/// <summary>
/// Simple constructor
/// </summary>
public PSIPIanalysissearchAnalysisSoftwareType(
string id, string name, string version, string uri, string org_id,
string contact_accession, string contact_name, string contact_cvRef,
string customizations)
{
// FuGECommonIdentifiableType
this.id = id;
this.name = name;
// FuGECommonProtocolSoftwareType
FuGECommonAuditContactRoleType contact_role = new FuGECommonAuditContactRoleType();
FuGECommonAuditContactRoleTypeRole role = new FuGECommonAuditContactRoleTypeRole();
FuGECommonOntologycvParamType cvParam =
new FuGECommonOntologycvParamType(contact_name, contact_accession, contact_cvRef);
role.cvParam = cvParam;
contact_role.role = role;
contact_role.Contact_ref = org_id;
ContactRole = contact_role;
this.version = version;
// PSIPIanalysissearchAnalysisSoftwareType
this.Customizations = customizations;
this.URI = uri;
}
/// <summary>
/// Simple constructor
/// </summary>
public FuGECollectionProviderType(
string id, string contact_ref, string accession, string name, string cvRef)
{
// FuGECommonIdentifiableType
this.id = id;
//this.name = name;
// FuGECommonAuditContactRoleType
FuGECommonAuditContactRoleType contact_role = new FuGECommonAuditContactRoleType();
FuGECommonAuditContactRoleTypeRole role = new FuGECommonAuditContactRoleTypeRole();
FuGECommonOntologycvParamType cvParam = new FuGECommonOntologycvParamType(name, accession, cvRef);
role.cvParam = cvParam;
contact_role.role = role;
contact_role.Contact_ref = contact_ref;
ContactRole = contact_role;
//Software_ref = ;
}
/// <summary>
/// Finds a given cvParam from an array
/// </summary>
/// <param name="acc">
/// A <see cref="System.String"/> with the accession of the cvParam to find
/// </param>
/// <param name="cvparams">
/// A <see cref="FuGECommonOntologycvParamType[]"/> with all the cvParams
/// </param>
/// <returns>
/// A <see cref="FuGECommonOntologycvParamType"/> with the desired cvParam or null if not found
/// </returns>
public static FuGECommonOntologycvParamType Find( string acc, FuGECommonOntologycvParamType[] cvparams ) {
if( cvparams == null )
return null;
foreach( FuGECommonOntologycvParamType cv in cvparams )
if( cv.accession == acc )
return cv;
return null;
}
/// <summary>
/// Simple constructor
/// </summary>
public FuGECollectionProviderType(
string id, string contact_ref, string accession, string name, string cvRef ) {
// FuGECommonIdentifiableType
this.id = id;
//this.name = name;
// FuGECommonAuditContactRoleType
FuGECommonAuditContactRoleType contact_role = new FuGECommonAuditContactRoleType();
FuGECommonAuditContactRoleTypeRole role = new FuGECommonAuditContactRoleTypeRole();
FuGECommonOntologycvParamType cvParam = new FuGECommonOntologycvParamType(name, accession, cvRef);
role.cvParam = cvParam;
contact_role.role = role;
contact_role.Contact_ref = contact_ref;
ContactRole = contact_role;
//Software_ref = ;
}
/// <summary>
/// Simple constructor
/// </summary>
public PSIPIanalysissearchAnalysisSoftwareType(
string id, string name, string version, string uri, string org_id,
string contact_accession, string contact_name, string contact_cvRef,
string customizations ) {
// FuGECommonIdentifiableType
this.id = id;
this.name = name;
// FuGECommonProtocolSoftwareType
FuGECommonAuditContactRoleType contact_role = new FuGECommonAuditContactRoleType();
FuGECommonAuditContactRoleTypeRole role = new FuGECommonAuditContactRoleTypeRole();
FuGECommonOntologycvParamType cvParam =
new FuGECommonOntologycvParamType(contact_name, contact_accession, contact_cvRef);
role.cvParam = cvParam;
contact_role.role = role;
contact_role.Contact_ref = org_id;
ContactRole = contact_role;
this.version = version;
// PSIPIanalysissearchAnalysisSoftwareType
this.Customizations = customizations;
this.URI = uri;
}
/// <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 );
}