OpenMS  2.8.0
PepXMLFileMascot.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 2002-2021.
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: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
40 #include <OpenMS/FORMAT/XMLFile.h>
42 
43 #include <vector>
44 
45 namespace OpenMS
46 {
54  class OPENMS_DLLAPI PepXMLFileMascot :
55  protected Internal::XMLHandler,
56  public Internal::XMLFile
57  {
58 public:
59 
62 
69  void load(const String & filename, std::map<String, std::vector<AASequence> > & peptides);
70 
71 protected:
72 
73  // Docu in base class
74  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
75 
76  // Docu in base class
77  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
78 
79  void matchModification_(double mass, String & modification_description);
80 
82 
83 
87 
90 
92  std::vector<std::pair<String, UInt> > actual_modifications_;
93 
95  std::map<String, std::vector<AASequence> > * peptides_;
96 
98  std::vector<AASequence> actual_aa_sequences_;
99 
101  std::vector<String> fixed_modifications_;
102 
104  std::vector<std::pair<String, double> > variable_modifications_;
106  };
107 
108 } // namespace OpenMS
109 
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
Base class for XML handlers.
Definition: XMLHandler.h:325
Used to load Mascot PepXML files.
Definition: PepXMLFileMascot.h:57
std::map< String, std::vector< AASequence > > * peptides_
The peptides together with the spectrum title.
Definition: PepXMLFileMascot.h:95
String actual_sequence_
The sequence of the actual peptide hit.
Definition: PepXMLFileMascot.h:89
String actual_title_
Pointer to fill in protein identifications.
Definition: PepXMLFileMascot.h:86
void matchModification_(double mass, String &modification_description)
void load(const String &filename, std::map< String, std::vector< AASequence > > &peptides)
Loads peptide sequences with modifications out of a PepXML file.
std::vector< std::pair< String, UInt > > actual_modifications_
The modifications of the actual peptide hit (position is 1-based)
Definition: PepXMLFileMascot.h:92
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
PepXMLFileMascot()
Constructor.
std::vector< String > fixed_modifications_
stores the fixed residue modifications
Definition: PepXMLFileMascot.h:101
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
std::vector< std::pair< String, double > > variable_modifications_
stores the variable residue modifications
Definition: PepXMLFileMascot.h:104
std::vector< AASequence > actual_aa_sequences_
stores the actual peptide sequences
Definition: PepXMLFileMascot.h:98
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47