示例#1
0
	private String GetPtmCsv (Peptide peptide) {
		String result = "";
		List<PTM> ptms = new List<PTM>();
		foreach( List<PTM> variant in peptide.Variants )
			foreach( PTM ptm in variant )
				if( !ptms.Contains(ptm) ) {
					ptms.Add(ptm);
					result += peptide.ToString()+"/"+ptm.ToString()+" ";
				}
		return result;
	}
示例#2
0
	private bool CheckPeptide( Peptide f ) {
		if( f.Proteins.Count == 0 )
			return false;
		if( Spectra.Count != 0 && (f.Psm == null || f.Psm.Count == 0) )
			return false;
		if( FilterDecoys && f.Decoy )
			return false;
		if (f.Sequence.Length < LengthThreshold)
			return false;
		if( Type == SourceType.Plgs && (int)f.Confidence < (int)PlgsThreshold )
			return false;
		return true;
	}
示例#3
0
	/// <summary>
	/// Removes invalid PSMs and their associated peptides (if neccessary).
	/// </summary>
	private void FilterPsms() {
		if( Spectra.Count == 0 )
			return;
		List<Spectrum> spectra = new List<Spectrum>();

		// Remove previous relations
		foreach( Peptide f in Peptides )
			f.Psm = new List<PSM>();
		
		foreach( Spectrum spectrum in Spectra ) {
			if( spectrum.Psm == null )
				continue;
			Spectrum tmp = null;
			foreach( PSM psm in spectrum.Psm ) {
				if( !CheckPsm(psm) )
					continue;
				if( tmp == null ) {
					tmp = new Spectrum();
					tmp.File = spectrum.File;
					tmp.ID = spectrum.ID;
					tmp.SpectrumID = spectrum.SpectrumID;
					tmp.Psm = new List<PSM>();
				}
				tmp.Psm.Add(psm);
				Peptide f = psm.Peptide;
				if( !f.Psm.Contains(psm) )
					f.Psm.Add(psm);
				if( f.Confidence < psm.Confidence )
					f.Confidence = psm.Confidence;
			}
			if( tmp != null )
				spectra.Add(tmp);
		}
		
		Spectra = spectra;
	}
示例#4
0
	private void LoadData( string xmlpath ) {
		SortedList<int,string> SortedAccession = new SortedList<int, string>();
	
		XmlDocument doc = new XmlDocument();
		doc.Load( xmlpath );
		
		// Load proteins
		XmlNodeList proteins = doc.GetElementsByTagName( "PROTEIN" );
		foreach( XmlElement element in proteins ) {
			int id = int.Parse(element.GetAttribute("ID"));
			if( SortedAccession.ContainsKey(id) )
				continue;
			string acc = element.GetElementsByTagName("ACCESSION")[0].InnerText;
			SortedAccession.Add( id, acc );
			if( m_SortedProteins.ContainsKey(acc) )
				continue;
			string entry = element.GetElementsByTagName("ENTRY")[0].InnerText;
			string desc = element.GetElementsByTagName("DESCRIPTION")[0].InnerText.Replace('+',' ');
			string seq = element.GetElementsByTagName("SEQUENCE")[0].InnerText.ToUpper();
			Protein p = new Protein(m_pid++, entry, acc, desc, seq);
			Proteins.Add( p );
			m_SortedProteins.Add( acc, p );
		}
		
