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 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) { 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 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 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; }