public void AddDbEntryProperty(string dbReferenceType, string dbReferenceId, string protertyType, string protertyValue)
{
DbReferenceType type = DbReferenceType.GetDbReferenceType(dbReferenceType);
if (type == null)
{
return;
}
dbEntries[type][dbReferenceId].AddProperty(protertyType, protertyValue);
}
private UniprotEntry CopyEntry()
{
UniprotEntry newEntry = new UniprotEntry();
DbReferenceType[] dbRefTypes = new DbReferenceType[dbEntries.Keys.Count];
dbEntries.Keys.CopyTo(dbRefTypes, 0);
foreach (DbReferenceType refType in dbRefTypes)
{
string[] dbRefIDs = Get(refType);
foreach (string id in dbRefIDs)
{
newEntry.AddDbEntry(refType.UniprotName, id);
foreach (KeyValuePair <string, List <string> > property in dbEntries[refType][id].properties)
{
foreach (string propertyValue in property.Value)
{
newEntry.AddDbEntryProperty(refType.UniprotName, id, property.Key, propertyValue);
}
}
}
}
if (features != null)
{
foreach (FeatureType type in GetAllFeatureTypes())
{
newEntry.AddFeatures(type, GetFeatures(type));
}
}
foreach (string kword in Keywords)
{
newEntry.AddKeyword(kword);
}
newEntry.ProteinFullNames = ProteinFullNames;
newEntry.ProteinShortNames = ProteinShortNames;
newEntry.ProteinEcNumbers = ProteinEcNumbers;
newEntry.Accessions = Accessions;
newEntry.GeneNamesAndTypes = GeneNamesAndTypes;
newEntry.OrganismNames = OrganismNames;
newEntry.UniprotNames = UniprotNames;
newEntry.Sequence = Sequence;
foreach (string taxId in taxonomyIds)
{
newEntry.AddTaxonomyId(taxId);
}
foreach (string hostTaxId in hostTaxonomyIds)
{
newEntry.AddHostTaxonomyId(hostTaxId);
}
return(newEntry);
}
public string[] GetNames(DbReferenceType key)
{
if (!dbEntries.ContainsKey(key))
{
return(new string[0]);
}
UniprotDbReference[] x = dbEntries[key].Values.ToArray();
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 List <UniprotEntry> ResolveIsoforms(Dictionary <string, List <string> > isoformToEnsembl)
{
DbReferenceType dbRefType = DbReferenceType.ensembl;
List <UniprotEntry> isoforms = new List <UniprotEntry>();
foreach (KeyValuePair <string, List <string> > isofToEnsembl in isoformToEnsembl)
{
UniprotEntry modEntry = CopyEntry();
modEntry.dbEntries.Remove(dbRefType);
Dictionary <string, UniprotDbReference> enstToData = new Dictionary <string, UniprotDbReference>();
foreach (string enst in isofToEnsembl.Value)
{
enstToData.Add(enst, dbEntries[dbRefType][enst]);
}
modEntry.dbEntries.Add(dbRefType, enstToData);
isoforms.Add(modEntry);
}
return(isoforms);
}
public void AddDbEntry(string dbReferenceType, string dbReferenceId)
{
if (dbEntries == null)
{
dbEntries = new Dictionary <DbReferenceType, Dictionary <string, UniprotDbReference> >();
}
DbReferenceType type = DbReferenceType.GetDbReferenceType(dbReferenceType);
if (type == null)
{
return;
}
if (!dbEntries.ContainsKey(type))
{
dbEntries.Add(type, new Dictionary <string, UniprotDbReference>());
}
if (!dbEntries[type].ContainsKey(dbReferenceId))
{
dbEntries[type].Add(dbReferenceId, new UniprotDbReference());
}
}
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,
bioGrid,
treeFam,
pro,
guideToPharmacology,
uniProtKb,
ccds,
maxqb,
prositeProrule,
geneReviews,
proteomes,
expressionAtlas,
bioMuta,
chEbi,
depod,
moonProt,
SwissPalm,
iPTMnet,
PhosphoSitePlus,
TopDownProteomics,
Genevisible,
CORUM,
ELM,
EPD,
DisGeNET,
MalaCards,
OpenTargets,
SIGNOR,
Araport,
CDD,
SFLD,
ESTHER,
SwissLipids,
GeneDB,
CollecTF,
WBParaSite,
IMGTGENEDB,
SAM,
ProteomicsDB,
VGNC,
CarbonylDB,
GlyConnect,
ComplexPortal,
MoonDB,
Rhea,
jPOST,
UniLectin
};
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 UniprotDbReference[] GetDbEntries(DbReferenceType key)
{
return(!dbEntries.ContainsKey(key) ? new UniprotDbReference[0] : dbEntries[key].Values.ToArray());
}
public string[] Get(DbReferenceType key)
{
return(!dbEntries.ContainsKey(key) ? new string[0] : dbEntries[key].Keys.ToArray());
}
