| OpenMS 2.5.0

ProtXMLFile.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 2002-2020.
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: Chris Bielow $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/METADATA/ProteinIdentification.h>
38 #include <OpenMS/METADATA/PeptideIdentification.h>
39 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
40 #include <OpenMS/FORMAT/XMLFile.h>
41
42 #include <vector>
43
44 namespace OpenMS
45 {
70 class OPENMS_DLLAPI ProtXMLFile :
71 protected Internal::XMLHandler,
72 public Internal::XMLFile
73 {
74 public:
75
77 typedef ProteinIdentification::ProteinGroup ProteinGroup;
78
80 ProtXMLFile();
81
91 void load(const String & filename, ProteinIdentification & protein_ids, PeptideIdentification & peptide_ids);
92
101 void store(const String & filename, const ProteinIdentification & protein_ids, const PeptideIdentification & peptide_ids, const String & document_id = "");
102
103 protected:
104
106 void resetMembers_();
107
109 void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
110
112 void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
113
115 void registerProtein_(const String & protein_name);
116
129 void matchModification_(const double mass, const String & origin, String & modification_description);
130
132
133 ProteinIdentification * prot_id_;
136 PeptideIdentification * pep_id_;
138 PeptideHit * pep_hit_;
140 ProteinGroup protein_group_;
141
142
144 };
145
146 } // namespace OpenMS
147
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
OpenMS::ProtXMLFile::pep_id_
PeptideIdentification * pep_id_
Pointer to peptide identification.
Definition: ProtXMLFile.h:136
OpenMS::ProtXMLFile
Used to load (storing not supported, yet) ProtXML files.
Definition: ProtXMLFile.h:70
XMLHandler.h
OpenMS::ProteinIdentification::ProteinGroup
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:81
OpenMS::ProtXMLFile::ProteinGroup
ProteinIdentification::ProteinGroup ProteinGroup
A protein group (set of indices into ProteinIdentification)
Definition: ProtXMLFile.h:77
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::ProtXMLFile::protein_group_
ProteinGroup protein_group_
protein group
Definition: ProtXMLFile.h:140
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::ProtXMLFile::pep_hit_
PeptideHit * pep_hit_
Temporary peptide hit.
Definition: ProtXMLFile.h:138