1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
|
// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_MZDATAFILE_H
#define OPENMS_FORMAT_MZDATAFILE_H
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/HANDLERS/MzDataHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/DocumentIdentifier.h>
namespace OpenMS
{
/**
@brief File adapter for MzData files
@ingroup FileIO
*/
class OPENMS_DLLAPI MzDataFile :
public Internal::XMLFile,
public ProgressLogger
{
public:
///Default constructor
MzDataFile();
///Destructor
~MzDataFile();
/// Mutable access to the options for loading/storing
PeakFileOptions & getOptions();
/// Non-mutable access to the options for loading/storing
const PeakFileOptions & getOptions() const;
/// set options for loading/storing
void setOptions(const PeakFileOptions &);
/**
@brief Loads a map from a MzData file.
@p map has to be a MSExperiment or have the same interface.
@exception Exception::FileNotFound is thrown if the file could not be opened
@exception Exception::ParseError is thrown if an error occurs during parsing
*/
template <typename MapType>
void load(const String & filename, MapType & map)
{
map.reset();
//set DocumentIdentifier
map.setLoadedFileType(filename);
map.setLoadedFilePath(filename);
Internal::MzDataHandler<MapType> handler(map, filename, schema_version_, *this);
handler.setOptions(options_);
parse_(filename, &handler);
}
/**
@brief Stores a map in a MzData file.
@p map has to be a MSExperiment or have the same interface.
@exception Exception::UnableToCreateFile is thrown if the file could not be created
*/
template <typename MapType>
void store(const String & filename, const MapType & map) const
{
Internal::MzDataHandler<MapType> handler(map, filename, schema_version_, *this);
handler.setOptions(options_);
save_(filename, &handler);
}
/**
@brief Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
@param filename File name of the file to be checked.
@param errors Errors during the validation are returned in this output parameter.
@param warnings Warnings during the validation are returned in this output parameter.
@exception Exception::FileNotFound is thrown if the file could not be opened
*/
bool isSemanticallyValid(const String & filename, StringList & errors, StringList & warnings);
private:
/// Options for loading / storing
PeakFileOptions options_;
};
} // namespace OpenMS
#endif // OPENMS_FOMAT_MZXMLFILE_H
|
