ProteoWizard
Pep2MzIdentTest.cpp
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1 //
2 // $Id: Pep2MzIdentTest.cpp 4129 2012-11-20 00:05:37Z chambm $
3 //
4 // Original author: Robert Burke <robert.burke@proteowizard.org>
5 //
6 // Copyright 2009 Spielberg Family Center for Applied Proteomics
7 // University of Southern California, Los Angeles, California 90033
8 //
9 // Licensed under the Apache License, Version 2.0 (the "License");
10 // you may not use this file except in compliance with the License.
11 // You may obtain a copy of the License at
12 //
13 // http://www.apache.org/licenses/LICENSE-2.0
14 //
15 // Unless required by applicable law or agreed to in writing, software
16 // distributed under the License is distributed on an "AS IS" BASIS,
17 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18 // See the License for the specific language governing permissions and
19 // limitations under the License.
20 //
21 
22 #include "Pep2MzIdent.hpp"
23 #include "Serializer_mzid.hpp"
24 #include <iostream>
25 #include <string>
26 
27 using namespace pwiz;
28 using namespace pwiz::identdata;
29 using namespace pwiz::data::pepxml;
30 
31 ostream* os_ = NULL;
32 
33 const char* samplePepXML =
34  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
35  "<msms_pipeline_analysis>\n"
36  "<msms_run_summary>\n"
37  "<spectrum_query start_scan=\"1\" end_scan=\"2\" precursor_neutral_mass=\"1.0\" assumed_charge=\"1\" retention_time_sec=\"2.0\">\n"
38  "<search_result>\n"
39  "<search_hit peptide=\"BUCKLEMYSHOE\">\n"
40  "<analysis_result analysis=\"peptideprophet\">\n"
41  "<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
42  "<search_score_summary>\n"
43  "</search_score_summary>\n"
44  "</peptideprophet_result>\n"
45  "</analysis_result>\n"
46  "</search_hit>\n"
47  "</search_result>\n"
48  "</spectrum_query>\n"
49  "<spectrum_query start_scan=\"3\" end_scan=\"4\" precursor_neutral_mass=\"3.0\" assumed_charge=\"1\" retention_time_sec=\"4.0\">\n"
50  "<search_result>\n"
51  "<search_hit peptide=\"SHUTTHEDOOR\">\n"
52  "<analysis_result analysis=\"peptideprophet\">\n"
53  "<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
54  "<search_score_summary>\n"
55  "</search_score_summary>\n"
56  "</peptideprophet_result>\n"
57  "</analysis_result>\n"
58  "</search_hit>\n"
59  "</search_result>\n"
60  "</spectrum_query>\n"
61  "<spectrum_query start_scan=\"5\" end_scan=\"6\" precursor_neutral_mass=\"5.0\" assumed_charge=\"1\" retention_time_sec=\"6.0\">\n"
62  "<search_result>\n"
63  "<search_hit peptide=\"PICKUPSTICKS\">\n"
64  "<analysis_result analysis=\"peptideprophet\">\n"
65  "<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
66  "<search_score_summary>\n"
67  "</search_score_summary>\n"
68  "</peptideprophet_result>\n"
69  "</analysis_result>\n"
70  "</search_hit>\n"
71  "</search_result>\n"
72  "</spectrum_query>\n"
73  "<spectrum_query start_scan=\"7\" end_scan=\"8\" precursor_neutral_mass=\"7.0\" assumed_charge=\"1\" retention_time_sec=\"8.0\">\n"
74  "<search_result>\n"
75  "<search_hit peptide=\"LAYTHEMSTRAIGHT\">\n"
76  "<analysis_result analysis=\"peptideprophet\">\n"
77  "<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
78  "<search_score_summary>\n"
79  "</search_score_summary>\n"
80  "</peptideprophet_result>\n"
81  "</analysis_result>\n"
82  "</search_hit>\n"
83  "</search_result>\n"
84  "</spectrum_query>\n"
85  "</msms_run_summary>\n"
86  "</msms_pipeline_analysis>\n";
87 
88 
89 void test()
90 {
91  istringstream iss(samplePepXML);
93  mspa.read(iss);
94 
95  Pep2MzIdent translator(mspa);
96  IdentDataPtr result(translator.translate());
97 
98  Serializer_mzIdentML serializer;
99  ostringstream oss;
100  serializer.write(oss, *result);
101 
102  if (os_)
103  *os_ << oss.str() << endl;
104 
105 }
106 
107 int main(int argc, char** argv)
108 {
109  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
110 
111  cout << "\ntesting Pep2MzIdent ... \n" << endl;
112  test();
113  return 0;
114 }