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PepXMLCat.hpp
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//
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// $Id: PepXMLCat.hpp 2503 2011-02-07 18:13:48Z chambm $
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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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