		// Load peptides
		SortedList<int,Peptide> SortedPeptides = new SortedList<int, Peptide>();
		XmlNodeList peptides = doc.GetElementsByTagName( "PEPTIDE" );
		foreach( XmlElement element in peptides ) {
			int id = int.Parse(element.GetAttribute("ID"));
			int pid = int.Parse(element.GetAttribute("PROT_ID"));
			int mid = 0;
			if( PlgsThreshold != Peptide.ConfidenceType.NoThreshold )
				mid = int.Parse(element.GetAttribute("QUERY_MASS_ID"));
			string seq = element.GetAttribute("SEQUENCE").ToUpper();
			Peptide f = new Peptide(id, seq);
			XmlNodeList mods = element.GetElementsByTagName( "MATCH_MODIFIER" );
			f.Runs.Add( m_Run );
			foreach( XmlElement mod in mods ) {
				PTM ptm = new PTM();
				string[] strs = mod.GetAttribute("NAME").Split(new char[]{'+'});
				ptm.Name = strs[0];
				string str = mod.GetAttribute("POS");
				ptm.Pos = str.Length == 0 ? -1 : int.Parse(str);
				if( strs.Length > 1 )
					ptm.Residues = strs[1];
				f.AddPTM( ptm );
			}
			Protein p = null;
			try {
				p = m_SortedProteins[SortedAccession[pid]];
			} catch {
				Notify( "Peptide '" + id + "' references unknown protein '" + pid + "'" );
			}
			if( p != null ) {
				p.Peptides.Add( f );
				f.Proteins.Add( p );
				if( !p.Sequence.Contains(f.Sequence) )
					throw new ApplicationException( "Inconsistent sequence data" );
			}
			Peptides.Add( f );
			if( PlgsThreshold != Peptide.ConfidenceType.NoThreshold )
				SortedPeptides.Add(mid,f);
		}
		if( PlgsThreshold == Peptide.ConfidenceType.NoThreshold )
			return;
		
		// Scores
		XmlNodeList scores = doc.GetElementsByTagName( "MASS_MATCH" );
		foreach( XmlElement element in scores ) {
			int id = int.Parse(element.GetAttribute("ID"));
			double score = double.Parse(element.GetAttribute("SCORE"), m_Format);
			SortedPeptides[id].Score = score;
		}
	}
示例#5
0
文件: Plgs.cs 项目: akrogp/EhuBio
        private void LoadData( string xmlpath )
        {
            SortedList<int,string> SortedAccession = new SortedList<int, string>();

            XmlDocument doc = new XmlDocument();
            doc.Load( xmlpath );

            // Load proteins
            XmlNodeList proteins = doc.GetElementsByTagName( "PROTEIN" );
            foreach( XmlElement element in proteins ) {
            int id = int.Parse(element.GetAttribute("ID"));
            if( SortedAccession.ContainsKey(id) )
                continue;
            string acc = element.GetElementsByTagName("ACCESSION")[0].InnerText;
            SortedAccession.Add( id, acc );
            if( m_SortedProteins.ContainsKey(acc) )
                continue;
            string entry = element.GetElementsByTagName("ENTRY")[0].InnerText;
            string desc = element.GetElementsByTagName("DESCRIPTION")[0].InnerText.Replace('+',' ');
            string seq = element.GetElementsByTagName("SEQUENCE")[0].InnerText.ToUpper();
            Protein p = new Protein(m_pid++, entry, acc, desc, seq);
            Proteins.Add( p );
            m_SortedProteins.Add( acc, p );
            }

            // Load peptides
            SortedList<int,Peptide> SortedPeptides = new SortedList<int, Peptide>();
            XmlNodeList peptides = doc.GetElementsByTagName( "PEPTIDE" );
            foreach( XmlElement element in peptides ) {
            int id = int.Parse(element.GetAttribute("ID"));
            int pid = int.Parse(element.GetAttribute("PROT_ID"));
            int mid = 0;
            if( PlgsThreshold != Peptide.ConfidenceType.NoThreshold )
                mid = int.Parse(element.GetAttribute("QUERY_MASS_ID"));
            string seq = element.GetAttribute("SEQUENCE").ToUpper();
            Peptide f = new Peptide(id, seq);
            XmlNodeList mods = element.GetElementsByTagName( "MATCH_MODIFIER" );
            f.Runs.Add( m_Run );
            foreach( XmlElement mod in mods ) {
                PTM ptm = new PTM();
                string[] strs = mod.GetAttribute("NAME").Split(new char[]{'+'});
                ptm.Name = strs[0];
                string str = mod.GetAttribute("POS");
                ptm.Pos = str.Length == 0 ? -1 : int.Parse(str);
                if( strs.Length > 1 )
                    ptm.Residues = strs[1];
                f.AddPTM( ptm );
            }
            Protein p = null;
            try {
                p = m_SortedProteins[SortedAccession[pid]];
            } catch {
                Notify( "Peptide '" + id + "' references unknown protein '" + pid + "'" );
            }
            if( p != null ) {
                p.Peptides.Add( f );
                f.Proteins.Add( p );
                if( !p.Sequence.Contains(f.Sequence) )
                    throw new ApplicationException( "Inconsistent sequence data" );
            }
            Peptides.Add( f );
            if( PlgsThreshold != Peptide.ConfidenceType.NoThreshold )
                SortedPeptides.Add(mid,f);
            }
            if( PlgsThreshold == Peptide.ConfidenceType.NoThreshold )
            return;

