ProteoWizard
SpectrumList_Bruker.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_BRUKER_HPP_
24#define _SPECTRUMLIST_BRUKER_HPP_
25
35#include <boost/container/flat_map.hpp>
36
37
38namespace pwiz {
39namespace msdata {
40namespace detail {
41
42using boost::shared_ptr;
43
44//
45// SpectrumList_Bruker
46//
48{
49 public:
50
51 virtual size_t size() const;
52 virtual const SpectrumIdentity& spectrumIdentity(size_t index) const;
53 virtual size_t find(const string& id) const;
54 virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const;
55 virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const;
56 virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
57 virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet& msLevelsToCentroid) const;
58 virtual bool hasIonMobility() const;
59 virtual bool hasPASEF() const;
60 virtual bool canConvertIonMobilityAndCCS() const;
61 virtual double ionMobilityToCCS(double inverseK0, double mz, int charge) const;
62 virtual double ccsToIonMobility(double ccs, double mz, int charge) const;
63
64#ifdef PWIZ_READER_BRUKER
66 const string& rootpath,
68 CompassDataPtr compassDataPtr,
69 const Reader::Config& config);
70
71 MSSpectrumPtr getMSSpectrumPtr(size_t index, vendor_api::Bruker::DetailLevel detailLevel) const;
72
73 private:
74
75 MSData& msd_;
76 bfs::path rootpath_;
78 mutable CompassDataPtr compassDataPtr_;
79 const Reader::Config config_;
80 size_t size_;
81 vector<bfs::path> sourcePaths_;
82
83 struct IndexEntry : public SpectrumIdentity
84 {
85 int source;
86 int collection; // -1 for an MS spectrum
87 int scan;
88 };
89
90 vector<IndexEntry> index_;
91
92 // idToIndexMap_["scan=<#>" or "file=<sourceFile::id>"] == index
93 boost::container::flat_map<string, size_t> idToIndexMap_;
94
95 void fillSourceList();
96 void createIndex();
97 //string findPrecursorID(int precursorMsLevel, size_t index) const;
98#endif // PWIZ_READER_BRUKER
99};
100
101} // detail
102} // msdata
103} // pwiz
104
105#endif // _SPECTRUMLIST_BRUKER_HPP_
#define PWIZ_API_DECL
Definition Export.hpp:32
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const
retrieve a spectrum by index
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData) const
retrieve a spectrum by index
virtual double ccsToIonMobility(double ccs, double mz, int charge) const
virtual const SpectrumIdentity & spectrumIdentity(size_t index) const
access to a spectrum index
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual double ionMobilityToCCS(double inverseK0, double mz, int charge) const
virtual bool canConvertIonMobilityAndCCS() const
virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel, const pwiz::util::IntegerSet &msLevelsToCentroid) const
virtual size_t find(const string &id) const
find id in the spectrum index (returns size() on failure)
virtual size_t size() const
returns the number of spectra
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
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