private static DbReferenceType[] CreateDbReferenceTypeList() { List <DbReferenceType> ft = new List <DbReferenceType> { go, kegg, pfam, pdb, wormBase, reactome, mgi, sgd, mim, prosite, interPro, prints, smart, flyBase, wormPep, ncbiTaxonomy, doi, pubMed, embl, refSeq, geneId, protClustDb, medLine, proteinModelPortal, smr, gene3D, panther, pirsf, supfam, uniGene, dip, intAct, pride, ensemblPlants, gramene, eggNog, oma, phylomeDb, string1, ctd, xenbase, hogenom, hovergen, orthoDb, ipi, geneTree, patric, arrayExpress, brenda, ec, germOnline, ensemblMetazoa, bioCyc, genomeReviews, pir, ensembl, bgee, ko, inParanoid, nextBio, hamap, tigrfams, ensemblBacteria, dmdm, geneCards, hgnc, nextProt, cleanEx, genevestigator, mint, uniProt, peptideAtlas, ensemblFungi, cygd, tair, ucsc, proMex, proDom, pdbSum, phosphoSite, hssp, tigr, ensemblProtists, dictyBase, hinvDb, pharmGkb, rgd, zfin, merops, cazy, dnasu, hpa, pseudoCap, tcdb, vectorBase, drugBank, swiss2Dpage, dosacCobs2Dpage, ucd2Dpage, legioList, orphanet, genoList, pomBase, phosSite, echoBase, ecoGene, world2Dpage, cornea2Dpage, tubercuList, reproduction2Dpage, agricola, agd, leproma, allergome, geneFarm, peroxiBase, eco2Dbase, cgd, glycoSuiteDb, siena2Dpage, pmapCutDb, bindingDb, pathwayInteractionDb, twoDBaseEcoli, ogp, maizeGdb, conoServer, disProt, aarhusGhent2Dpage, euPathDb, phci2Dpage, compluyeast2Dpage, reBase, arachnoServer, euHcvDb, pmma2Dpage, pptaseDb, ratHeart2Dpage, anu2Dpage, ruleBase, saas, pirsr, pirnr, genpept, evolutionaryTrace, uniPathway, genomeRnai, paxDb, signaLink, hamapRule, chiTars, chEmbl, sabioRk, mycoClap, geneWiki, uniCarbKb }; allDbReferenceTypeStrings = new string[ft.Count]; allDbReferenceTypeStrings = new string[ft.Count]; for (int i = 0; i < allDbReferenceTypeStrings.Length; i++) { allDbReferenceTypeStrings[i] = ft[i].UniprotName; } int[] o = ArrayUtils.Order(allDbReferenceTypeStrings); allDbReferenceTypeStrings = ArrayUtils.SubArray(allDbReferenceTypeStrings, o); DbReferenceType[] result = new DbReferenceType[ft.Count]; for (int i = 0; i < result.Length; i++) { result[i] = ft[o[i]]; result[i].Index = i; } return(result); }
public string[] GetNames(DbReferenceType key) { if (!dbEntries.ContainsKey(key)) { return(new string[0]); } UniprotDbReference[] x = ArrayUtils.GetValues(dbEntries[key]); string[] result = new string[x.Length]; for (int i = 0; i < x.Length; i++) { result[i] = x[i].GetPropertyValues("entry name")[0]; } return(result); }
public void AddDbEntry(string dbReferenceType, string dbReferenceId) { if (dbEntries == null) { dbEntries = new Dictionary <DbReferenceType, Dictionary <string, UniprotDbReference> >(); } DbReferenceType type = DbReferenceType.GetDbReferenceType(dbReferenceType); if (!dbEntries.ContainsKey(type)) { dbEntries.Add(type, new Dictionary <string, UniprotDbReference>()); } if (!dbEntries[type].ContainsKey(dbReferenceId)) { dbEntries[type].Add(dbReferenceId, new UniprotDbReference()); } }
public string[] GetNames(DbReferenceType key) { if (!dbEntries.ContainsKey(key)){ return new string[0]; } UniprotDbReference[] x = ArrayUtils.GetValues(dbEntries[key]); string[] result = new string[x.Length]; for (int i = 0; i < x.Length; i++){ result[i] = x[i].GetPropertyValues("entry name")[0]; } return result; }
