ProteoWizard
SpectrumList_TitleMaker.hpp
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1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
6//
7// Copyright 2009 Vanderbilt University - Nashville, TN 37232
8//
9// Licensed under the Apache License, Version 2.0 (the "License");
10// you may not use this file except in compliance with the License.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
22
23#ifndef _SPECTRUMLIST_TITLEMAKER_HPP_
24#define _SPECTRUMLIST_TITLEMAKER_HPP_
25
26
29
30
31namespace pwiz {
32namespace analysis {
33
34
35/// SpectrumList implementation to add (or replace) a spectrum title to each spectrum
36/// according to a user-specified format.
38{
39 public:
40
41 /// The format string recognizes some keywords to replace with the appropriate field:
42 /// <RunId> - Run::id
43 /// <Index> - SpectrumIdentity::index
44 /// <Id> - SpectrumIdentity::id (nativeID)
45 /// <ScanNumber> - if the nativeID can be represented as a single number, that number, else index
46 /// <ActivationType> - for the first precursor, Activation::cvParamChild("dissociation method")
47 /// <IsolationMz> - for the first precursor, IsolationWindow::cvParam("isolation target m/z")
48 /// <SelectedIonMz> - for the first selected ion of the first precursor, SelectedIon::cvParam("selected ion m/z")
49 /// <ChargeState> - for the first selected ion of the first precursor, SelectedIon::cvParam("charge state")
50 /// <SpectrumType> - Spectrum::cvParamChild("spectrum type")
51 /// <ScanStartTimeInSeconds> - for the first scan, Scan::cvParam("scan start time") converted to seconds
52 /// <ScanStartTimeInMinutes> - for the first scan, Scan::cvParam("scan start time") converted to minutes
53 /// <BasePeakMz> - Spectrum::cvParam("base peak m/z")
54 /// <BasePeakIntensity> - Spectrum::cvParam("base peak intensity")
55 /// <TotalIonCurrent> - Spectrum::cvParam("total ion current")
56 /// <IonMobility> - Scan::cvParam("ion mobility drift time") or Scan::cvParam("inverse reduced ion mobility")
57 SpectrumList_TitleMaker(const msdata::MSData& msd, const std::string& format);
58
59 static bool accept(const msdata::SpectrumListPtr& inner) {return true;}
60
61 virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData = false) const;
62
63 private:
65 const std::string format_;
67};
68
69
70} // namespace analysis
71} // namespace pwiz
72
73
74#endif // _SPECTRUMLIST_TITLEMAKER_HPP_
#define PWIZ_API_DECL
Definition Export.hpp:32
SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user...
SpectrumList_TitleMaker(const msdata::MSData &msd, const std::string &format)
The format string recognizes some keywords to replace with the appropriate field: <RunId> - Run::id <...
static bool accept(const msdata::SpectrumListPtr &inner)
virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData=false) const
retrieve a spectrum by index
Inheritable pass-through implementation for wrapping a SpectrumList.
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition MSData.hpp:711
boost::shared_ptr< Spectrum > SpectrumPtr
Definition MSData.hpp:573
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition MSData.hpp:850