| OpenMS 2.5.0

RNPxlReport.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: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.h>
39 #include <OpenMS/DATASTRUCTURES/ListUtilsIO.h>
40
41 #include <OpenMS/METADATA/PeptideIdentification.h>
42 #include <OpenMS/KERNEL/MSSpectrum.h>
43 #include <OpenMS/KERNEL/MSExperiment.h>
44 #include <OpenMS/CONCEPT/Constants.h>
45
46 namespace OpenMS
47 {
48
50 struct OPENMS_DLLAPI RNPxlReportRow
51 {
52 bool no_id;
53 double rt;
54 double original_mz;
55 String accessions;
56 String RNA;
57 String peptide;
58 double best_localization_score;
59 String localization_scores;
60 String best_localization;
61 Int charge;
62 double score;
63 double peptide_weight;
64 double RNA_weight;
65 double xl_weight;
66 double abs_prec_error;
67 double rel_prec_error;
68 RNPxlMarkerIonExtractor::MarkerIonsType marker_ions;
69 double m_H;
70 double m_2H;
71 double m_3H;
72 double m_4H;
73 int rank;
74 String getString(const String& separator) const;
75
76 };
77
79 struct OPENMS_DLLAPI RNPxlReportRowHeader
80 {
81 static String getString(const String& separator);
82 };
83
85 struct OPENMS_DLLAPI RNPxlReport
86 {
87 static std::vector<RNPxlReportRow> annotate(const PeakMap& spectra, std::vector<PeptideIdentification>& peptide_ids, double marker_ions_tolerance);
88 };
89
90 }
91
92
OpenMS::RNPxlReportRow::RNA
String RNA
Definition: RNPxlReport.h:56
Constants.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RNPxlReportRow::best_localization
String best_localization
Definition: RNPxlReport.h:60
OpenMS::RNPxlReportRow::localization_scores
String localization_scores
Definition: RNPxlReport.h:59
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::RNPxlReportRow::charge
Int charge
Definition: RNPxlReport.h:61
StandardTypes.h
OpenMS::RNPxlReportRow::peptide_weight
double peptide_weight
Definition: RNPxlReport.h:63
OpenMS::RNPxlReportRow::original_mz
double original_mz
Definition: RNPxlReport.h:54
OpenMS::RNPxlReportRowHeader
create header line
Definition: RNPxlReport.h:79
OpenMS::RNPxlReportRow::no_id
bool no_id
Definition: RNPxlReport.h:52
OpenMS::RNPxlReportRow::abs_prec_error
double abs_prec_error
Definition: RNPxlReport.h:66
OpenMS::RNPxlReportRow::best_localization_score
double best_localization_score
Definition: RNPxlReport.h:58
OpenMS::RNPxlReportRow
struct to hold a single report line
Definition: RNPxlReport.h:50
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::RNPxlReportRow::m_4H
double m_4H
Definition: RNPxlReport.h:72
MSExperiment.h
OpenMS::RNPxlReportRow::accessions
String accessions
Definition: RNPxlReport.h:55
OpenMS::RNPxlReportRow::rel_prec_error
double rel_prec_error
Definition: RNPxlReport.h:67
MSSpectrum.h
OpenMS::RNPxlReport
create report
Definition: RNPxlReport.h:85
OpenMS::RNPxlReportRow::m_2H
double m_2H
Definition: RNPxlReport.h:70
OpenMS::RNPxlReportRow::rank
int rank
Definition: RNPxlReport.h:73
OpenMS::RNPxlReportRow::score
double score
Definition: RNPxlReport.h:62
RNPxlMarkerIonExtractor.h
OpenMS::RNPxlReportRow::rt
double rt
Definition: RNPxlReport.h:53
int
OpenMS::RNPxlReportRow::RNA_weight
double RNA_weight
Definition: RNPxlReport.h:64
ListUtilsIO.h
OpenMS::RNPxlReportRow::peptide
String peptide
Definition: RNPxlReport.h:57
OpenMS::RNPxlMarkerIonExtractor::MarkerIonsType
std::map< String, std::vector< std::pair< double, double > > > MarkerIonsType
name to mass-intensity pair
Definition: RNPxlMarkerIonExtractor.h:49
OpenMS::RNPxlReportRow::marker_ions
RNPxlMarkerIonExtractor::MarkerIonsType marker_ions
Definition: RNPxlReport.h:68
OpenMS::RNPxlReportRow::xl_weight
double xl_weight
Definition: RNPxlReport.h:65
OpenMS::RNPxlReportRow::m_H
double m_H
Definition: RNPxlReport.h:69
OpenMS::RNPxlReportRow::m_3H
double m_3H
Definition: RNPxlReport.h:71