 if (m_IgOptions->m_IsProtein) { in Run()
376 ::Create((m_IgOptions->m_IsProtein)? eBlastp: eBlastn)); in Run()
379 int num_genes = (m_IgOptions->m_IsProtein) ? 1 : 3; in Run()
499 if (m_IgOptions->m_IsProtein) { in x_SetupVSearch()
1444 CSeqDB::ESeqType db_type = (m_IgOptions->m_IsProtein)? in x_AnnotateDomain()
1519 CBl2Seq bl2seq(q_loc, s_loc, (m_IgOptions->m_IsProtein)? eBlastp: eBlastn); in x_AnnotateDomain()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/blast/seqdb_writer/
H A Dbuild_db.hpp586 bool m_IsProtein; member in CBuildDatabase
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/blast/seqdb_writer/
H A Dbuild_db.hpp586 bool m_IsProtein; member in CBuildDatabase
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/igblast/
H A Digblastp_app.cpp177 ig_opts->m_IsProtein, -1, false); in Run()
H A Digblastn_app.cpp277 … CBlastFormatUtil::GetBlastDbInfo(db_info, l_full_db_list, l_ig_opts->m_IsProtein, -1, false); in Main()
837 if (!(m_ig_opts->m_IsProtein) && total_elements > 1) { in Run()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/
H A Dseqdbalias.hpp1275 bool m_IsProtein; member in CSeqDBAliasFile
H A Dseqdbalias.cpp60 m_IsProtein (prot_nucl == 'p'), in CSeqDBAliasFile()
1710 string extn = (m_IsProtein ? ".pin" : ".nin"); in GetAliasFileValues()
1851 ddc.Log("m_IsProtein", m_IsProtein); in DebugDump()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/
H A Dseqdbalias.hpp1275 bool m_IsProtein; member in CSeqDBAliasFile
H A Dseqdbalias.cpp60 m_IsProtein (prot_nucl == 'p'), in CSeqDBAliasFile()
1710 string extn = (m_IsProtein ? ".pin" : ".nin"); in GetAliasFileValues()
1851 ddc.Log("m_IsProtein", m_IsProtein); in DebugDump()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/igblast/
H A Digblast.hpp66 bool m_IsProtein; // search molecular type member in CIgBlastOptions
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/igblast/
H A Digblast.hpp66 bool m_IsProtein; // search molecular type member in CIgBlastOptions
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/align_format/
H A Dtabular.cpp2258 bool is_protein = ig_opts->m_IsProtein; in SetIgAnnotation()

12