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;
}
