Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
PeptideIdentification.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2013.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Nico Pfeifer $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
36 #define OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
37 
41 
42 #include <string>
43 #include <map>
44 
45 namespace OpenMS
46 {
63  class OPENMS_DLLAPI PeptideIdentification :
64  public MetaInfoInterface
65  {
66 public:
67 
70 
72 
76  virtual ~PeptideIdentification();
80  PeptideIdentification & operator=(const PeptideIdentification & source);
82  bool operator==(const PeptideIdentification & rhs) const;
84  bool operator!=(const PeptideIdentification & rhs) const;
86 
88  const std::vector<PeptideHit> & getHits() const;
90  void insertHit(const PeptideHit & hit);
92  void setHits(const std::vector<PeptideHit> & hits);
93 
95  DoubleReal getSignificanceThreshold() const;
97  void setSignificanceThreshold(DoubleReal value);
98 
100  String getScoreType() const;
102  void setScoreType(const String & type);
103 
105  bool isHigherScoreBetter() const;
107  void setHigherScoreBetter(bool value);
108 
110  const String & getIdentifier() const;
112  void setIdentifier(const String & id);
113 
115  void assignRanks();
116 
122  void sort();
123 
125  bool empty() const;
126 
128 
129 
131  void getReferencingHits(const String & protein_accession, std::vector<PeptideHit> & peptide_hits) const;
132 
134  void getReferencingHits(const std::vector<String> & accessions, std::vector<PeptideHit> & peptide_hits) const;
135 
137  void getReferencingHits(const std::vector<ProteinHit> & protein_hits, std::vector<PeptideHit> & peptide_hits) const;
138 
140  void getNonReferencingHits(const String & protein_accession, std::vector<PeptideHit> & peptide_hits) const;
141  void getNonReferencingHits(const std::vector<String> & accessions, std::vector<PeptideHit> & peptide_hits) const;
142  void getNonReferencingHits(const std::vector<ProteinHit> & protein_hits, std::vector<PeptideHit> & peptide_hits) const;
144 
145 protected:
147  std::vector<PeptideHit> hits_;
151  };
152 
153 } //namespace OpenMS
154 #endif // OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
A more convenient string class.
Definition: String.h:56
String score_type_
The score type (Mascot, Sequest, e-value, p-value)
Definition: PeptideIdentification.h:149
std::vector< PeptideHit > hits_
A list containing the peptide hits.
Definition: PeptideIdentification.h:147
Representation of a peptide hit.
Definition: PeptideHit.h:54
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
PeptideHit HitType
Hit type definition.
Definition: PeptideIdentification.h:69
String id_
Identifier by which ProteinIdentification and PeptideIdentification are matched.
Definition: PeptideIdentification.h:146
DoubleReal significance_threshold_
the peptide significance threshold
Definition: PeptideIdentification.h:148
bool higher_score_better_
The score orientation.
Definition: PeptideIdentification.h:150
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:19 using doxygen 1.8.5