            // Scores
            XmlNodeList scores = doc.GetElementsByTagName( "MASS_MATCH" );
            foreach( XmlElement element in scores ) {
            int id = int.Parse(element.GetAttribute("ID"));
            double score = double.Parse(element.GetAttribute("SCORE"), m_Format);
            SortedPeptides[id].Score = score;
            }
        }
示例#6
0
文件: mzId1_0.cs 项目: akrogp/EhuBio
        /// <summary>
        /// Loads a mzIdentML file
        /// </summary>
        protected override 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 );
                }
            }
        }
示例#7
0
文件: Mapper.cs 项目: akrogp/EhuBio
 private String GetPtmCsv(Peptide peptide)
 {
     String result = "";
     List<PTM> ptms = new List<PTM>();
     foreach( List<PTM> variant in peptide.Variants )
     foreach( PTM ptm in variant )
         if( !ptms.Contains(ptm) ) {
             ptms.Add(ptm);
             result += peptide.ToString()+"/"+ptm.ToString()+" ";
         }
     return result;
 }
示例#8
0
文件: Mapper.cs 项目: akrogp/EhuBio
 private bool CheckPeptide( Peptide f )
 {
     if( f.Proteins.Count == 0 )
     return false;
     if( Spectra.Count != 0 && (f.Psm == null || f.Psm.Count == 0) )
     return false;
     if( FilterDecoys && f.Decoy )
     return false;
     if (f.Sequence.Length < LengthThreshold)
     return false;
     if( Type == SourceType.Plgs && (int)f.Confidence < (int)PlgsThreshold )
     return false;
     return true;
 }
示例#9
0
文件: Mapper.cs 项目: akrogp/EhuBio
 protected bool CheckPsm( bool passThreshold, int rank, Peptide.ConfidenceType confidence, double score, string type )
 {
     if( RequirePassTh && !passThreshold )
     return false;
     if( RankThreshold != 0 && (rank == 0 || rank > RankThreshold) )
     return false;
     if( Type >= SourceType.mzIdentML110 && Type <= SourceType.mzIdentML120 && (int)confidence < (int)SeqThreshold )
     return false;
     if( type == "Mascot expectation value" && score > MascotThreshold )
     return false;
     if( type == "X!Tandem expect" && score > XTandemThreshold )
     return false;
     return true;
 }
示例#10
0
	/// <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 );
				}
			}
	}
示例#11
0
	/// <summary>
	/// Checks for the presence of the given peptide in the peptide list of the protein
	/// </summary>
	public bool HasPeptide( Peptide fo ) {
		return Peptides.Contains( fo );
	}
示例#12
0
文件: mzId1_1.cs 项目: akrogp/EhuBio
 private SortedList<string, Peptide> LoadPeptides()
 {
     SortedList<string,Peptide> SortedPeptides = new SortedList<string, Peptide>();
     int id = 1;
     foreach( PeptideType pep in m_mzid.ListPeptides ) {
     Peptide p = new Peptide( id++, pep.PeptideSequence );
     p.Confidence = Peptide.ConfidenceType.NoThreshold;
     SortedPeptides.Add( pep.id, p );
     p.Runs.Add( m_Run );
     if( pep.Modification != null )
         foreach( ModificationType mod in pep.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( CVParamType param in mod.cvParam )
                 if( param.cvRef.Equals("UNIMOD") )
                     ptm.Name = param.name;
             p.AddPTM( ptm );
         }
     p.DBRef = pep.id;
     Peptides.Add( p );
     }
     return SortedPeptides;
 }
示例#13
0
文件: mzId1_1.cs 项目: akrogp/EhuBio
        private void GetPsmScore(
		SpectrumIdentificationItemType item,
		out double score, out string type, out Peptide.ConfidenceType confidence )
        {
            score = -1.0;
            type = "N/A";
            confidence = item.passThreshold ? Peptide.ConfidenceType.PassThreshold : Peptide.ConfidenceType.NoThreshold;
            if( item.Items == null )
            return;
            foreach( AbstractParamType param in item.Items ) {
            if( !(param is CVParamType) )
                continue;
            CVParamType cv = param as CVParamType;
            if( cv.accession == "MS:1001155" ) {
                score = double.Parse(cv.value, m_Format);
                type = "ProteomeDiscoverer/SEQUEST Confidence XCorr";
                if( score >= m_GreenTh[item.chargeState-1] )
                    confidence = Peptide.ConfidenceType.Green;
                else if( score >= m_YellowTh[item.chargeState-1] )
                    confidence = Peptide.ConfidenceType.Yellow;
                else
                    confidence = Peptide.ConfidenceType.Red;
                break;
            } else if( cv.accession == "MS:1001172" ) {
                score = double.Parse(cv.value, m_Format);
                type = "Mascot expectation value";
                break;
            } else if( cv.accession == "MS:1001330" ) {
                score = double.Parse( cv.value, m_Format );
                type = "X!Tandem expect";
                break;
            }
            }
        }
示例#14
0
	/// <summary>
	/// Removes peptides with low score, duplicated (same sequence) or not voted (multirun)
	/// </summary>
	private void FilterPeptides() {
		List<Peptide> peptides = new List<Peptide>();
		int id = 1;
		
