ProteoWizard
pwiz
data
proteome
Reader_FASTA.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 _READER_FASTA_HPP_
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#define _READER_FASTA_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include "
ProteomeData.hpp
"
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#include "
Reader.hpp
"
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namespace
pwiz
{
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namespace
proteome
{
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/// FASTA -> ProteomeData stream serialization
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class
PWIZ_API_DECL
Reader_FASTA
:
public
Reader
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{
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public
:
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/// Reader_FASTA configuration
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struct
PWIZ_API_DECL
Config
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{
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/// read with a side-by-side index
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bool
indexed
;
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Config
() {}
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};
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/// constructor
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Reader_FASTA
(
const
Config& config = Config());
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const
char
*
getType
()
const
{
return
"FASTA"
;}
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virtual
std::string identify(
const
std::string& uri,
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boost::shared_ptr<std::istream> uriStreamPtr)
const
;
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/// fill in the ProteomeData structure
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virtual
void
read
(
const
std::string& uri,
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boost::shared_ptr<std::istream> uriStreamPtr,
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ProteomeData
& result)
const
;
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private
:
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Config
config_
;
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Reader_FASTA
(
Reader_FASTA
&);
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Reader_FASTA
& operator=(
Reader_FASTA
&);
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};
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PWIZ_API_DECL
std::ostream&
operator<<
(std::ostream& os,
const
Reader_FASTA::Config
& config);
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}
// namespace proteome
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}
// namespace pwiz
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#endif // _READER_FASTA_HPP_
Reader.hpp
pwiz::proteome::operator<<
PWIZ_API_DECL std::ostream & operator<<(std::ostream &os, const data::Diff< ProteomeData, DiffConfig > &diff)
pwiz::proteome::Reader_FASTA
FASTA -> ProteomeData stream serialization.
Definition:
Reader_FASTA.hpp:38
pwiz
Definition:
ChromatogramList_Filter.hpp:36
pwiz::proteome
Definition:
AminoAcid.hpp:35
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition:
Export.hpp:32
Export.hpp
pwiz::proteome::Reader
interface for file readers
Definition:
Reader.hpp:36
pwiz::proteome::Reader_FASTA::Config::Config
Config()
Definition:
Reader_FASTA.hpp:48
pwiz::proteome::ProteomeData
Definition:
ProteomeData.hpp:88
ProteomeData.hpp
pwiz::proteome::Reader_FASTA::Config::indexed
bool indexed
read with a side-by-side index
Definition:
Reader_FASTA.hpp:46
pwiz::proteome::Reader_FASTA::getType
const char * getType() const
Definition:
Reader_FASTA.hpp:54
pwiz::proteome::Reader_FASTA::Config
Reader_FASTA configuration.
Definition:
Reader_FASTA.hpp:43
pwiz::proteome::Reader_FASTA::config_
Config config_
Definition:
Reader_FASTA.hpp:65
pwiz::identdata::IO::read
PWIZ_API_DECL void read(std::istream &is, CV &cv)
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