| /dports/biology/p5-Bio-DB-NCBIHelper/Bio-DB-NCBIHelper-1.7.7/bin/ |
| H A D | bp_download_query_genbank | 58 my $gifile;
67 'gi|gifile|gis:s' => \$gifile,
94 if( $gifile ) {
96 open my $fh, '<', $gifile or die "Could not read file '$gifile': $!\n";
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| /dports/biology/ncbi-toolkit/ncbi/demo/ |
| H A D | formatdb.c | 708 CharPtr gifile; in Main() local
721 if ((gifile = FindBlastDBFile(options->gi_file)) == NULL) { in Main()
727 gi_list = GetGisFromFile(gifile, &gi_list_total); in Main()
728 gifile = MemFree(gifile); in Main()
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| H A D | blastpgp.c | 1184 options->gifile = StringSave(myargs[ARG_GILIST].strvalue); in PGPReadBlastOptions()
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| H A D | megablast.c | 1435 options->gifile = StringSave(myargs[ARG_GILIST].strvalue); in Main_old()
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| H A D | blastall.c | 2107 options->gifile = StringSave(myargs[ARG_GILIST].strvalue); in Main_old()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/unit_test/ |
| H A D | writedb_unit_test.cpp | 2226 ofstream gifile(tmp_gifile.GetFileName().c_str()); in BOOST_AUTO_TEST_CASE() local
2227 gifile << "129295" << endl; in BOOST_AUTO_TEST_CASE()
2228 gifile << "555" << endl; in BOOST_AUTO_TEST_CASE()
2229 gifile << "55" << endl; in BOOST_AUTO_TEST_CASE()
2230 gifile.close(); in BOOST_AUTO_TEST_CASE()
2267 gifile << "P01013.1" << endl; // GI 129295 in BOOST_AUTO_TEST_CASE()
2269 gifile.close(); in BOOST_AUTO_TEST_CASE()
2481 ofstream gifile(tmp_gifile.GetFileName().c_str()); in BOOST_AUTO_TEST_CASE() local
2483 gifile << "556" << endl; in BOOST_AUTO_TEST_CASE()
2484 gifile << "555" << endl; in BOOST_AUTO_TEST_CASE()
[all …]
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/unit_test/ |
| H A D | writedb_unit_test.cpp | 2226 ofstream gifile(tmp_gifile.GetFileName().c_str()); in BOOST_AUTO_TEST_CASE() local
2227 gifile << "129295" << endl; in BOOST_AUTO_TEST_CASE()
2228 gifile << "555" << endl; in BOOST_AUTO_TEST_CASE()
2229 gifile << "55" << endl; in BOOST_AUTO_TEST_CASE()
2230 gifile.close(); in BOOST_AUTO_TEST_CASE()
2267 gifile << "P01013.1" << endl; // GI 129295 in BOOST_AUTO_TEST_CASE()
2269 gifile.close(); in BOOST_AUTO_TEST_CASE()
2481 ofstream gifile(tmp_gifile.GetFileName().c_str()); in BOOST_AUTO_TEST_CASE() local
2483 gifile << "556" << endl; in BOOST_AUTO_TEST_CASE()
2484 gifile << "555" << endl; in BOOST_AUTO_TEST_CASE()
[all …]
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| /dports/biology/ncbi-toolkit/ncbi/tools/ |
| H A D | readdb.h | 1165 CharPtr gifile; /* Path to a file with the gi list, should member
1990 CharPtr oidlist, CharPtr gifile));
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| H A D | blastdef.h | 1146 CharPtr gifile; /* name of file containing list of gis on server */ member
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| H A D | blastool.c | 1501 options->gifile = NULL; in BLASTOptionNewEx()
1659 MemFree(options->gifile); in BLASTOptionDelete()
2802 if (gi_list || options->gifile || options->gilist) in BlastProcessGiLists()
2814 if (options->gifile) { in BlastProcessGiLists()
2816 if ((tmp_list = GetGisFromFile(options->gifile, &ngis))) { in BlastProcessGiLists()
2861 if (!options->gifile && !gi_list) in BlastProcessGiLists()
6412 out->gifile = 0; in BLAST_Wizard()
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| H A D | readdb.c | 4310 && (rdfp_list->oidlist || rdfp_list->gifile || in readdb_get_totals_ex3()
4317 && (rdfp_list->oidlist || rdfp_list->gifile || in readdb_get_totals_ex3()
4470 ASSERT(rdfp->gifile == NULL && temp->gifile == NULL); in readdb_merge_gifiles()
4700 rdfp->gifile = MemFree(rdfp->gifile); in readdb_destruct_element()
5199 if (rdfp->gifile) { in readdb_seqid2fasta()
12254 if (rdfp->gilist || rdfp->gifile) { in s_HasGiList()
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| H A D | blast.c | 5626 GetGisFromFile (CharPtr gifile, Int4Ptr gi_list_size) in GetGisFromFile() argument
5632 if ( !(gilist = Int4ListReadFromFile(gifile))) in GetGisFromFile()
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| /dports/biology/ncbi-toolkit/ncbi/network/blast3/client/ |
| H A D | netblap3.c | 818 parameters->gifile = StringSave(options->gifile); in BlastOptionsToParameters()
2788 if (parameters->gifile) in parametersToOptions()
2790 options->gifile = StringSave(parameters->gifile); in parametersToOptions()
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| H A D | objblst3.h | 132 CharPtr gifile; member
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| H A D | objblst3.c | 980 MemFree(ptr -> gifile); in BlastParametersFree()
1206 ptr -> gifile = av.ptrvalue; in BlastParametersAsnRead()
1576 if (ptr -> gifile != NULL) { in BlastParametersAsnWrite()
1577 av.ptrvalue = ptr -> gifile; in BlastParametersAsnWrite()
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| H A D | blstspc.asn | 162 gifile VisibleString OPTIONAL, -- file with list of gis on server side
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/seqdb_reader/ |
| H A D | seqdb_unit_test.cpp | 1671 ifstream gifile(fn.c_str()); in BOOST_AUTO_TEST_CASE() local
1672 BOOST_REQUIRE(gifile); in BOOST_AUTO_TEST_CASE()
1676 while ( !gifile.eof() ) { in BOOST_AUTO_TEST_CASE()
1678 gifile >> tgi; in BOOST_AUTO_TEST_CASE()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/seqdb_reader/ |
| H A D | seqdb_unit_test.cpp | 1671 ifstream gifile(fn.c_str()); in BOOST_AUTO_TEST_CASE() local
1672 BOOST_REQUIRE(gifile); in BOOST_AUTO_TEST_CASE()
1676 while ( !gifile.eof() ) { in BOOST_AUTO_TEST_CASE()
1678 gifile >> tgi; in BOOST_AUTO_TEST_CASE()
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