		// Remove previous relations
		foreach( Protein p in Proteins )
			p.Peptides.Clear();
		
		// Filters duplicated (same sequence) peptides
		SortedList<string,Peptide> SortedPeptides = new SortedList<string, Peptide>();
		foreach( Peptide f in Peptides ) {
			// Low score peptide
			if( !CheckPeptide(f) ) {
				if( f.Psm != null )
					foreach( PSM psm in f.Psm )
						psm.Spectrum.Psm.Remove(psm);
				continue;
			}
			// Duplicated peptide, new protein?
			if( SortedPeptides.ContainsKey(f.Sequence) ) {
				Peptide fo = SortedPeptides[f.Sequence];
				if( (int)f.Confidence > (int)fo.Confidence )
					fo.Confidence = f.Confidence;
				if( !fo.Runs.Contains(f.Runs[0]) )
					fo.Runs.Add(f.Runs[0]);
				fo.AddVariant( f.LastVariant );
				bool dp = false;	// duplicated protein?, needed for PLGS
				foreach( Protein po in fo.Proteins )
					if( po.ID == f.Proteins[0].ID ) {
						dp = true;
						break;
					}
				if( !dp )
					fo.Proteins.Add( f.Proteins[0] );
				if( fo.Psm == null )
					fo.Psm = f.Psm;
				else if( f.Psm != null )
					fo.Psm.AddRange(f.Psm);
				if( fo.Psm != null )
					foreach( PSM psm in fo.Psm )
						psm.Peptide = fo;
			// New peptide
			} else {
				f.ID = id++;
				SortedPeptides.Add( f.Sequence, f );
				peptides.Add( f );
			}
		}
		
		// Vote peptides
		if( RunsThreshold > 1 ) {
			Peptides = new List<Peptide>();
			foreach( Peptide f in peptides )
				if( f.Runs.Count >= RunsThreshold )
					Peptides.Add(f);
		} else
			Peptides = peptides;
		
		// Asigns new peptides to proteins
		foreach( Peptide f in Peptides )
			foreach( Protein p in f.Proteins )
				p.Peptides.Add(f);
	}
示例#15
0
	private void WriteProteinDetails( TextWriter w, Protein p ) {
		Tag tr = new Tag( "tr", true );
		Tag td = new Tag( "td", "colspan" );
		Tag th = new Tag( "th", "rowspan" );
		Tag a = new Tag( "a", "href" );
		int i;
		
