ProteoWizard
pwiz
analysis
passive
PepXMLCat.hpp
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//
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// $Id$
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//
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//
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// Original author: Darren Kessner <darren@proteowizard.org>
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//
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// Copyright 2007 Spielberg Family Center for Applied Proteomics
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// Cedars-Sinai Medical Center, Los Angeles, California 90048
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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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#ifndef _PEPXMLCAT_HPP_
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#define _PEPXMLCAT_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include <string>
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#include <ostream>
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#include <vector>
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#include <utility>
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namespace
pwiz
{
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namespace
analysis {
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class
PWIZ_API_DECL
PepxmlRecordReader
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{
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public
:
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struct
PWIZ_API_DECL
Config
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{
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std::string
pepxmlfile
;
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char
delim
;
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char
record
;
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char
quote
;
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bool
headers
;
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Config
();
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};
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struct
PWIZ_API_DECL
record
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{
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int
index
;
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int
hit_rank
;
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std::string
spectrum
;
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double
mz
;
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// Tandem
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double
hyperscore
;
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double
nextscore
;
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double
expect
;
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// SEQUEST
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double
xcorr
;
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double
deltacn
;
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double
deltacnstar
;
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double
spscore
;
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int
sprank
;
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// PHENYX
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double
zscore
;
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double
origScore
;
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// MASCOT
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double
ionscore
;
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double
id_score
;
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double
homology_score
;
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// COMET
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double
dot_product
;
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double
delta
;
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//double zscore; covered above
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std::vector<std::pair< std::string, std::string> >
search_scores
;
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// PROBID
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double
bays_score
;
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// double zscore; covered above
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std::string
m_ions
;
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std::string
peptide
;
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std::string
protein
;
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int
ntt
;
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record
();
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};
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typedef
std::vector<record>
set
;
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typedef
std::vector<record>::iterator
iterator
;
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typedef
std::vector<record>::const_iterator
const_iterator
;
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PepxmlRecordReader
(
const
Config
& _config);
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virtual
~
PepxmlRecordReader
();
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bool
open(
const
std::string& file);
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void
close();
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void
