ProteoWizard
Index_mzML.hpp
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1 //
2 // $Id$
3 //
4 //
5 // Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
6 //
7 // Copyright 2011 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.
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13 // http://www.apache.org/licenses/LICENSE-2.0
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21 
22 
23 #ifndef _INDEX_MZML_HPP_
24 #define _INDEX_MZML_HPP_
25 
26 
28 #include "MSData.hpp"
29 #include <boost/shared_ptr.hpp>
30 #include <iosfwd>
31 #include <map>
32 
33 
34 namespace pwiz {
35 namespace msdata {
36 
37 struct SpectrumIdentityFromXML; // forward ref
38 
40 {
41  Index_mzML(boost::shared_ptr<std::istream> is, const MSData& msd);
42 
43  void recreate();
44 
45  size_t spectrumCount() const;
46  const SpectrumIdentityFromXML& spectrumIdentity(size_t index) const;
47  size_t findSpectrumId(const std::string& id) const;
48  IndexList findSpectrumBySpotID(const std::string& spotID) const;
49  const std::map<std::string,std::string>& legacyIdRefToNativeId() const;
50 
51  size_t chromatogramCount() const;
52  const ChromatogramIdentity& chromatogramIdentity(size_t index) const;
53  size_t findChromatogramId(const std::string& id) const;
54 
55  private:
56  struct Impl;
57  boost::shared_ptr<Impl> impl_;
58 };
59 
60 
61 typedef boost::shared_ptr<Index_mzML> Index_mzML_Ptr;
62 
63 
64 } // namespace msdata
65 } // namespace pwiz
66 
67 
68 #endif // _INDEX_MZML_HPP_
pwiz
Definition: ChromatogramList_Filter.hpp:36
MSData.hpp
pwiz::msdata::IndexList
Definition: MSData.hpp:628
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition: Export.hpp:32
pwiz::msdata::ChromatogramIdentity
Identifying information for a chromatogram.
Definition: MSData.hpp:490
Export.hpp
pwiz::msdata::Index_mzML::chromatogramCount
size_t chromatogramCount() const
pwiz::msdata::Index_mzML::findChromatogramId
size_t findChromatogramId(const std::string &id) const
pwiz::msdata::Index_mzML
Definition: Index_mzML.hpp:40
pwiz::msdata::Index_mzML::Index_mzML
Index_mzML(boost::shared_ptr< std::istream > is, const MSData &msd)
pwiz::msdata::SpectrumIdentityFromXML
Identifying information for a spectrum subclassed to add private information for faster file IO in mz...
Definition: IO.hpp:44
pwiz::msdata::Index_mzML::findSpectrumBySpotID
IndexList findSpectrumBySpotID(const std::string &spotID) const
pwiz::msdata::Index_mzML::findSpectrumId
size_t findSpectrumId(const std::string &id) const
pwiz::msdata::Index_mzML::spectrumCount
size_t spectrumCount() const
pwiz::msdata::Index_mzML::spectrumIdentity
const SpectrumIdentityFromXML & spectrumIdentity(size_t index) const
pwiz::msdata::Index_mzML::chromatogramIdentity
const ChromatogramIdentity & chromatogramIdentity(size_t index) const
pwiz::msdata::Index_mzML::legacyIdRefToNativeId
const std::map< std::string, std::string > & legacyIdRefToNativeId() const
pwiz::msdata::MSData
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition: MSData.hpp:850
pwiz::msdata::Index_mzML::recreate
void recreate()
pwiz::msdata::Index_mzML_Ptr
boost::shared_ptr< Index_mzML > Index_mzML_Ptr
Definition: Index_mzML.hpp:61
pwiz::msdata::Index_mzML::impl_
boost::shared_ptr< Impl > impl_
Definition: Index_mzML.hpp:56