/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/demo/ |
H A D | blastinput_demo.cpp | 115 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()
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/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | blastalign.c | 194 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()
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H A D | fastacmd.c | 224 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | seqinfosrc_bioseq.cpp | 54 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()
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H A D | seqinfosrc_bioseq.hpp | 64 CBioseqSeqInfoSrc(const objects::CBioseq& bs, bool is_prot); 70 CBioseqSeqInfoSrc(const objects::CBioseq_set& bss, bool is_prot);
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H A D | bioseq_extract_data_priv.hpp | 123 CBlastQuerySourceBioseqSet(const objects::CBioseq_set& bss, bool is_prot); 129 CBlastQuerySourceBioseqSet(const objects::CBioseq& bioseq, bool is_prot);
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H A D | bioseq_extract_data_priv.cpp | 231 (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()
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H A D | local_db_adapter.cpp | 166 bool is_prot = Blast_SubjectIsProtein(p) ? true : false; in MakeSeqInfoSrc() local 167 m_SeqInfoSrc = new CBioseqSeqInfoSrc(*subject_bioseqs, is_prot); in MakeSeqInfoSrc()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | seqinfosrc_bioseq.cpp | 54 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()
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H A D | seqinfosrc_bioseq.hpp | 64 CBioseqSeqInfoSrc(const objects::CBioseq& bs, bool is_prot); 70 CBioseqSeqInfoSrc(const objects::CBioseq_set& bss, bool is_prot);
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H A D | bioseq_extract_data_priv.hpp | 123 CBlastQuerySourceBioseqSet(const objects::CBioseq_set& bss, bool is_prot); 129 CBlastQuerySourceBioseqSet(const objects::CBioseq& bioseq, bool is_prot);
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H A D | bioseq_extract_data_priv.cpp | 231 (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()
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H A D | local_db_adapter.cpp | 166 bool is_prot = Blast_SubjectIsProtein(p) ? true : false; in MakeSeqInfoSrc() local 167 m_SeqInfoSrc = new CBioseqSeqInfoSrc(*subject_bioseqs, is_prot); in MakeSeqInfoSrc()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/ |
H A D | writedb.cpp | 280 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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/ |
H A D | writedb.cpp | 280 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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/blast_format/ |
H A D | vecscreen_run_unit_test.cpp | 63 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/blast_format/ |
H A D | vecscreen_run_unit_test.cpp | 63 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()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | salign.c | 87 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 …]
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H A D | salign.h | 28 Boolean is_prot; member 49 NLM_EXTERN MashPtr MashNew (Boolean is_prot);
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H A D | bandalgn.c | 753 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 …]
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H A D | bandalgn.h | 422 …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…
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blast/ |
H A D | cleanup-blastdb-volumes.py | 67 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")
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blast/ |
H A D | cleanup-blastdb-volumes.py | 67 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")
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/dports/biology/ncbi-toolkit/ncbi/network/wwwblast/Src/ |
H A D | wblast2.c | 749 (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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
H A D | best_placement.cpp | 139 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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