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
|
// --------------------------------------------------------------------------
// 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: Alexandra Zerck $
// $Authors: Eva Lange $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
#include <OpenMS/FORMAT/MzMLFile.h>
///////////////////////////
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerCWT.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(PeakPickerCWT, "$Id: PeakPickerCWT_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
PeakPickerCWT* ptr = 0;
PeakPickerCWT* nullPointer = 0;
START_SECTION((PeakPickerCWT()))
ptr = new PeakPickerCWT();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION((virtual ~PeakPickerCWT()))
delete ptr;
END_SECTION
//load input and output data
MzMLFile mz_ml_file;
MSExperiment<Peak1D> input, output;
mz_ml_file.load(OPENMS_GET_TEST_DATA_PATH("PeakPickerCWT_test.mzML"),input);
mz_ml_file.load(OPENMS_GET_TEST_DATA_PATH("PeakPickerCWT_test_output.mzML"),output);
//set data type (this is not stored correctly in mzData)
for (Size s=0; s<output.size(); ++s)
{
output[s].setType(SpectrumSettings::PEAKS);
}
//set up PeakPicker
PeakPickerCWT pp;
Param param;
param.setValue("peak_width",0.15);
param.setValue("signal_to_noise",3.);
pp.setParameters(param);
START_SECTION((void pick(const MSSpectrum<> &input, MSSpectrum<> &output)))
MSSpectrum<> spec;
pp.pick(input[0],spec);
// TEST_EQUAL(spec.SpectrumSettings::operator==(output[0]), true)-> are not equal as peak picking step is written to the spectrum settings
for (Size p=0; p<spec.size(); ++p)
{
TEST_REAL_SIMILAR(spec[p].getMZ(), output[0][p].getMZ())
TEST_REAL_SIMILAR(spec[p].getIntensity(), output[0][p].getIntensity())
}
END_SECTION
START_SECTION((void pickExperiment(const MSExperiment<> &input, MSExperiment<> &output)))
MSExperiment<> exp;
pp.pickExperiment(input,exp);
TEST_EQUAL(exp.ExperimentalSettings::operator==(input), true)
for (Size s=0; s<exp.size(); ++s)
{
// TEST_EQUAL(exp[s].SpectrumSettings::operator==(output[s]), true) -> are not equal as peak picking step is written to the spectrum settings
for (Size p=0; p<exp[s].size(); ++p)
{
TEST_REAL_SIMILAR(exp[s][p].getMZ(), output[s][p].getMZ())
TEST_REAL_SIMILAR(exp[s][p].getIntensity(), output[s][p].getIntensity())
}
}
END_SECTION
START_SECTION(DoubleReal estimatePeakWidth(const MSExperiment<>& input))
DoubleReal peak_width = pp.estimatePeakWidth(input);
TEST_REAL_SIMILAR(peak_width,0.15)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
