ProteoWizard
pwiz
data
proteome
Serializer_FASTA.hpp
Go to the documentation of this file.
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//
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// $Id$
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//
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//
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// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
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//
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// Copyright 2009 Vanderbilt University - Nashville, TN 37232
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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 _SERIALIZER_FASTA_HPP_
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#define _SERIALIZER_FASTA_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include "
ProteomeData.hpp
"
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#include "
pwiz/data/common/MemoryIndex.hpp
"
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#include "
pwiz/utility/misc/IterationListener.hpp
"
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namespace
pwiz
{
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namespace
proteome
{
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/// ProteomeData <-> FASTA stream serialization
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class
PWIZ_API_DECL
Serializer_FASTA
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{
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public
:
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/// Serializer_FASTA configuration
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struct
PWIZ_API_DECL
Config
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{
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data::IndexPtr
indexPtr
;
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Config
() : indexPtr(new data::MemoryIndex) {}
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};
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Serializer_FASTA
(
const
Config& config = Config());
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/// write ProteomeData object to ostream as FASTA
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void
write
(std::ostream& os,
const
ProteomeData
& pd,
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const
pwiz::util::IterationListenerRegistry
* iterationListenerRegistry)
const
;
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/// read in ProteomeData object from a FASTA istream
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void
read
(boost::shared_ptr<std::istream> is,
ProteomeData
& pd)
const
;
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private
:
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Config
config_
;
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Serializer_FASTA
(
Serializer_FASTA
&);
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Serializer_FASTA
& operator=(
Serializer_FASTA
&);
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};
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}
// namespace proteome
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}
// namespace pwiz
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#endif // _SERIALIZER_FASTA_HPP_
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IterationListener.hpp
pwiz::proteome::Serializer_FASTA::Config::indexPtr
data::IndexPtr indexPtr
Definition:
Serializer_FASTA.hpp:45
pwiz
Definition:
ChromatogramList_Filter.hpp:36
pwiz::proteome
Definition:
AminoAcid.hpp:35
pwiz::data::IndexPtr
boost::shared_ptr< Index > IndexPtr
Definition:
Index.hpp:72
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition:
Export.hpp:32
pwiz::proteome::Serializer_FASTA
ProteomeData <-> FASTA stream serialization.
Definition:
Serializer_FASTA.hpp:38
pwiz::identdata::IO::write
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
Export.hpp
pwiz::proteome::ProteomeData
Definition:
ProteomeData.hpp:88
pwiz::proteome::Serializer_FASTA::Config::Config
Config()
Definition:
Serializer_FASTA.hpp:47
pwiz::util::IterationListenerRegistry
handles registration of IterationListeners and broadcast of update messages
Definition:
IterationListener.hpp:65
pwiz::proteome::Serializer_FASTA::config_
Config config_
Definition:
Serializer_FASTA.hpp:60
ProteomeData.hpp
pwiz::proteome::Serializer_FASTA::Config
Serializer_FASTA configuration.
Definition:
Serializer_FASTA.hpp:43
MemoryIndex.hpp
pwiz::identdata::IO::read
PWIZ_API_DECL void read(std::istream &is, CV &cv)
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