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Pep2MzIdentTest.cpp
Go to the documentation of this file.
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//
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// $Id: Pep2MzIdentTest.cpp 4129 2012-11-20 00:05:37Z chambm $
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//
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// Original author: Robert Burke <robert.burke@proteowizard.org>
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//
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// Copyright 2009 Spielberg Family Center for Applied Proteomics
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// University of Southern California, Los Angeles, California 90033
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//
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// Licensed under the Apache License, Version 2.0 (the "License");
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// you may not use this file except in compliance with the License.
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// You may obtain a copy of the License at
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//
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// http://www.apache.org/licenses/LICENSE-2.0
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//
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// Unless required by applicable law or agreed to in writing, software
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// distributed under the License is distributed on an "AS IS" BASIS,
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// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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// See the License for the specific language governing permissions and
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// limitations under the License.
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//
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#include "
Pep2MzIdent.hpp
"
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#include "
Serializer_mzid.hpp
"
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#include <iostream>
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#include <string>
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using namespace
pwiz;
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using namespace
pwiz::identdata;
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using namespace
pwiz::data::pepxml;
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ostream*
os_
= NULL;
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const
char
*
samplePepXML
=
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"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
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"<msms_pipeline_analysis>\n"
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"<msms_run_summary>\n"
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"<spectrum_query start_scan=\"1\" end_scan=\"2\" precursor_neutral_mass=\"1.0\" assumed_charge=\"1\" retention_time_sec=\"2.0\">\n"
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"<search_result>\n"
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"<search_hit peptide=\"BUCKLEMYSHOE\">\n"
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"<analysis_result analysis=\"peptideprophet\">\n"
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"<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
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"<search_score_summary>\n"
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"</search_score_summary>\n"
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"</peptideprophet_result>\n"
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"</analysis_result>\n"
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"</search_hit>\n"
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"</search_result>\n"
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"</spectrum_query>\n"
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"<spectrum_query start_scan=\"3\" end_scan=\"4\" precursor_neutral_mass=\"3.0\" assumed_charge=\"1\" retention_time_sec=\"4.0\">\n"
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"<search_result>\n"
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"<search_hit peptide=\"SHUTTHEDOOR\">\n"
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"<analysis_result analysis=\"peptideprophet\">\n"
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"<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
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"<search_score_summary>\n"
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"</search_score_summary>\n"
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"</peptideprophet_result>\n"
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"</analysis_result>\n"
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"</search_hit>\n"
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"</search_result>\n"
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"</spectrum_query>\n"
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"<spectrum_query start_scan=\"5\" end_scan=\"6\" precursor_neutral_mass=\"5.0\" assumed_charge=\"1\" retention_time_sec=\"6.0\">\n"
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"<search_result>\n"
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"<search_hit peptide=\"PICKUPSTICKS\">\n"
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"<analysis_result analysis=\"peptideprophet\">\n"
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"<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
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"<search_score_summary>\n"
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"</search_score_summary>\n"
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"</peptideprophet_result>\n"
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"</analysis_result>\n"
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"</search_hit>\n"
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"</search_result>\n"
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"</spectrum_query>\n"
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"<spectrum_query start_scan=\"7\" end_scan=\"8\" precursor_neutral_mass=\"7.0\" assumed_charge=\"1\" retention_time_sec=\"8.0\">\n"
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"<search_result>\n"
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"<search_hit peptide=\"LAYTHEMSTRAIGHT\">\n"
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"<analysis_result analysis=\"peptideprophet\">\n"
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"<peptideprophet_result probability=\"0.900\" all_ntt_prob=\"(0,0,0.900)\">\n"
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"<search_score_summary>\n"
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"</search_score_summary>\n"
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"</peptideprophet_result>\n"
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"</analysis_result>\n"
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"</search_hit>\n"
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"</search_result>\n"
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"</spectrum_query>\n"
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"</msms_run_summary>\n"
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"</msms_pipeline_analysis>\n"
;
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void
test
()
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{
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istringstream iss(
samplePepXML
);
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MSMSPipelineAnalysis
mspa;
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mspa.
read
(iss);
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Pep2MzIdent
translator(mspa);
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IdentDataPtr
result(translator.
translate
());
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Serializer_mzIdentML
serializer;
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ostringstream oss;
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serializer.
write
(oss, *result);
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if
(
os_
)
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*
os_
<< oss.str() << endl;
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}
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int
main
(
int
argc,
char
** argv)
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{
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if
(argc>1 && !strcmp(argv[1],
"-v"
))
os_
= &cout;
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cout <<
"\ntesting Pep2MzIdent ... \n"
<< endl;
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test
();
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return
0;
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}
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