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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