/// <summary>
/// Loads a mzIdentML file
/// </summary>
override protected void Load( string mzid ) {
m_mzid = new mzidFile1_0();
m_mzid.Load( mzid );
// Proteins
SortedList<string,string> SortedAccession = new SortedList<string, string>();
foreach( PSIPIanalysissearchDBSequenceType element in m_mzid.ListProteins ) {
if( SortedAccession.ContainsKey(element.id) )
continue;
string acc = element.accession;
SortedAccession.Add( element.id, acc );
if( m_SortedProteins.ContainsKey(acc) )
continue;
FuGECommonOntologycvParamType cv;
cv = FuGECommonOntologycvParamType.Find( "MS:1001352", element.cvParam );
string entry = cv == null ? "" : cv.value;
cv = FuGECommonOntologycvParamType.Find( "MS:1001088", element.cvParam );
string desc = cv == null ? "" : cv.value;
string seq = element.seq;//.ToUpper();
Protein p = new Protein(m_pid++, entry, acc, desc, seq);
p.DBRef = element.id;
Proteins.Add( p );
m_SortedProteins.Add( acc, p );
}
// Peptides
SortedList<string,Peptide> SortedPeptides = new SortedList<string, Peptide>();
int id = 1;
foreach( PSIPIpolypeptidePeptideType element in m_mzid.ListPeptides ) {
string seq = element.peptideSequence;//.ToUpper();
Peptide f = new Peptide(id++, seq);
f.Confidence = Peptide.ConfidenceType.PassThreshold; // It will be filtered later if neccessary
SortedPeptides.Add( element.id, f );
f.Runs.Add( m_Run );
if( element.Modification != null )
foreach( PSIPIpolypeptideModificationType mod in element.Modification ) {
PTM ptm = new PTM();
ptm.Pos = mod.locationSpecified ? mod.location : -1;
if( mod.residues != null )
foreach( string residue in mod.residues )
ptm.Residues += residue;
foreach( FuGECommonOntologycvParamType param in mod.cvParam )
if( param.cvRef.Equals("UNIMOD") )
ptm.Name = param.name;
f.AddPTM( ptm );
}
Peptides.Add( f );
}
// Relations
if( m_mzid.Data.DataCollection.AnalysisData.SpectrumIdentificationList.Length != 1 )
throw new ApplicationException( "Multiple spectrum identification lists not supported" );
foreach( PSIPIanalysissearchSpectrumIdentificationResultType idres in
m_mzid.Data.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult )
foreach( PSIPIanalysissearchSpectrumIdentificationItemType item in idres.SpectrumIdentificationItem ) {
if( !item.passThreshold )
continue;
Peptide f = SortedPeptides[item.Peptide_ref];
if( item.PeptideEvidence == null )
continue;
f.Confidence = Peptide.ConfidenceType.PassThreshold;
foreach( PSIPIanalysisprocessPeptideEvidenceType relation in item.PeptideEvidence ) {
Protein p = m_SortedProteins[SortedAccession[relation.DBSequence_Ref]];
if( f.Proteins.Contains(p) )
continue;
f.Names.Add( relation.DBSequence_Ref, relation.id );
p.Peptides.Add( f );
f.Proteins.Add( p );
}
}
}
/// <summary>
/// Save results to a mzIdentML file
/// </summary>
public void SaveMzid(
string mzid,
string org_id, string org_name,
string owner_name, string owner_email ) {
// Previous file is required for including MS data
if( m_mzid == null || m_InputFiles.Count > 1 )
return;
#region Organization
FuGECommonAuditOrganizationType org = new FuGECommonAuditOrganizationType();
org.id = "UPV/EHU";
org.name = "University of the Basque Country";
foreach( FuGECommonAuditOrganizationType o in m_mzid.ListOrganizations )
if( o.id == org.id ) {
m_mzid.ListOrganizations.Remove( o );
break;
}
