private int AddPassThreshold( List<ProteinAmbiguityGroupType> groups )
{
int count = 0;
CVParamType cv;
bool pass;
foreach( ProteinAmbiguityGroupType pag in groups ) {
cv = new CVParamType();
cv.cvRef = "PSI-MS";
cv.accession = "MS:1002415";
cv.name = "protein group passes threshold";
pass = false;
foreach( ProteinDetectionHypothesisType pdh in pag.ProteinDetectionHypothesis ) {
if( !pdh.passThreshold )
continue;
foreach( AbstractParamType item in pdh.Items )
if( item.name == "leading protein" ) {
pass = true;
break;
}
if( pass )
break;
}
if( pass ) {
count++;
cv.value = "true";
} else
cv.value = "false";
pag.Items = new AbstractParamType[]{cv};
}
return count;
}
protected override List<ProteinAmbiguityGroupType> BuildProteinDetectionList()
{
List<ProteinAmbiguityGroupType> groups = BuildPags();
int count = AddPassThreshold(groups);
CVParamType cv = new CVParamType();
cv.cvRef = "PSI-MS";
cv.accession = "MS:1002404";
cv.name = "count of identified proteins";
cv.value = count.ToString();
m_mzid.Data.DataCollection.AnalysisData.ProteinDetectionList.Items = new AbstractParamType[]{cv};
return groups;
}
/// <summary>
/// Helper method for including an additional analysis software to the list
/// </summary>
public void AddAnalysisSoftware(
string id, string name, string version, string uri, string cv, string accession, string customizations )
{
AnalysisSoftwareType sw = new AnalysisSoftwareType();
sw.id = id;
sw.name = name;
sw.version = version;
sw.uri = uri;
if( cv != null && accession != null ) {
CVParamType p = new CVParamType();
p.cvRef = cv;
p.accession = accession;
p.name = name;
sw.SoftwareName.Item = p;
}
if( customizations != null )
sw.Customizations = customizations;
ListSW.Add( sw );
}
/// <summary>
/// Save results to a mzIdentML file
/// </summary>
public void SaveMzid( string fpath )
{
if( m_mzid == null || m_InputFiles.Count > 1 )
return;
#region Organization
OrganizationType org = new OrganizationType();
org.id = "UPV/EHU";
org.name = "University of the Basque Country";
foreach( OrganizationType o in m_mzid.ListOrganizations )
if( o.id == org.id ) {
m_mzid.ListOrganizations.Remove( o );
break;
}
CVParamType url = new CVParamType();
url.accession = "MS:1000588";
url.name = "contact URL";
url.cvRef = "PSI-MS";
url.value = "http://www.ehu.es";
org.Item = url;
m_mzid.ListOrganizations.Add( org );
#endregion
#region Software author
PersonType person = new PersonType();
person.id = "PAnalyzer_Author";
person.firstName = "Gorka";
person.lastName = "Prieto";
CVParamType email = new CVParamType();
email.accession = "MS:1000589";
email.name = "contact email";
email.cvRef = "PSI-MS";
email.value = "*****@*****.**";
//person.Items.Add(email);
person.Item = email;
AffiliationType aff = new AffiliationType();
aff.organization_ref = org.id;
//person.Affiliation.Add(aff);
person.Affiliation = new AffiliationType[]{aff};
foreach( PersonType 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
AnalysisSoftwareType sw = new AnalysisSoftwareType();
sw.id = m_Software.Name;
sw.name = m_Software.ToString();
sw.uri = m_Software.Url;
sw.version = m_Software.Version;
CVParamType swname = new CVParamType();
swname.name = "PAnalyzer";
swname.cvRef = "PSI-MS";
swname.accession = "MS:1002076";
sw.SoftwareName = new ParamType();
sw.SoftwareName.Item = swname;
RoleType role = new RoleType();
CVParamType contacttype = new CVParamType();
contacttype.accession = "MS:1001271";
contacttype.cvRef = "PSI-MS";
contacttype.name = "researcher";
role.cvParam = contacttype;
sw.ContactRole = new ContactRoleType();
sw.ContactRole.contact_ref = person.id;
sw.ContactRole.Role = role;
sw.Customizations = m_Software.Customizations;
AnalysisSoftwareType old = null;
foreach( AnalysisSoftwareType s in m_mzid.ListSW )
if( s.id == m_Software.Name ) {
old = s;
break;
}
if( old != null )
m_mzid.ListSW.Remove(old);
m_mzid.ListSW.Add( sw );
#endregion
#region Protein detection protocol
if( m_mzid.Data.AnalysisCollection.ProteinDetection == null || m_mzid.Data.AnalysisProtocolCollection.ProteinDetectionProtocol == null )
return;
