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Searched refs:is_prot (Results 1 – 25 of 119) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/demo/
H A Dblastinput_demo.cpp115 void PrintReport(CNcbiOstream& out, bool is_prot, CStopWatch& sw) const { in PrintReport() argument
118 out << "Number of " << (is_prot ? "residues" : "bases") << ": " in PrintReport()
144 bool is_prot = static_cast<bool>(args["mol_type"].AsString() == "prot"); in Run() local
145 const EProgram kProgram = is_prot ? eBlastp : eBlastn; in Run()
147 const SDataLoaderConfig dlconfig(is_prot); in Run()
171 stats->PrintReport(out, is_prot, sw); in Run()
/dports/biology/ncbi-toolkit/ncbi/demo/
H A Dblastalign.c194 Boolean is_prot; in Main() local
207 is_prot = (Boolean) myargs[MYARGPROT].intvalue; in Main()
220 while ((septmp = FastaToSeqEntry (ifp, (Boolean)(is_prot==FALSE))) != NULL) in Main()
275 msh = MashNew (is_prot); in Main()
284 if(is_prot ||(Boolean) myargs[MYARGTRS].intvalue ) { in Main()
300 if (!is_prot) { in Main()
305 msh->is_prot = is_prot; in Main()
312 if(is_prot) { in Main()
318 if(msh->translate_prot || msh->is_prot) { in Main()
337 if (is_prot) in Main()
H A Dfastacmd.c224 Uint1 is_prot; in Main() local
243 is_prot = READDB_DB_IS_PROT; in Main()
245 is_prot = READDB_DB_IS_NUC; in Main()
247 is_prot = READDB_DB_UNKNOWN; in Main()
267 rv = Fastacmd_Search_ex (searchstr, database, is_prot, batchfile, dupl, in Main()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dseqinfosrc_bioseq.cpp54 CBioseqSeqInfoSrc::CBioseqSeqInfoSrc(const objects::CBioseq& bs, bool is_prot) in CBioseqSeqInfoSrc() argument
55 : m_DataSource(*x_BioseqSetFromBioseq(bs), is_prot) in CBioseqSeqInfoSrc()
59 bool is_prot) in CBioseqSeqInfoSrc() argument
60 : m_DataSource(bss, is_prot) in CBioseqSeqInfoSrc()
H A Dseqinfosrc_bioseq.hpp64 CBioseqSeqInfoSrc(const objects::CBioseq& bs, bool is_prot);
70 CBioseqSeqInfoSrc(const objects::CBioseq_set& bss, bool is_prot);
H A Dbioseq_extract_data_priv.hpp123 CBlastQuerySourceBioseqSet(const objects::CBioseq_set& bss, bool is_prot);
129 CBlastQuerySourceBioseqSet(const objects::CBioseq& bioseq, bool is_prot);
H A Dbioseq_extract_data_priv.cpp231 (const objects::CBioseq_set& bss, bool is_prot) in CBlastQuerySourceBioseqSet() argument
232 : m_IsProt(is_prot) in CBlastQuerySourceBioseqSet()
243 (const objects::CBioseq& bioseq, bool is_prot) in CBlastQuerySourceBioseqSet() argument
244 : m_IsProt(is_prot) in CBlastQuerySourceBioseqSet()
H A Dlocal_db_adapter.cpp166 bool is_prot = Blast_SubjectIsProtein(p) ? true : false; in MakeSeqInfoSrc() local
167 m_SeqInfoSrc = new CBioseqSeqInfoSrc(*subject_bioseqs, is_prot); in MakeSeqInfoSrc()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dseqinfosrc_bioseq.cpp54 CBioseqSeqInfoSrc::CBioseqSeqInfoSrc(const objects::CBioseq& bs, bool is_prot) in CBioseqSeqInfoSrc() argument
55 : m_DataSource(*x_BioseqSetFromBioseq(bs), is_prot) in CBioseqSeqInfoSrc()
59 bool is_prot) in CBioseqSeqInfoSrc() argument
60 : m_DataSource(bss, is_prot) in CBioseqSeqInfoSrc()
H A Dseqinfosrc_bioseq.hpp64 CBioseqSeqInfoSrc(const objects::CBioseq& bs, bool is_prot);
70 CBioseqSeqInfoSrc(const objects::CBioseq_set& bss, bool is_prot);
H A Dbioseq_extract_data_priv.hpp123 CBlastQuerySourceBioseqSet(const objects::CBioseq_set& bss, bool is_prot);
