| /dports/biology/ncbi-toolkit/ncbi/network/taxon1/common/ |
| H A D | checkid.c | 96 if(orp->taxname == NULL) { in CheckTaxId()
104 if(StringICmp(orp->taxname, tdp->org->taxname) != 0) { in CheckTaxId()
108 orp->taxname, tdp->org->taxname, tax_id); in CheckTaxId()
127 (orp->taxname == NULL)? "" : orp->taxname, in CheckTaxId()
136 tdp->org->taxname, tax_id); in CheckTaxId()
140 if(orp->taxname == NULL) { in CheckTaxId()
143 tdp->org->taxname); in CheckTaxId()
147 else if(StringICmp(orp->taxname, tdp->org->taxname) != 0) { in CheckTaxId()
151 orp->taxname, tdp->org->taxname, tax_id); in CheckTaxId()
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqfeat/ |
| H A D | Org_ref.cpp | 177 string taxname = ""; in x_GetTaxnameAfterFirstTwoWords() local
179 taxname = GetTaxname(); in x_GetTaxnameAfterFirstTwoWords()
182 size_t pos = NStr::Find (taxname, " "); in x_GetTaxnameAfterFirstTwoWords()
184 taxname = ""; in x_GetTaxnameAfterFirstTwoWords()
186 taxname = taxname.substr(pos + 1); in x_GetTaxnameAfterFirstTwoWords()
187 NStr::TruncateSpacesInPlace(taxname); in x_GetTaxnameAfterFirstTwoWords()
188 pos = NStr::Find (taxname, " "); in x_GetTaxnameAfterFirstTwoWords()
190 taxname = ""; in x_GetTaxnameAfterFirstTwoWords()
192 taxname = taxname.substr(pos + 1); in x_GetTaxnameAfterFirstTwoWords()
196 return taxname; in x_GetTaxnameAfterFirstTwoWords()
[all …]
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqfeat/ |
| H A D | Org_ref.cpp | 177 string taxname = ""; in x_GetTaxnameAfterFirstTwoWords() local
179 taxname = GetTaxname(); in x_GetTaxnameAfterFirstTwoWords()
182 size_t pos = NStr::Find (taxname, " "); in x_GetTaxnameAfterFirstTwoWords()
184 taxname = ""; in x_GetTaxnameAfterFirstTwoWords()
186 taxname = taxname.substr(pos + 1); in x_GetTaxnameAfterFirstTwoWords()
187 NStr::TruncateSpacesInPlace(taxname); in x_GetTaxnameAfterFirstTwoWords()
188 pos = NStr::Find (taxname, " "); in x_GetTaxnameAfterFirstTwoWords()
190 taxname = ""; in x_GetTaxnameAfterFirstTwoWords()
192 taxname = taxname.substr(pos + 1); in x_GetTaxnameAfterFirstTwoWords()
196 return taxname; in x_GetTaxnameAfterFirstTwoWords()
[all …]
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/asnval/TestRes.asnval/tests/test1/test-cases/ |
| H A D | reject.sqn | 89 taxname "Uncultured bacterium" ,
175 taxname "Uncultured bacterium" ,
247 taxname "Uncultured bacterium" ,
277 taxname "Uncultured bacterium" ,
307 taxname "Uncultured bacterium" ,
337 taxname "Uncultured bacterium" ,
367 taxname "Uncultured bacterium" ,
397 taxname "Uncultured bacterium" ,
427 taxname "Uncultured bacterium" ,
457 taxname "Uncultured bacterium" ,
[all …]
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/alnreader_test_cases/ |
| H A D | rw-855.asn | 11 taxname "Eclectus roratus",
42 taxname "Psittacula himalayana"
70 taxname "Psittacula derbyana"
98 taxname "Psittacula longicauda"
126 taxname "Psittacula alexandri"
155 taxname "Psittacula alexandri"
184 taxname "Psittacula roseata"
253 taxname "Psittacula krameri",
290 taxname "Psittacula krameri",
327 taxname "Psittacula krameri",
[all …]
|
| H A D | aln-nexus-14.asn | 11 taxname "animal 1"
29 taxname "animal 2"
47 taxname "animal 3"
65 taxname "animal 4"
83 taxname "animal 5"
|
| H A D | aln-phylip-17.asn | 11 taxname "animal 1"
29 taxname "animal 2"
47 taxname "animal 3"
65 taxname "animal 4"
83 taxname "animal 5"
|
| H A D | aln-fasta-5.asn | 11 taxname "animal 1"
29 taxname "animal 2"
47 taxname "animal 3"
65 taxname "animal 4"
83 taxname "animal 5"
|
| H A D | aln-fasta-6.asn | 11 taxname "animal 1"
30 taxname "animal 2"
49 taxname "animal 3"
68 taxname "animal 4"
87 taxname "animal 5"
|
| H A D | aln-fasta-7.asn | 11 taxname "animal 1"
30 taxname "animal 2"
49 taxname "animal 3"
68 taxname "animal 4"
87 taxname "animal 5"
|
| H A D | aln-fasta-8.asn | 11 taxname "animal 1"
30 taxname "animal 2"
49 taxname "animal 3"
68 taxname "animal 4"
87 taxname "animal 5"
|
| H A D | aln-fasta-src-22.asn | 11 taxname "val1"
35 taxname "val1"
54 taxname "val1"
73 taxname "val1"
|
| H A D | aln-fasta-src-27.asn | 11 taxname "val1"
30 taxname "val1"
49 taxname "val1"
68 taxname "val1"
|