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
m_mzid.Data.DataCollection.AnalysisData.ProteinDetectionList.id = "PDL_PAnalyzer";
List<ProteinAmbiguityGroupType> groups = BuildProteinDetectionList();
m_mzid.Data.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup = groups.ToArray();
#endregion
#region References
BibliographicReferenceType pa = new BibliographicReferenceType();
pa.authors = "Gorka Prieto, Kerman Aloria, Nerea Osinalde, Asier Fullaondo, Jesus M. Arizmendi and Rune Matthiesen";
pa.id = pa.doi = "10.1186/1471-2105-13-288";
pa.issue = "288";
pa.name = pa.title = "PAnalyzer: A software tool for protein inference in shotgun proteomics";
pa.publication = "BMC Bioinformatics";
pa.publisher = "BioMed Central Ltd.";
pa.volume = "13";
pa.year = 2012;
List<BibliographicReferenceType> refs = new List<BibliographicReferenceType>();
refs.Add( pa );
if( m_mzid.Data.BibliographicReference != null )
foreach( BibliographicReferenceType r in m_mzid.Data.BibliographicReference ) {
if( r.doi != null && r.doi == pa.doi )
continue;
refs.Add( r );
}
m_mzid.Data.BibliographicReference = refs.ToArray();
#endregion
m_mzid.Save( fpath );
Notify( "Saved to " + fpath );
}
// TODO: Support empty PDH in input mzid
protected virtual List<ProteinAmbiguityGroupType> BuildProteinDetectionList()
{
int gid = 1;
SortedList<string,ProteinDetectionHypothesisType> list = new SortedList<string, ProteinDetectionHypothesisType>();
List<ProteinAmbiguityGroupType> groups = new List<ProteinAmbiguityGroupType>();
foreach( ProteinAmbiguityGroupType grp in m_mzid.Data.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup )
foreach( ProteinDetectionHypothesisType pdh in grp.ProteinDetectionHypothesis )
list.Add( pdh.dBSequence_ref, pdh );
foreach( Protein p in Proteins ) {
ProteinAmbiguityGroupType g = new ProteinAmbiguityGroupType();
CVParamType ev = new CVParamType();
ev.accession = "MS:1001600";
ev.cvRef = "PSI-MS";
ev.name = "Protein Inference Confidence Category";
switch( p.Evidence ) {
case Protein.EvidenceType.Conclusive:
ev.value = "conclusive"; break;
case Protein.EvidenceType.Indistinguishable:
ev.value = "indistinguishable"; break;
case Protein.EvidenceType.Group:
ev.value = "ambiguous group"; break;
case Protein.EvidenceType.NonConclusive:
ev.value = "non conclusive"; break;
default:
continue;
}
g.id = "PAG_" + gid; gid++;
if( p.Subset.Count == 0 ) {
//g.ProteinDetectionHypothesis.Add(list[p.DBRef]);
g.ProteinDetectionHypothesis = new ProteinDetectionHypothesisType[]{list[p.DBRef]};
g.Items = new CVParamType[]{ev};
} else {
List<ProteinDetectionHypothesisType> listpdh = new List<ProteinDetectionHypothesisType>();
foreach( Protein p2 in p.Subset ) {
ProteinDetectionHypothesisType pdh = list[p2.DBRef];
pdh.Items = new CVParamType[]{ev};
listpdh.Add( pdh );
}
g.ProteinDetectionHypothesis = listpdh.ToArray();
}
groups.Add( g );
}
return groups;
}
private void UpdatePdhCvs( ProteinDetectionHypothesisType pdh, Protein.EvidenceType evidence )
{
List<AbstractParamType> list = new List<AbstractParamType>();
foreach( AbstractParamType item in pdh.Items )
if( !item.name.Contains("PAnalyzer") && !item.name.Contains("leading") )
list.Add( item );
CVParamType ev = new CVParamType(), ld = new CVParamType();
ev.cvRef = "PSI-MS";
ld.cvRef = "PSI-MS";
switch( evidence ) {
case Protein.EvidenceType.Conclusive:
ev.accession = "MS:1002213";
ev.name = "PAnalyzer:conclusive protein";
ld.accession = "MS:1002401";
ld.name = "leading protein";
break;
case Protein.EvidenceType.Indistinguishable:
ev.accession = "MS:1002214";
ev.name = "PAnalyzer:indistinguishable protein";
ld.accession = "MS:1002401";
ld.name = "leading protein";
break;
case Protein.EvidenceType.Group:
ev.accession = "MS:1002216";
ev.name = "PAnalyzer:ambiguous group member";
ld.accession = "MS:1002401";
ld.name = "leading protein";
break;
case Protein.EvidenceType.NonConclusive:
ev.accession = "MS:1002215";
ev.name = "PAnalyzer:non-conclusive protein";
ld.accession = "MS:1002402";
ld.name = "non-leading protein";
break;
default: // filtered
return;
}
list.Add(ld);
list.Add(ev);
pdh.Items = list.ToArray();
}
