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PeptideIdentification.h (Maintainer: Nico Pfeifer)

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00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 // --------------------------------------------------------------------------
00005 //                   OpenMS Mass Spectrometry Framework
00006 // --------------------------------------------------------------------------
00007 //  Copyright (C) 2003-2008 -- Oliver Kohlbacher, Knut Reinert
00008 //
00009 //  This library is free software; you can redistribute it and/or
00010 //  modify it under the terms of the GNU Lesser General Public
00011 //  License as published by the Free Software Foundation; either
00012 //  version 2.1 of the License, or (at your option) any later version.
00013 //
00014 //  This library is distributed in the hope that it will be useful,
00015 //  but WITHOUT ANY WARRANTY; without even the implied warranty of
00016 //  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
00017 //  Lesser General Public License for more details.
00018 //
00019 //  You should have received a copy of the GNU Lesser General Public
00020 //  License along with this library; if not, write to the Free Software
00021 //  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
00022 //
00023 // --------------------------------------------------------------------------
00024 // $Maintainer: Nico Pfeifer $
00025 // --------------------------------------------------------------------------
00026 
00027 #ifndef OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
00028 #define OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
00029 
00030 #include <OpenMS/METADATA/PeptideHit.h>
00031 #include <OpenMS/METADATA/MetaInfoInterface.h>
00032 #include <OpenMS/METADATA/ProteinHit.h>
00033 
00034 #include <string>
00035 #include <map>
00036 
00037 namespace OpenMS
00038 {     
00052   class PeptideIdentification
00053     : public MetaInfoInterface
00054   {
00055     public:
00056       
00058       typedef PeptideHit HitType;
00059       
00061 
00062 
00063       PeptideIdentification();
00065       virtual ~PeptideIdentification();
00067       PeptideIdentification(const PeptideIdentification& source);
00069       PeptideIdentification& operator=(const PeptideIdentification& source);    
00071       bool operator == (const PeptideIdentification& rhs) const;
00073       bool operator != (const PeptideIdentification& rhs) const;
00075   
00077       const std::vector<PeptideHit>& getHits() const;
00079       void insertHit(const PeptideHit& hit);
00081       void setHits(const std::vector<PeptideHit>& hits);
00082       
00084       Real getSignificanceThreshold() const;
00086       void setSignificanceThreshold(Real value);
00087      
00089       String getScoreType() const;   
00091       void setScoreType(const String& type);    
00092      
00094       bool isHigherScoreBetter() const;   
00096       void setHigherScoreBetter(bool value);
00097       
00099       const String& getIdentifier() const;
00101       void setIdentifier(const String& id);
00102 
00104       void assignRanks();
00106       void sort();
00108       bool empty() const;
00109       
00111 
00112       void getReferencingHits(const String& protein_accession, std::vector<PeptideHit>& peptide_hits) const;      
00113       void getReferencingHits(const std::vector<String>& accessions, std::vector<PeptideHit>& peptide_hits) const;
00114       void getReferencingHits(const std::vector<ProteinHit>& protein_hits, std::vector<PeptideHit>& peptide_hits) const;
00115 
00116       void getNonReferencingHits(const String& protein_accession, std::vector<PeptideHit>& peptide_hits) const;     
00117       void getNonReferencingHits(const std::vector<String>& accessions, std::vector<PeptideHit>& peptide_hits) const;
00118       void getNonReferencingHits(const std::vector<ProteinHit>& protein_hits, std::vector<PeptideHit>& peptide_hits) const;
00120       
00121     protected:
00122       String id_;                          
00123       std::vector<PeptideHit> hits_;       
00124       Real significance_threshold_;        
00125       String score_type_;                  
00126       bool higher_score_better_;           
00127   };
00128 
00129 } //namespace OpenMS
00130 #endif // OPENMS_METADATA_PEPTIDEIDENTIFICATION_H

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