ProteoWizard
SpectrumList_UIMF.hpp
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1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers .@. 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_UIMF_
24#define _SPECTRUMLIST_UIMF_
25
26
34#include <boost/container/flat_map.hpp>
35//#include "pwiz/analysis/spectrum_processing/SpectrumList_3D.hpp"
36
37
38#ifdef PWIZ_READER_UIMF
39#include "pwiz_aux/msrc/utility/vendor_api/UIMF/UIMFReader.hpp"
41#include <boost/thread.hpp>
42using namespace pwiz::vendor_api::UIMF;
43#endif // PWIZ_READER_UIMF
44
45
46namespace pwiz {
47namespace msdata {
48namespace detail {
49
50using boost::shared_ptr;
51
53{
54 public:
55
56 virtual size_t size() const;
57 virtual const SpectrumIdentity& spectrumIdentity(size_t index) const;
58 virtual size_t find(const string& id) const;
59 virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const;
60 virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const;
61
62 //virtual pwiz::analysis::Spectrum3DPtr spectrum3d(double scanStartTime, const boost::icl::interval_set<double>& driftTimeRanges) const;
63
64#ifdef PWIZ_READER_UIMF
65 SpectrumList_UIMF(const MSData& msd, UIMFReaderPtr rawfile, const Reader::Config& config);
66
67 private:
68
69 const MSData& msd_;
70 UIMFReaderPtr rawfile_;
71 Reader::Config config_;
72 mutable size_t size_;
73 mutable boost::mutex readMutex;
74
75 mutable util::once_flag_proxy indexInitialized_;
76
77 struct IndexEntry : public SpectrumIdentity
78 {
79 };
80
81 mutable vector<IndexEntry> index_;
82 mutable map<string, size_t> idToIndexMap_;
83 mutable boost::container::flat_map<double, size_t> scanTimeToFrameMap_;
84
85 void createIndex() const;
86#endif // PWIZ_READER_UIMF
87};
88
89
90} // detail
91} // msdata
92} // pwiz
93
94#endif // _SPECTRUMLIST_UIMF_
#define PWIZ_API_DECL
Definition Export.hpp:32
common functionality for base SpectrumList implementations
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const
retrieve a spectrum by index
virtual size_t find(const string &id) const
find id in the spectrum index (returns size() on failure)
virtual const SpectrumIdentity & spectrumIdentity(size_t index) const
access to a spectrum index
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const
retrieve a spectrum by index
virtual size_t size() const
returns the number of spectra
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
Reader configuration.
Definition Reader.hpp:45
Identifying information for a spectrum.
Definition MSData.hpp:471