129 CBlastQuerySourceBioseqSet(const objects::CBioseq& bioseq, bool is_prot);
H A Dbioseq_extract_data_priv.cpp231 (const objects::CBioseq_set& bss, bool is_prot) in CBlastQuerySourceBioseqSet() argument
232 : m_IsProt(is_prot) in CBlastQuerySourceBioseqSet()
243 (const objects::CBioseq& bioseq, bool is_prot) in CBlastQuerySourceBioseqSet() argument
244 : m_IsProt(is_prot) in CBlastQuerySourceBioseqSet()
H A Dlocal_db_adapter.cpp166 bool is_prot = Blast_SubjectIsProtein(p) ? true : false; in MakeSeqInfoSrc() local
167 m_SeqInfoSrc = new CBioseqSeqInfoSrc(*subject_bioseqs, is_prot); in MakeSeqInfoSrc()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/
H A Dwritedb.cpp280 bool is_prot, in s_ComputeNumSequencesAndDbLength() argument
289 CSeqDB::ESeqType dbtype(is_prot ? CSeqDB::eProtein : CSeqDB::eNucleotide); in s_ComputeNumSequencesAndDbLength()
361 bool is_prot(seq_type == CWriteDB::eProtein ? true : false); in s_CreateAliasFilePriv() local
365 fnamestr << file_name << (is_prot ? ".pal" : ".nal"); in s_CreateAliasFilePriv()
390 if (!s_ComputeNumSequencesAndDbLength(file_name, is_prot, &dbsize, &num_seqs)){ in s_CreateAliasFilePriv()
411 s_PrintAliasFileCreationLog(file_name, is_prot, num_seqs); in s_CreateAliasFilePriv()
419 bool is_prot(seq_type == CWriteDB::eProtein ? true : false); in CWriteDB_CreateAliasFile() local
426 s_DoesBlastDbExist(vol_name, is_prot); in CWriteDB_CreateAliasFile()
433 s_ComputeNumSequencesAndDbLength(concatenated_blastdb_name, is_prot, in CWriteDB_CreateAliasFile()
436 fname << file_name << (is_prot ? ".pal" : ".nal"); in CWriteDB_CreateAliasFile()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/
H A Dwritedb.cpp280 bool is_prot, in s_ComputeNumSequencesAndDbLength() argument
289 CSeqDB::ESeqType dbtype(is_prot ? CSeqDB::eProtein : CSeqDB::eNucleotide); in s_ComputeNumSequencesAndDbLength()
361 bool is_prot(seq_type == CWriteDB::eProtein ? true : false); in s_CreateAliasFilePriv() local
365 fnamestr << file_name << (is_prot ? ".pal" : ".nal"); in s_CreateAliasFilePriv()
390 if (!s_ComputeNumSequencesAndDbLength(file_name, is_prot, &dbsize, &num_seqs)){ in s_CreateAliasFilePriv()
411 s_PrintAliasFileCreationLog(file_name, is_prot, num_seqs); in s_CreateAliasFilePriv()
419 bool is_prot(seq_type == CWriteDB::eProtein ? true : false); in CWriteDB_CreateAliasFile() local
426 s_DoesBlastDbExist(vol_name, is_prot); in CWriteDB_CreateAliasFile()
433 s_ComputeNumSequencesAndDbLength(concatenated_blastdb_name, is_prot, in CWriteDB_CreateAliasFile()
436 fname << file_name << (is_prot ? ".pal" : ".nal"); in CWriteDB_CreateAliasFile()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/blast_format/
H A Dvecscreen_run_unit_test.cpp63 const bool is_prot = false; in BOOST_AUTO_TEST_CASE() local
64 SDataLoaderConfig config(is_prot, SDataLoaderConfig::eUseGenbankDataLoader); in BOOST_AUTO_TEST_CASE()
88 const bool is_prot = false; in BOOST_AUTO_TEST_CASE() local
89 SDataLoaderConfig config(is_prot, SDataLoaderConfig::eUseGenbankDataLoader); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/blast_format/
H A Dvecscreen_run_unit_test.cpp63 const bool is_prot = false; in BOOST_AUTO_TEST_CASE() local
64 SDataLoaderConfig config(is_prot, SDataLoaderConfig::eUseGenbankDataLoader); in BOOST_AUTO_TEST_CASE()
88 const bool is_prot = false; in BOOST_AUTO_TEST_CASE() local