print_headers(std::ostream& os)
const
;
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const_iterator
begin()
const
;
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const_iterator
end()
const
;
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iterator
begin();
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iterator
end();
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friend
PWIZ_API_DECL
std::ostream&
operator<<
(std::ostream& os,
PepxmlRecordReader
& prr);
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private
:
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Config
config
;
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set
recordset
;
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std::string
search_engine
;
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};
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PWIZ_API_DECL
std::ostream&
operator<<
(std::ostream& os,
PepxmlRecordReader
& prr);
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}
// namespace analysis
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}
// namespace pwiz
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#endif // _PEPXMLCAT_HPP_
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pwiz::analysis::PepxmlRecordReader::recordset
set recordset
Definition:
PepXMLCat.hpp:121
pwiz::analysis::PepxmlRecordReader::Config::headers
bool headers
Definition:
PepXMLCat.hpp:47
pwiz::analysis::PepxmlRecordReader::iterator
std::vector< record >::iterator iterator
Definition:
PepXMLCat.hpp:101
pwiz::analysis::PepxmlRecordReader::record::hyperscore
double hyperscore
Definition:
PepXMLCat.hpp:60
pwiz::analysis::PepxmlRecordReader::record::deltacn
double deltacn
Definition:
PepXMLCat.hpp:67
pwiz::analysis::PepxmlRecordReader
Definition:
PepXMLCat.hpp:37
pwiz
Definition:
ChromatogramList_Filter.hpp:36
pwiz::analysis::PepxmlRecordReader::record::expect
double expect
Definition:
PepXMLCat.hpp:62
pwiz::analysis::PepxmlRecordReader::record::spscore
double spscore
Definition:
PepXMLCat.hpp:69
pwiz::analysis::PepxmlRecordReader::record::m_ions
std::string m_ions
Definition:
PepXMLCat.hpp:92
pwiz::analysis::PepxmlRecordReader::record::xcorr
double xcorr
Definition:
PepXMLCat.hpp:66
pwiz::analysis::PepxmlRecordReader::search_engine
std::string search_engine
Definition:
PepXMLCat.hpp:122
pwiz::analysis::PepxmlRecordReader::record::zscore
double zscore
Definition:
PepXMLCat.hpp:73
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition:
Export.hpp:32
pwiz::analysis::PepxmlRecordReader::Config::quote
char quote
Definition:
PepXMLCat.hpp:46
pwiz::analysis::PepxmlRecordReader::Config::record
char record
Definition:
PepXMLCat.hpp:45
pwiz::analysis::PepxmlRecordReader::const_iterator
std::vector< record >::const_iterator const_iterator
Definition:
PepXMLCat.hpp:102
pwiz::analysis::PepxmlRecordReader::record::peptide
std::string peptide
Definition:
PepXMLCat.hpp:93
Export.hpp
pwiz::analysis::PepxmlRecordReader::Config
Definition:
PepXMLCat.hpp:41
pwiz::analysis::PepxmlRecordReader::record::bays_score
double bays_score
Definition:
PepXMLCat.hpp:89
pwiz::analysis::PepxmlRecordReader::record::delta
double delta
Definition:
PepXMLCat.hpp:83
pwiz::analysis::PepxmlRecordReader::record::protein
std::string protein
Definition:
PepXMLCat.hpp:94
pwiz::analysis::PepxmlRecordReader::record::dot_product
double dot_product
Definition:
PepXMLCat.hpp:82
pwiz::analysis::PepxmlRecordReader::record::search_scores
std::vector< std::pair< std::string, std::string > > search_scores
Definition:
PepXMLCat.hpp:86
pwiz::analysis::PepxmlRecordReader::record::nextscore
double nextscore
Definition:
PepXMLCat.hpp:61
pwiz::analysis::PepxmlRecordReader::record::hit_rank
int hit_rank
Definition:
PepXMLCat.hpp:55
pwiz::analysis::PepxmlRecordReader::record::index
int index
Definition:
PepXMLCat.hpp:54
pwiz::proteome::AminoAcid::Info::record
const PWIZ_API_DECL Record & record(Type type)
returns the amino acid's Record by type
pwiz::analysis::PepxmlRecordReader::record::mz
double mz
Definition:
PepXMLCat.hpp:57
pwiz::analysis::operator<<
PWIZ_API_DECL std::ostream & operator<<(std::ostream &os, PepxmlRecordReader &prr)
pwiz::analysis::PepxmlRecordReader::record::deltacnstar
double deltacnstar
Definition:
PepXMLCat.hpp:68
pwiz::analysis::PepxmlRecordReader::record::ionscore
double ionscore
Definition:
PepXMLCat.hpp:77
pwiz::analysis::PepxmlRecordReader::set
std::vector< record > set
Definition:
PepXMLCat.hpp:100
pwiz::analysis::PepxmlRecordReader::Config::pepxmlfile
std::string pepxmlfile
Definition:
PepXMLCat.hpp:43
pwiz::analysis::PepxmlRecordReader::Config::delim
char delim
Definition:
PepXMLCat.hpp:44
pwiz::analysis::PepxmlRecordReader::record::homology_score
double homology_score
Definition:
PepXMLCat.hpp:79
pwiz::analysis::PepxmlRecordReader::record::ntt
int ntt
Definition:
PepXMLCat.hpp:95
pwiz::analysis::PepxmlRecordReader::record
Definition:
PepXMLCat.hpp:52
pwiz::analysis::PepxmlRecordReader::record::origScore
double origScore
Definition:
PepXMLCat.hpp:74
pwiz::analysis::PepxmlRecordReader::record::id_score
double id_score
Definition:
PepXMLCat.hpp:78
pwiz::analysis::PepxmlRecordReader::record::sprank
int sprank
Definition:
PepXMLCat.hpp:70
pwiz::analysis::PepxmlRecordReader::config
Config config
Definition:
PepXMLCat.hpp:120
pwiz::analysis::PepxmlRecordReader::record::spectrum
std::string spectrum
Definition:
PepXMLCat.hpp:56
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