m_mzid.ListOrganizations.Add( org );
#endregion
#region Software author
FuGECommonAuditPersonType person = new FuGECommonAuditPersonType();
person.id = "PAnalyzer_Author";
person.firstName = "Gorka";
person.lastName = "Prieto";
person.email = "*****@*****.**";
FuGECommonAuditPersonTypeAffiliations aff = new FuGECommonAuditPersonTypeAffiliations();
aff.Organization_ref = org.id;
person.affiliations = new FuGECommonAuditPersonTypeAffiliations[]{aff};
foreach( FuGECommonAuditPersonType p in m_mzid.ListPeople )
if( p.id == person.id ) {
m_mzid.ListPeople.Remove( p );
break;
}
m_mzid.ListPeople.Add( person );
#endregion
#region Analysis software
PSIPIanalysissearchAnalysisSoftwareType sw = new PSIPIanalysissearchAnalysisSoftwareType();
sw.id = m_Software.Name;
sw.name = m_Software.ToString();
sw.URI = m_Software.Url;
sw.version = m_Software.Version;
ParamType swname = new ParamType();
FuGECommonOntologycvParamType item = new FuGECommonOntologycvParamType();
item.name = "PAnalyzer";
item.cvRef = "PSI-MS";
item.accession = "MS:1002076";
swname.Item = item;
sw.SoftwareName = swname;
FuGECommonAuditContactRoleType contact = new FuGECommonAuditContactRoleType();
contact.Contact_ref = person.id;
FuGECommonAuditContactRoleTypeRole role = new FuGECommonAuditContactRoleTypeRole();
FuGECommonOntologycvParamType contacttype = new FuGECommonOntologycvParamType();
contacttype.accession = "MS:1001271";
contacttype.cvRef = "PSI-MS";
contacttype.name = "researcher";
role.cvParam = contacttype;
contact.role = role;
sw.ContactRole = contact;
sw.Customizations = m_Software.Customizations;
foreach( PSIPIanalysissearchAnalysisSoftwareType s in m_mzid.ListSW )
if( s.id == m_Software.Name ) {
m_mzid.ListSW.Remove( sw );
break;
}
m_mzid.ListSW.Add( sw );
#endregion
#region Protein detection protocol
m_mzid.Data.AnalysisCollection.ProteinDetection.ProteinDetectionList_ref = "PDL_PAnalyzer";
m_mzid.Data.AnalysisCollection.ProteinDetection.ProteinDetectionProtocol_ref = "PDP_PAnalyzer";
m_mzid.Data.AnalysisProtocolCollection.ProteinDetectionProtocol.AnalysisSoftware_ref = sw.id;
m_mzid.Data.AnalysisProtocolCollection.ProteinDetectionProtocol.id = "PDP_PAnalyzer";
#endregion
#region Protein detection list
List<PSIPIanalysisprocessProteinAmbiguityGroupType> listGroup =
new List<PSIPIanalysisprocessProteinAmbiguityGroupType>();
int hit = 1;
foreach( Protein p in Proteins ) {
if( p.Evidence == Protein.EvidenceType.Filtered )
continue;
PSIPIanalysisprocessProteinAmbiguityGroupType grp = new PSIPIanalysisprocessProteinAmbiguityGroupType();
grp.id = "PAG_hit_" + (hit++);
int num = (p.Subset.Count == 0 ? 1 : p.Subset.Count);
grp.ProteinDetectionHypothesis = new PSIPIanalysisprocessProteinDetectionHypothesisType[num];
if( p.Subset.Count == 0 )
grp.ProteinDetectionHypothesis[0] = BuildHypothesis( p, p.Evidence );
else {
int i = 0;
foreach( Protein p2 in p.Subset )
grp.ProteinDetectionHypothesis[i++] = BuildHypothesis( p2, p.Evidence );
}
listGroup.Add( grp );
}
PSIPIanalysisprocessProteinDetectionListType analysis = new PSIPIanalysisprocessProteinDetectionListType();
analysis.id = "PDL_PAnalyzer";
analysis.ProteinAmbiguityGroup = listGroup.ToArray();
m_mzid.Data.DataCollection.AnalysisData.ProteinDetectionList = analysis;
#endregion
m_mzid.Save( mzid );
Notify( "Saved to " + mzid );
}