89 SDataLoaderConfig config(is_prot, SDataLoaderConfig::eUseGenbankDataLoader); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dsalign.c87 msp->is_prot = is_prot; in MashNew()
90 if (msp->is_prot) in MashNew()
152 Boolean is_prot; in CC_CreatBandStruct() local
154 is_prot = (Boolean)(msp->is_prot || msp->translate_prot); in CC_CreatBandStruct()
173 Boolean is_prot; in BandAlignTwoSeqLocsFunc() local
180 is_prot = (Boolean)(msp->is_prot || msp->translate_prot); in BandAlignTwoSeqLocsFunc()
549 if(is_prot) { in BlastTwoSeqLocs()
563 if (is_prot) in BlastTwoSeqLocs()
569 if (!is_prot) { in BlastTwoSeqLocs()
587 if (!is_prot) { in BlastTwoSeqLocs()
[all …]
H A Dsalign.h28 Boolean is_prot; member
49 NLM_EXTERN MashPtr MashNew (Boolean is_prot);
H A Dbandalgn.c753 if (is_prot) { in ChangeGlobalBandMatrix()
776 if(is_prot) { in ChangeGlobalBandMatrix()
845 static Uint1Ptr load_data (SeqLocPtr slp,Boolean is_prot) in load_data() argument
853 if (is_prot) in load_data()
876 if (is_prot) { in CreatBandStruct()
886 seq1 = load_data(slp1, is_prot); in CreatBandStruct()
887 seq2 = load_data(slp2, is_prot); in CreatBandStruct()
898 } else if (is_prot) { in CreatBandStruct()
954 options = BLASTOptionNew((is_prot == FALSE) ? "blastn":"blastp", TRUE); in SetLowUpFromBlast()
955 …while ((seqalign = BlastTwoSequencesByLoc(slp1, slp2,NULL, options))==NULL && (is_prot==FALSE && o… in SetLowUpFromBlast()
[all …]
H A Dbandalgn.h422 …tPtr CreatBandStruct(SeqLocPtr slp1, SeqLocPtr slp2, Int4Ptr PNTR W, Boolean is_prot, Int2 method);
424 NLM_EXTERN void SetLowUpFromBlast(PSUGapOptionsPtr opt, Boolean is_prot, Int2 type, Int2 width, Seq…
426 …ByLoc(GlobalBandStructPtr gbsp, SeqLocPtr slp1, SeqLocPtr slp2, Boolean is_prot, Int2 band_method…
434 NLM_EXTERN Int2 ChangeGlobalBandMatrix(GlobalBandStructPtr gbsp, Boolean is_prot, CharPtr matrix_na…
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blast/
H A Dcleanup-blastdb-volumes.py67 def find_blastdb(name: str, is_prot: bool) -> str:
69 alias_file = "{}.{}al".format(name, "p" if is_prot else "n")
70 index_file = "{}.{}in".format(name, "p" if is_prot else "n")
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blast/
H A Dcleanup-blastdb-volumes.py67 def find_blastdb(name: str, is_prot: bool) -> str:
69 alias_file = "{}.{}al".format(name, "p" if is_prot else "n")
70 index_file = "{}.{}in".format(name, "p" if is_prot else "n")
/dports/biology/ncbi-toolkit/ncbi/network/wwwblast/Src/
H A Dwblast2.c749 (is_prot == FALSE) ? " value=1" : ""); in Blast2SeqMainPage()
751 (is_prot == FALSE) ? " value=-2" : ""); in Blast2SeqMainPage()
767 (is_prot == FALSE) ? " value=1" : ""); in Blast2SeqMainPage()
769 (is_prot == FALSE) ? " value=-2" : ""); in Blast2SeqMainPage()
1627 if (is_prot == TRUE) { in PrintParam()
2229 is_prot = (is_aa1 || is_aa2); in Main()
2236 is_prot = TRUE; in Main()
2320 wordsize = (is_prot == TRUE) ? 3 : 11; in Main()
2444 if (is_prot) { in Main()
2552 NULL, NULL, NULL, is_prot, options, mtrx, in Main()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/
H A Dbest_placement.cpp139 const bool is_prot = isProtSS(aln); in GetScore() local
145 const auto num_frameshifts = !is_prot ? 0 : aln.GetNumFrameshifts(); in GetScore()
577 const bool is_prot = isProtSS(aln); in GetCoverage() local
583 * (is_prot ? 3 : 1); in GetCoverage()

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