OpenMS
IndexedMzMLDecoder.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2023.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
38 #include <OpenMS/CONCEPT/Types.h>
41 
42 namespace OpenMS
43 {
44 
58  class OPENMS_DLLAPI IndexedMzMLDecoder
59  {
60  public:
61 
63  typedef std::vector< std::pair<std::string, std::streampos> > OffsetVector;
64 
80  int parseOffsets(const String& filename, std::streampos indexoffset, OffsetVector & spectra_offsets, OffsetVector& chromatograms_offsets);
81 
107  std::streampos findIndexListOffset(const String& filename, int buffersize = 1023);
108 
109  protected:
110 
146  int domParseIndexedEnd_(const std::string& in, OffsetVector & spectra_offsets, OffsetVector& chromatograms_offsets);
147  };
148 
149 }
A class to analyze indexedmzML files and extract the offsets of individual tags.
Definition: IndexedMzMLDecoder.h:59
int domParseIndexedEnd_(const std::string &in, OffsetVector &spectra_offsets, OffsetVector &chromatograms_offsets)
Extract data from a string containing an <indexList> tag.
std::streampos findIndexListOffset(const String &filename, int buffersize=1023)
Tries to extract the indexList offset from an indexedmzML.
int parseOffsets(const String &filename, std::streampos indexoffset, OffsetVector &spectra_offsets, OffsetVector &chromatograms_offsets)
Tries to extract the offsets of all spectra and chromatograms from an indexedmzML.
std::vector< std::pair< std::string, std::streampos > > OffsetVector
The vector containing binary offsets.
Definition: IndexedMzMLDecoder.h:63
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48