| H A D | aln-fasta-9.asn | 11 taxname "animal 1"
29 taxname "animal 2"
58 taxname "animal 4"
76 taxname "animal 5"
|
| H A D | aln-fasta-src-10.asn | 11 taxname "val1",
37 taxname "val1",
63 taxname "val1",
89 taxname "val1",
|
| H A D | aln-fasta-src-18.asn | 11 taxname "val1"
35 taxname "val1"
59 taxname "val1"
83 taxname "val1"
|
| H A D | aln-fasta-src-19.asn | 11 taxname "val1"
35 taxname "val1"
59 taxname "val1"
83 taxname "val1"
|
| H A D | aln-fasta-src-2.asn | 11 taxname "val1",
37 taxname "val1",
63 taxname "val1",
89 taxname "val1",
|
| H A D | aln-fasta-src-20.asn | 11 taxname "val1"
35 taxname "val1"
59 taxname "val1"
83 taxname "val1"
|
| H A D | aln-fasta-src-21.asn | 11 taxname "val1"
35 taxname "val1"
59 taxname "val1"
83 taxname "val1"
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
| H A D | constrainttree.cpp | 32 StrVector taxname; in readConstraint() local
34 getTaxaName(taxname); in readConstraint()
42 for(it = taxname.begin(); it != taxname.end(); it++) in readConstraint()
80 StrVector taxname; in initFromTree() local
82 getTaxaName(taxname); in initFromTree()
84 for (it = taxname.begin(); it != taxname.end(); it++) in initFromTree()
85 taxname_index[(*it)] = it - taxname.begin(); in initFromTree()
89 convertSplits(taxname, sg); in initFromTree()
|
| H A D | mtreeset.cpp | 401 vector<string> taxname(front()->leafNum); in convertSplits() local
406 front()->getTaxaName(taxname); in convertSplits()
430 if (sort_taxa) sort(taxname.begin(), taxname.end()); in convertSplits()
432 for (its = taxname.begin(); its != taxname.end(); its++) in convertSplits()
449 if (tree->leafNum != taxname.size()) in convertSplits()
457 if ((*it2)->name != taxname[i]) { in convertSplits()
466 tree->convertSplits(taxname, *isg); in convertSplits()
549 vector<string> taxname(front()->leafNum); in computeRFDist() local
553 front()->getTaxaName(taxname); in computeRFDist()
561 (*it)->convertSplits(taxname, *sg); in computeRFDist()
[all …]
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | valid_biosource.cpp | 1030 string taxname; in ValidateSubSource() local
1381 auto pos = NStr::Find(taxname, " "); in s_IsSalmonellaGenus()
1417 string taxname; in ValidateOrgRef() local
1423 taxname = orgref.GetTaxname(); in ValidateOrgRef()
1451 if (ContainsSgml(taxname)) { in ValidateOrgRef()
1493 string taxname_search = taxname; in ValidateOrgRef()
1560 if (s_IsSalmonellaGenus(taxname) && NStr::Find(taxname, subname) == string::npos) { in ValidateOrgRef()
1580 if (NStr::Equal(taxname, mismatch)) { in s_MatchOrgname()
1628 (const string& taxname, in ValidateTaxNameOrgname() argument
2509 rq->SetTaxname(taxname); in ValidateTentativeName()
[all …]
|
| /dports/biology/ncbi-toolkit/ncbi/access/ |
| H A D | tax3api.c | 607 else if ((rval = StringCmp (orp1->taxname, orp2->taxname)) != 0) in OrgRefCompare()
800 t->taxname = MemFree (t->taxname); in TaxFixItemFree()
849 if (taxname == NULL) { in MakeUnculturedName()
875 StringCat(name, taxname); in MakeUnculturedName()
1004 org->taxname = MemFree (org->taxname); in MakeTaxFixRequestList()
1153 tmp = func(t->taxname); in TryNewSuggestedFixes()
1460 t->taxname = StandardFixes (biop->org->taxname); in BuildBlankTaxFixList()
1776 else if (StringICmp(b1->org->taxname, b2->org->taxname) == 0) in DoOrgIdsMatch()
2002 request->taxname = NULL; in Taxon3GetOrgRefByName()
2207 } else if (StringCmp (orig_org->taxname, response_org->taxname) != 0) { in Taxon3CheckOrgInSeqEntry()
[all …]
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
| H A D | create_defline.cpp | 1431 const CTempString& taxname, in x_EndsWithStrain() argument
1452 char ch = taxname[pos - 1]; in x_EndsWithStrain()
1458 && taxname[taxname.size() - 1] == '\'') { in x_EndsWithStrain()
2074 if (taxname.empty()) return str; in s_RemoveBracketedOrgFromEnd()
2259 CTempString taxname = m_Taxname; in x_SetTitleFromProteinIdx() local
2272 if ((taxname.empty() || in x_SetTitleFromProteinIdx()
2469 if ((taxname.empty() || in x_SetTitleFromProtein()
2973 CTempString taxname in s_TitleEndsInOrganism() argument
2981 len2 = taxname.length(); in s_TitleEndsInOrganism()
3111 if ((taxname.empty() || in x_AdjustProteinTitleSuffixIdx()
[all …]
|