OpenMS  3.0.0
PercolatorInfile.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 2002-2022.
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: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/TextFile.h>
39 
40 #include <vector>
41 
42 namespace OpenMS
43 {
44 
49  class OPENMS_DLLAPI PercolatorInfile
50  {
51  public:
52  static void store(const String& pin_file,
53  const std::vector<PeptideIdentification>& peptide_ids,
54  const StringList& feature_set,
55  const std::string& enz,
56  int min_charge,
57  int max_charge);
58 
59  // uses spectrum_reference, if empty uses spectrum_id, if also empty fall back to using index
60  static String getScanIdentifier(const PeptideIdentification& pid, size_t index);
61 
62  protected:
63 
64  //id <tab> label <tab> scannr <tab> calcmass <tab> expmass <tab> feature1 <tab> ... <tab> featureN <tab> peptide <tab> proteinId1 <tab> .. <tab> proteinIdM
65  static TextFile preparePin_(
66  const std::vector<PeptideIdentification>& peptide_ids,
67  const StringList& feature_set,
68  const std::string& enz,
69  int min_charge,
70  int max_charge);
71 
72 
73  static Int getScanNumber_(const String& scan_identifier);
74 
75  static bool isEnz_(const char& n, const char& c, const std::string& enz);
76 
77  static Size countEnzymatic_(const String& peptide, const std::string& enz);
78 
79  };
80 } // namespace OpenMS
TextFile.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::PercolatorInfile
Class for storing Percolator tab-delimited input files.
Definition: PercolatorInfile.h:49
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
PeptideIdentification.h