ProteoWizard
pwiz
analysis
spectrum_processing
SpectrumList_TitleMaker.hpp
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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 <a.t> 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 _SPECTRUMLIST_TITLEMAKER_HPP_
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#define _SPECTRUMLIST_TITLEMAKER_HPP_
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#include "
pwiz/utility/misc/Export.hpp
"
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#include "
pwiz/data/msdata/SpectrumListWrapper.hpp
"
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namespace
pwiz
{
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namespace
analysis {
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/// SpectrumList implementation to add (or replace) a spectrum title to each spectrum
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/// according to a user-specified format.
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class
PWIZ_API_DECL
SpectrumList_TitleMaker
:
public
msdata::SpectrumListWrapper
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{
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public
:
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/// The format string recognizes some keywords to replace with the appropriate field:
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/// <RunId> - Run::id
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/// <Index> - SpectrumIdentity::index
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/// <Id> - SpectrumIdentity::id (nativeID)
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/// <ScanNumber> - if the nativeID can be represented as a single number, that number, else index
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/// <ActivationType> - for the first precursor, Activation::cvParamChild("dissociation method")
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/// <IsolationMz> - for the first precursor, IsolationWindow::cvParam("isolation target m/z")
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/// <SelectedIonMz> - for the first selected ion of the first precursor, SelectedIon::cvParam("selected ion m/z")
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/// <ChargeState> - for the first selected ion of the first precursor, SelectedIon::cvParam("charge state")
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/// <SpectrumType> - Spectrum::cvParamChild("spectrum type")
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/// <ScanStartTimeInSeconds> - for the first scan, Scan::cvParam("scan start time") converted to seconds
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/// <ScanStartTimeInMinutes> - for the first scan, Scan::cvParam("scan start time") converted to minutes
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/// <BasePeakMz> - Spectrum::cvParam("base peak m/z")
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/// <BasePeakIntensity> - Spectrum::cvParam("base peak intensity")
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/// <TotalIonCurrent> - Spectrum::cvParam("total ion current")
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/// <IonMobility> - Scan::cvParam("ion mobility drift time") or Scan::cvParam("inverse reduced ion mobility")
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SpectrumList_TitleMaker
(
const
msdata::MSData
& msd,
const
std::string&
format
);
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static
bool
accept
(
const
msdata::SpectrumListPtr
& inner) {
return
true
;}
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virtual
msdata::SpectrumPtr
spectrum(
size_t
index,
bool
getBinaryData =
false
)
const
;
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private
:
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const
msdata::MSData
&
msd_
;
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const
std::string
format_
;
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cv::CVID
nativeIdFormat_
;
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};
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}
// namespace analysis
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}
// namespace pwiz
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#endif // _SPECTRUMLIST_TITLEMAKER_HPP_
pwiz::msdata::SpectrumListPtr
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition:
MSData.hpp:711
pwiz
Definition:
ChromatogramList_Filter.hpp:36
pwiz::msdata::SpectrumListWrapper
Inheritable pass-through implementation for wrapping a SpectrumList.
Definition:
SpectrumListWrapper.hpp:37
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition:
Export.hpp:32
Export.hpp
pwiz::analysis::SpectrumList_TitleMaker::format_
const std::string format_
Definition:
SpectrumList_TitleMaker.hpp:65
pwiz::msdata::detail::Bruker::format
PWIZ_API_DECL Reader_Bruker_Format format(const std::string &path)
returns Bruker format of 'path' if it is a Bruker directory; otherwise returns empty string
pwiz::msdata::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition:
MSData.hpp:573
pwiz::analysis::SpectrumList_TitleMaker::accept
static bool accept(const msdata::SpectrumListPtr &inner)
Definition:
SpectrumList_TitleMaker.hpp:59
pwiz::analysis::SpectrumList_TitleMaker::nativeIdFormat_
cv::CVID nativeIdFormat_
Definition:
SpectrumList_TitleMaker.hpp:66
pwiz::analysis::SpectrumList_TitleMaker
SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user...
Definition:
SpectrumList_TitleMaker.hpp:37
pwiz::msdata::MSData
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition:
MSData.hpp:849
pwiz::analysis::SpectrumList_TitleMaker::msd_
const msdata::MSData & msd_
Definition:
SpectrumList_TitleMaker.hpp:64
SpectrumListWrapper.hpp
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