ProteoWizard
Index_mzML.hpp
Go to the documentation of this file.
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.
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 _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
34namespace pwiz {
35namespace msdata {
36
37struct 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
61typedef boost::shared_ptr<Index_mzML> Index_mzML_Ptr;
62
63
64} // namespace msdata
65} // namespace pwiz
66
67
68#endif // _INDEX_MZML_HPP_
#define PWIZ_API_DECL
Definition Export.hpp:32
boost::shared_ptr< Index_mzML > Index_mzML_Ptr
Identifying information for a chromatogram.
Definition MSData.hpp:490
const std::map< std::string, std::string > & legacyIdRefToNativeId() const
size_t chromatogramCount() const
size_t findChromatogramId(const std::string &id) const
const SpectrumIdentityFromXML & spectrumIdentity(size_t index) const
Index_mzML(boost::shared_ptr< std::istream > is, const MSData &msd)
size_t findSpectrumId(const std::string &id) const
boost::shared_ptr< Impl > impl_
IndexList findSpectrumBySpotID(const std::string &spotID) const
size_t spectrumCount() const
const ChromatogramIdentity & chromatogramIdentity(size_t index) const
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition MSData.hpp:850
Identifying information for a spectrum subclassed to add private information for faster file IO in mz...
Definition IO.hpp:44