public UniprotDbReference[] GetDbEntries(DbReferenceType key) { return !dbEntries.ContainsKey(key) ? new UniprotDbReference[0] : ArrayUtils.GetValues(dbEntries[key]); }
public UniprotDbReference[] GetDbEntries(DbReferenceType[] keys) { List<UniprotDbReference> result = new List<UniprotDbReference>(); foreach (DbReferenceType key in keys){ result.AddRange(GetDbEntries(key)); } return result.ToArray(); }
public string[] Get(DbReferenceType[] keys) { List<string> result = new List<string>(); foreach (DbReferenceType key in keys){ result.AddRange(Get(key)); } return result.ToArray(); }
public string[] Get(DbReferenceType key) { return !dbEntries.ContainsKey(key) ? new string[0] : ArrayUtils.GetKeys(dbEntries[key]); }
public void AddDbEntryProperty(string dbReferenceType, string dbReferenceId, string protertyType, string protertyValue) { DbReferenceType type = DbReferenceType.GetDbReferenceType(dbReferenceType); dbEntries[type][dbReferenceId].AddProperty(protertyType, protertyValue); }
public UniprotDbReference[] GetDbEntries(DbReferenceType key) { return(!dbEntries.ContainsKey(key) ? new UniprotDbReference[0] : ArrayUtils.GetValues(dbEntries[key])); }
public string[] Get(DbReferenceType key) { return(!dbEntries.ContainsKey(key) ? new string[0] : ArrayUtils.GetKeys(dbEntries[key])); }
private static DbReferenceType[] CreateDbReferenceTypeList() { List<DbReferenceType> ft = new List<DbReferenceType>{ go, kegg, pfam, pdb, wormBase, reactome, mgi, sgd, mim, prosite, interPro, prints, smart, flyBase, wormPep, ncbiTaxonomy, doi, pubMed, embl, refSeq, geneId, protClustDb, medLine, proteinModelPortal, smr, gene3D, panther, pirsf, supfam, uniGene, dip, intAct, pride, ensemblPlants, gramene, eggNog, oma, phylomeDb, string1, ctd, xenbase, hogenom, hovergen, orthoDb, ipi, geneTree, patric, arrayExpress, brenda, ec, germOnline, ensemblMetazoa, bioCyc, genomeReviews, pir, ensembl, bgee, ko, inParanoid, nextBio, hamap, tigrfams, ensemblBacteria, dmdm, geneCards, hgnc, nextProt, cleanEx, genevestigator, mint, uniProt, peptideAtlas, ensemblFungi, cygd, tair, ucsc, proMex, proDom, pdbSum, phosphoSite, hssp, tigr, ensemblProtists, dictyBase, hinvDb, pharmGkb, rgd, zfin, merops, cazy, dnasu, hpa, pseudoCap, tcdb, vectorBase, drugBank, swiss2Dpage, dosacCobs2Dpage, ucd2Dpage, legioList, orphanet, genoList, pomBase, phosSite, echoBase, ecoGene, world2Dpage, cornea2Dpage, tubercuList, reproduction2Dpage, agricola, agd, leproma, allergome, geneFarm, peroxiBase, eco2Dbase, cgd, glycoSuiteDb, siena2Dpage, pmapCutDb, bindingDb, pathwayInteractionDb, twoDBaseEcoli, ogp, maizeGdb, conoServer, disProt, aarhusGhent2Dpage, euPathDb, phci2Dpage, compluyeast2Dpage, reBase, arachnoServer, euHcvDb, pmma2Dpage, pptaseDb, ratHeart2Dpage, anu2Dpage, ruleBase, saas, pirsr, pirnr, genpept, evolutionaryTrace, uniPathway, genomeRnai, paxDb, signaLink, hamapRule, chiTars, chEmbl, sabioRk, mycoClap, geneWiki, uniCarbKb }; allDbReferenceTypeStrings = new string[ft.Count]; allDbReferenceTypeStrings = new string[ft.Count]; for (int i = 0; i < allDbReferenceTypeStrings.Length; i++){ allDbReferenceTypeStrings[i] = ft[i].UniprotName; } int[] o = ArrayUtils.Order(allDbReferenceTypeStrings); allDbReferenceTypeStrings = ArrayUtils.SubArray(allDbReferenceTypeStrings, o); DbReferenceType[] result = new DbReferenceType[ft.Count]; for (int i = 0; i < result.Length; i++){ result[i] = ft[o[i]]; result[i].Index = i; } return result; }