ProteoWizard
PepXMLCat.hpp
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1//
2// $Id$
3//
4//
5// Original author: Darren Kessner <darren@proteowizard.org>
6//
7// Copyright 2007 Spielberg Family Center for Applied Proteomics
8// Cedars-Sinai Medical Center, Los Angeles, California 90048
9//
10// Licensed under the Apache License, Version 2.0 (the "License");
11// you may not use this file except in compliance with the License.
12// You may obtain a copy of the License at
13//
14// http://www.apache.org/licenses/LICENSE-2.0
15//
16// Unless required by applicable law or agreed to in writing, software
17// distributed under the License is distributed on an "AS IS" BASIS,
18// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19// See the License for the specific language governing permissions and
20// limitations under the License.
21//
22
23
24#ifndef _PEPXMLCAT_HPP_
25#define _PEPXMLCAT_HPP_
26
28#include <string>
29#include <ostream>
30#include <vector>
31#include <utility>
32
33namespace pwiz {
34namespace analysis {
35
36
38{
39public:
40
42 {
43 std::string pepxmlfile;
44 char delim;
45 char record;
46 char quote;
47 bool headers;
48
50 };
51
53 {
54 int index;
56 std::string spectrum;
57 double mz;
58
59 // Tandem
60 double hyperscore;
61 double nextscore;
62 double expect;
63
64
65 // SEQUEST
66 double xcorr;
67 double deltacn;
69 double spscore;
70 int sprank;
71
72 // PHENYX
73 double zscore;
74 double origScore;
75
76 // MASCOT
77 double ionscore;
78 double id_score;
80
81 // COMET
83 double delta;
84 //double zscore; covered above
85
86 std::vector<std::pair< std::string, std::string> > search_scores;
87
88 // PROBID
89 double bays_score;
90 // double zscore; covered above
91
92 std::string m_ions;
93 std::string peptide;
94 std::string protein;
95 int ntt;
96
98 };
99
100 typedef std::vector<record> set;
101 typedef std::vector<record>::iterator iterator;
102 typedef std::vector<record>::const_iterator const_iterator;
103
104 PepxmlRecordReader(const Config& _config);
106
107 bool open(const std::string& file);
108 void close();
109
110 void print_headers(std::ostream& os) const;
111
114
117
118 friend PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, PepxmlRecordReader& prr);
119private:
122 std::string search_engine;
123};
124
125PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, PepxmlRecordReader& prr);
126
127
128} // namespace analysis
129} // namespace pwiz
130
131#endif // _PEPXMLCAT_HPP_
132
133
#define PWIZ_API_DECL
Definition Export.hpp:32
std::vector< record >::iterator iterator
const_iterator begin() const
friend PWIZ_API_DECL std::ostream & operator<<(std::ostream &os, PepxmlRecordReader &prr)
PepxmlRecordReader(const Config &_config)
bool open(const std::string &file)
std::vector< record >::const_iterator const_iterator
const_iterator end() const
void print_headers(std::ostream &os) const
PWIZ_API_DECL std::ostream & operator<<(std::ostream &os, PepxmlRecordReader &prr)
std::vector< std::pair< std::string, std::string > > search_scores
Definition PepXMLCat.hpp:86