		w.WriteLine( "<table>\n<caption><a name=\""+p.Accession+"\"/>Protein "+p.Accession+"</caption>" );
		//w.WriteLine( "<col width=\"10%\"/><col width=\"5%\"/><col width=\"10%\"/><col width=\"75%\"/>" );
		w.WriteLine( tr.Render(th.Render("Name")+td.Render("3",p.EntryEx)) );
		w.WriteLine( tr.Render(th.Render("Description")+td.Render("3",p.Desc)) );
		w.WriteLine( tr.Render(th.Render("Sequence")+td.Render("3","<pre>"+p.ParseSeq(10)+"</pre>")) );
		w.WriteLine( tr.Render(th.Render("Evidence")+td.Render("3",p.Evidence.ToString())) );
		w.Write( tr+th.Render("Peptide list")+"<td colspan=\"3\">" );
		if( p.Peptides.Count > 0 ) {
			for( i = 0; i < p.Peptides.Count-1; i++ )
				w.Write( a.Render("#"+p.Accession+"__"+p.Peptides[i].ID,p.Peptides[i].ToString()) + ", " );
			w.Write( a.Render("#"+p.Accession+"__"+p.Peptides[i].ID,p.Peptides[i].ToString()) );
		}
		w.WriteLine( "</td>"+tr );
		if( p.Peptides.Count == 0 ) {
			w.WriteLine( "</table><br/>" );
			return;
		}
		int rows = 8;
		if( Spectra.Count != 0 )
			rows++;
		w.Write( tr+th.Render((p.Peptides.Count*rows).ToString(),"Peptides") );
		bool first = true;
		foreach( Peptide f in p.Peptides ) {
			if( first )
				first = false;
			else
				w.Write( tr.ToString() );
			w.Write( th.Render(rows.ToString(),f.ToString()) );
			w.WriteLine( th.Render("<a name=\""+p.Accession+"__"+f.ID+"\"/>Confidence")+td.Render(f.Confidence.ToString())+tr );
			tr.Hold = true;
			w.WriteLine( tr.Render(th.Render("Decoy")+td.Render(f.Decoy.ToString())) );
			w.Write( tr+th.Render("Runs")+td );
			for( i = 0; i < f.Runs.Count-1; i++ )
				w.Write( f.Runs[i].ToString() + ", " );
			w.WriteLine( f.Runs[i].ToString()+td+tr );
			w.WriteLine( tr.Render(th.Render("Relation")+td.Render(f.Relation.ToString())) );
			w.Write( tr+th.Render("Proteins")+td );
			for( i = 0; i < f.Proteins.Count-1; i++ )
				w.Write( a.Render("#"+f.Proteins[i].Accession,f.Proteins[i].EntryEx) + ", " );
			w.WriteLine( a.Render("#"+f.Proteins[i].Accession,f.Proteins[i].EntryEx)+td.ToString()+tr );
			w.WriteLine( tr.Render(th.Render("Sequence")+td.Render("<pre>"+f.Sequence+"</pre>")) );
			w.WriteLine( tr.Render(th.Render("Position")+td.Render(f.GetPositions(p))) );
			w.Write( tr+th.Render("PTMs")+td );
			if( f.Variants.Count == 1 )
				w.Write( Peptide.Variant2Str(f.LastVariant) );
			else {
        		i = 1;
        		foreach( List<PTM> v in f.Variants )
        			w.Write( "Variant #"+(i++)+": "+Peptide.Variant2Str(v)+"<br/>" );
        	}
			w.WriteLine( td.ToString()+tr );
			if( Spectra.Count != 0 ) {
				w.Write( tr+th.Render("PSMs")+td );
				if( f.Psm != null ) {
					for( i = 0; i < f.Psm.Count-1; i++ )
						w.Write( a.Render("#PSM"+f.Psm[i].ID,f.Psm[i].ID.ToString()) + ", " );
					w.WriteLine( a.Render("#PSM"+f.Psm[i].ID,f.Psm[i].ID.ToString()) );
				}
				w.WriteLine( td.ToString()+tr );
			}
			tr.Hold = false;
		}
		w.WriteLine( "</table><br/>" );
	}
示例#16
0
文件: Protein.cs 项目: akrogp/EhuBio
 /// <summary>
 /// Checks for the presence of the given peptide in the peptide list of the protein
 /// </summary>
 public bool HasPeptide( Peptide fo )
 {
     return Peptides.Contains( fo );
 }