public Affiliation(AffiliationType kind, int group, int radio)
{
this.kind = kind;
this.time = DateTime.Now;
this.group = group;
this.radio = radio;
}
public Affiliation(AffiliationType kind, int group, int radio)
{
this.kind = kind;
this.time = DateTime.Now;
this.group = group;
this.radio = radio;
}
/// <summary>
/// Add a new affiliation to the list.
/// </summary>
/// <param name="type"></param>
/// <param name="node"></param>
/// <returns></returns>
public OwnerAffiliation AddAffiliation(AffiliationType type, string node)
{
OwnerAffiliation afil = CreateChildElement <OwnerAffiliation>();
afil.Type = type;
afil.Node = node;
return(afil);
}
public Affiliation(string node, Jid jid, AffiliationType affiliation)
: this(jid, affiliation)
{
this.Node = node;
}
/// <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 );
}
public void OwnerModifyAffiliation(Jid to, Jid from, string node, Jid affiliate, AffiliationType affiliation, IqHandler cb)
{
owner.PubSubIq pubsubIq = new owner.PubSubIq(IqType.set, to);
if (from != null)
{
pubsubIq.From = from;
}
owner.Affiliates aff = new owner.Affiliates(node);
aff.AddAffiliate(new owner.Affiliate(affiliate, affiliation));
pubsubIq.PubSub.Affiliates = aff;
if (cb == null)
{
m_connection.Send(pubsubIq);
}
else
{
m_connection.IqGrabber.SendIq(pubsubIq, cb);
}
}
public Affiliation(Jid jid, AffiliationType affiliation)
{
this.Jid = jid;
this.AffiliationType = affiliation;
}
public Affiliate(Jid jid, AffiliationType affiliation) : this()
{
Jid = jid;
Affiliation = affiliation;
}
public void OwnerModifyAffiliation(Jid to, Jid from, string node, Jid affiliate, AffiliationType affiliation, IqCB cb)
{
this.OwnerModifyAffiliation(to, from, node, affiliate, affiliation, cb, null);
}
public void OwnerModifyAffiliation(Jid to, Jid from, string node, Jid affiliate, AffiliationType affiliation, IqCB cb, object cbArgs)
{
owner.PubSubIq pubsubIq = new owner.PubSubIq(IqType.set, to);
if (from != null)
pubsubIq.From = from;
owner.Affiliates aff = new owner.Affiliates(node);
aff.AddAffiliate(new owner.Affiliate(affiliate, affiliation));
pubsubIq.PubSub.Affiliates = aff;
if (cb == null)
m_connection.Send(pubsubIq);
else
m_connection.IqGrabber.SendIq(pubsubIq, cb, cbArgs);
}
public Affiliate(Jid jid, AffiliationType affiliation) : this()
{
Jid = jid;
Affiliation = affiliation;
}
public void OwnerModifyAffiliation(Jid to, string node, Jid affiliate, AffiliationType affiliation, IqCB cb, object cbArgs)
{
OwnerModifyAffiliation(to, null, node, affiliate, affiliation, cb, cbArgs);
}
public void OwnerModifyAffiliation(Jid to, Jid from, string node, Jid affiliate, AffiliationType affiliation, IqCB cb)
{
OwnerModifyAffiliation(to, from, node, affiliate, affiliation, cb, null);
}
/*
Owner modifies a single affiliation
<iq type='set'
from='[email protected]/elsinore'
to='pubsub.shakespeare.lit'
id='ent2'>
<pubsub xmlns='http://jabber.org/protocol/pubsub#owner'>
<affiliates node='blogs/princely_musings'/>
<affiliate jid='*****@*****.**' affiliation='owner'/>
</affiliates>
</pubsub>
</iq>
*/
public void OwnerModifyAffiliation(Jid to, string node, Jid affiliate, AffiliationType affiliation)
{
OwnerModifyAffiliation(to, null, node, affiliate, affiliation, null, null);
}
public Affiliation(Jid jid, AffiliationType affiliation)
{
this.Jid = jid;
this.AffiliationType = affiliation;
}
public Affiliation(Jid jid, AffiliationType affiliation)
{
Jid = jid;
AffiliationType = affiliation;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="a"></param>
/// <param name="idata"></param>
public AffiliationObj(AffiliationType a, IdentDataObj idata)
: base(idata)
{
OrganizationRef = a.organization_ref;
}
public Affiliation(Jid jid, AffiliationType affiliation)
{
Jid = jid;
AffiliationType = affiliation;
}
public Affiliate(Jid jid, AffiliationType affiliation)
: this()
{
this.Jid = jid;
this.Affiliation = affiliation;
}
/*
* Owner modifies a single affiliation
*
* <iq type='set'
* from='[email protected]/elsinore'
* to='pubsub.shakespeare.lit'
* id='ent2'>
* <pubsub xmlns='http://jabber.org/protocol/pubsub#owner'>
* <affiliates node='blogs/princely_musings'/>
* <affiliate jid='*****@*****.**' affiliation='owner'/>
* </affiliates>
* </pubsub>
* </iq>
*
*/
public void OwnerModifyAffiliation(Jid to, string node, Jid affiliate, AffiliationType affiliation)
{
this.OwnerModifyAffiliation(to, null, node, affiliate, affiliation, null, null);
}
public Affiliate(Jid jid, AffiliationType affiliation) : this()
{
this.Jid = jid;
this.Affiliation = affiliation;
}
public void OwnerModifyAffiliation(Jid to, string node, Jid affiliate, AffiliationType affiliation, IqHandler cb)
{
OwnerModifyAffiliation(to, null, node, affiliate, affiliation, cb);
}
public Affiliation(string node, Jid jid, AffiliationType affiliation) : this(jid, affiliation)
{
Node = node;
}
public void OwnerModifyAffiliation(Jid to, string node, Jid affiliate, AffiliationType affiliation, IqCB cb)
{
OwnerModifyAffiliation(to, null, node, affiliate, affiliation, cb, null);
}
public void OwnerModifyAffiliation(Jid to, string node, Jid affiliate, AffiliationType affiliation, IqCB cb, object cbArgs)
{
this.OwnerModifyAffiliation(to, null, node, affiliate, affiliation, cb, cbArgs);
}
public void OwnerModifyAffiliation(Jid to, Jid from, string node, Jid affiliate, AffiliationType affiliation)
{
OwnerModifyAffiliation(to, from, node, affiliate, affiliation, null, null);
}
public void OwnerModifyAffiliation(Jid to, Jid from, string node, Jid affiliate, AffiliationType affiliation, IqCB cb, object cbArgs)
{
var pubsubIq = new Owner.PubSubIq(IQType.Set, to);
if (from != null)
{
pubsubIq.From = from;
}
var aff = new Owner.Affiliates(node);
aff.AddAffiliate(new Owner.Affiliate(affiliate, affiliation));
pubsubIq.PubSub.Affiliates = aff;
if (cb == null)
{
this.m_connection.Send(pubsubIq);
}
else
{
this.m_connection.IqGrabber.SendIq(pubsubIq, cb, cbArgs);
}
}
public ChurchAtt(String n, AffiliationType t)
{
name = n; aff_type = t; bAffiliation = true;
}
