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);
}
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 (var 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;
}
private void EndElement(IEquatable <string> qName, HandleUniprotEntry handle, bool isTrembl)
{
if (qName.Equals("sequence"))
{
entry.Sequence = StringUtils.RemoveWhitespace(sequence.ToString());
sequence = null;
}
else if (qName.Equals("keyword"))
{
entry.AddKeyword(StringUtils.RemoveWhitespace(keyword.ToString()));
keyword = null;
}
else if (qName.Equals("molecule") && dbReferenceType.Equals("Ensembl"))
{
string mol = molecule.ToString().Trim();
entry.AddDbEntryProperty(dbReferenceType, dbReferenceId, "isoform ID", mol);
if (!isoformToEnst.ContainsKey(mol))
{
isoformToEnst.Add(mol, new List <string>());
}
isoformToEnst[mol].Add(dbReferenceId);
molecule = null;
}
else if (qName.Equals("entry"))
{
entry.Accessions = accessions.ToArray();
entry.ProteinFullNames = proteinFullNames.ToArray();
entry.ProteinShortNames = proteinShortNames.ToArray();
entry.ProteinEcNumbers = proteinEcNumbers.ToArray();
entry.GeneNamesAndTypes = gnames.ToArray();
entry.OrganismNames = onames.ToArray();
entry.UniprotNames = unames.ToArray();
entry.IsTrembl = isTrembl;
if (resolveIsoforms)
{
if (numIsoforms > 1 && isoformToEnst.Count > 1)
{
List <UniprotEntry> isoEntries = entry.ResolveIsoforms(isoformToEnst);
foreach (UniprotEntry e in isoEntries)
{
handle(e);
}
}
else
{
handle(entry);
}
}
else
{
handle(entry);
}
}
else if (qName.Equals("dbReference"))
{
inDbRef = false;
}
else if (qName.Equals("accession"))
{
accessions.Add(StringUtils.RemoveWhitespace(accession.ToString()));
accession = null;
}
else if (qName.Equals("location"))
{
if (inFeature)
{
//inFeatureLocation = false;
entry.AddFeatureLocation(featureBegin, featureEnd);
}
}
else if (qName.Equals("variation"))
{
if (inFeature)
{
entry.AddFeatureVariation(StringUtils.RemoveWhitespace(variation.ToString()));
variation = null;
}
}
else if (qName.Equals("original"))
{
if (inFeature)
{
entry.AddFeatureOriginal(StringUtils.RemoveWhitespace(original.ToString()));
original = null;
}
}
else if (qName.Equals("feature"))
{
inFeature = false;
foreach (FeatureType type in entry.GetAllFeatureTypes())
{
int c = entry.GetFeatureCount(type);
if (!featureCounts.ContainsKey(type))
{
featureCounts.Add(type, 0);
}
featureCounts[type] += c;
}
}
else if (qName.Equals("fullName") && inProteinRecommendedName)
{
proteinFullNames.Add(proteinFullName.ToString().Trim());
proteinFullName = null;
}
else if (qName.Equals("shortName") && inProteinRecommendedName)
{
proteinShortNames.Add(proteinShortName.ToString().Trim());
proteinShortName = null;
}
else if (qName.Equals("ecNumber") && inProteinRecommendedName)
{
proteinEcNumbers.Add(proteinEcNumber.ToString().Trim());
proteinEcNumber = null;
}
else if (qName.Equals("name") && inGene)
{
gnames.Add(new Tuple <string, string>(gname.ToString().Trim(), gnameType.Trim()));
gname = null;
gnameType = null;
}
else if (qName.Equals("name") && inOrganism)
{
string on = oname?.ToString().Trim();
if (@on?.Length > 0)
{
onames.Add(@on);
oname = null;
}
}
else if (qName.Equals("name") && level == 1)
{
unames.Add(uname.ToString().Trim());
uname = null;
}
else if (qName.Equals("protein"))
{
inProtein = false;
}
else if (qName.Equals("recommendedName") && inProtein)
{
inProteinRecommendedName = false;
}
else if (qName.Equals("gene"))
{
inGene = false;
}
else if (qName.Equals("organism"))
{
inOrganism = false;
}
else if (qName.Equals("organismHost"))
{
inOrganismHost = false;
}
}