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
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
// --------------------------------------------------------------------------
// 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: Chris Bielow $
// $Authors: Chris Bielow, Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FILTERING/TRANSFORMERS/SpectraMerger.h>
#include <algorithm>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page TOPP_SpectraMerger SpectraMerger
@brief Allows to add up several spectra.
<center>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. predecessor tools </td>
<td VALIGN="middle" ROWSPAN=2> \f$ \longrightarrow \f$ SpectraMerger \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> any tool operating on MS peak data @n (in mzML format) </td>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> any tool operating on MS peak data @n (in mzML format)</td>
</tr>
</table>
</center>
@experimental This TOPP-tool is not well tested and not all features might be properly implemented and tested!
This tool can add several consecutive scans, increasing S/N ratio (for MS1 and above) or merge scans which stem from similar precursors (for MS2 and above).
In any case, the number of scans will be reduced.
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_SpectraMerger.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_SpectraMerger.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPSpectraMerger :
public TOPPBase
{
public:
TOPPSpectraMerger() :
TOPPBase("SpectraMerger", "Merges spectra (each MS level separately), increasing S/N ratios.")
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Input mzML file.");
setValidFormats_("in", StringList::create("mzML"));
registerOutputFile_("out", "<file>", "", "Output mzML file with merged spectra.");
setValidFormats_("out", StringList::create("mzML"));
registerStringOption_("merging_method", "<method>", "block_method", "Method of merging which should be used.", false);
setValidStrings_("merging_method", StringList::create("precursor_method,block_method"));
registerSubsection_("algorithm", "Algorithm section for merging spectra");
}
Param getSubsectionDefaults_(const String & /*section*/) const
{
return SpectraMerger().getParameters();
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in(getStringOption_("in"));
String out(getStringOption_("out"));
String merging_method(getStringOption_("merging_method"));
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
FileHandler fh;
FileTypes::Type in_type = fh.getType(in);
PeakMap exp;
fh.loadExperiment(in, exp, in_type, log_type_);
exp.sortSpectra();
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
SpectraMerger merger;
merger.setParameters(getParam_().copy("algorithm:", true));
if (merging_method == "precursor_method")
{
merger.mergeSpectraPrecursors(exp);
}
else if (merging_method == "block_method")
{
merger.mergeSpectraBlockWise(exp);
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
fh.storeExperiment(out, exp, log_type_);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPSpectraMerger tool;
return tool.main(argc, argv);
}
/// @endcond
|
