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
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
|
// --------------------------------------------------------------------------
// 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: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmIdentification.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentTransformer.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <iostream>
using namespace std;
using namespace OpenMS;
/////////////////////////////////////////////////////////////
START_TEST(MapAlignmentAlgorithmIdentification, "$Id: MapAlignmentAlgorithmIdentification_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
MapAlignmentAlgorithmIdentification* ptr = 0;
MapAlignmentAlgorithmIdentification* nullPointer = 0;
MapAlignmentAlgorithm* base_nullPointer = 0;
START_SECTION((MapAlignmentAlgorithmIdentification()))
ptr = new MapAlignmentAlgorithmIdentification();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION((virtual ~MapAlignmentAlgorithmIdentification()))
delete ptr;
END_SECTION
START_SECTION((static MapAlignmentAlgorithm* create()))
TEST_NOT_EQUAL(MapAlignmentAlgorithmIdentification::create(), base_nullPointer)
END_SECTION
START_SECTION((static String getProductName()))
TEST_EQUAL(MapAlignmentAlgorithmIdentification::getProductName(), "identification")
END_SECTION
START_SECTION((virtual void alignPeptideIdentifications(std::vector<std::vector<PeptideIdentification> >&, std::vector<TransformationDescription>&)))
{
vector<vector<PeptideIdentification> > peptides(2);
vector<ProteinIdentification> proteins;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("MapAlignmentAlgorithmIdentification_test_1.idXML"), proteins, peptides[0]);
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("MapAlignmentAlgorithmIdentification_test_2.idXML"), proteins, peptides[1]);
// cout << "Input:\n";
// for (Size i = 0; i < peptides[0].size(); ++i)
// {
// cout << left << setw(20)
// << peptides[0][i].getHits()[0].getSequence().toString() + ":"
// << peptides[0][i].getMetaValue("RT") << "\t"
// << peptides[1][i].getMetaValue("RT") << endl;
// }
vector<TransformationDescription> transforms(2);
MapAlignmentAlgorithm* aligner = Factory<MapAlignmentAlgorithm>::create(
"identification");
Param params = aligner->getParameters();
params.setValue("peptide_score_threshold", 0.0);
aligner->setParameters(params);
aligner->setLogType(ProgressLogger::CMD);
aligner->alignPeptideIdentifications(peptides, transforms);
params.clear();
params.setValue("num_breakpoints", 10);
aligner->fitModel("b_spline", params, transforms);
MapAlignmentTransformer::transformPeptideIdentifications(peptides, transforms);
// cout << "Output (transformed):\n";
// for (Size i = 0; i < peptides[0].size(); ++i)
// {
// cout << left << setw(20)
// << peptides[0][i].getHits()[0].getSequence().toString() + ":"
// << peptides[0][i].getMetaValue("RT") << "\t"
// << peptides[1][i].getMetaValue("RT") << endl;
// }
for (Size i = 0; i < peptides[0].size(); ++i)
{
TEST_REAL_SIMILAR(peptides[0][i].getMetaValue("RT"),
peptides[1][i].getMetaValue("RT"));
}
}
END_SECTION
START_SECTION((virtual void alignPeakMaps(std::vector<MSExperiment<> >&, std::vector<TransformationDescription>&)))
{
// largely the same as "alignPeptideIdentifications"
NOT_TESTABLE;
}
END_SECTION
START_SECTION((virtual void alignFeatureMaps(std::vector<FeatureMap<> >&, std::vector<TransformationDescription>&)))
{
// largely the same as "alignPeptideIdentifications"
NOT_TESTABLE;
}
END_SECTION
START_SECTION((virtual void alignConsensusMaps(std::vector<ConsensusMap>&, std::vector<TransformationDescription>&)))
{
// largely the same as "alignPeptideIdentifications"
NOT_TESTABLE;
}
END_SECTION
START_SECTION((virtual void setReference(Size reference_index=0, const String& reference_file="")))
{
MapAlignmentAlgorithm* aligner = Factory<MapAlignmentAlgorithm>::create(
"identification");
aligner->setReference(1); // nothing happens
TEST_EXCEPTION(Exception::FileNotFound,
aligner->setReference(0, "not-a-real-file.idXML"));
}
END_SECTION
// can't test protected methods...
// START_SECTION((DoubleReal median_(DoubleList&, bool)))
// {
// DoubleList values;
// TEST_EXCEPTION(Exception::IllegalArgument, median_(values)); // empty list
// // -1.0, -0.5, ..., 2.0 scrambled:
// values << 0.5 << -1.0 << 0.0 << 1.5 << 1.0 << -0.5 << 2.0;
// TEST_EQUAL(median_(values, false), 0.5);
// TEST_EQUAL(median_(values, true), 0.5); // should be sorted now
// values << 2.5; // even number of values
// TEST_EQUAL(median_(values, true), 0.75);
// }
// END_SECTION
// START_SECTION((void computeMedians_(SeqToList&, SeqToValue&, bool)))
// {
// map<String, DoubleList> seq_to_list;
// map<String, DoubleReal> seq_to_value;
// seq_to_list["ABC"] << -1.0 << 2.5 << 0.5 << -3.5;
// seq_to_list["DEF"] << 1.5 << -2.5 << -1;
// computeMedians_(seq_to_list, seq_to_value, false);
// TEST_EQUAL(seq_to_value.size(), 2);
// TEST_EQUAL(seq_to_value["ABC"], -0.25);
// TEST_EQUAL(seq_to_value["DEF"], -1);
// seq_to_value.clear();
// computeMedians_(seq_to_list, seq_to_value, true); // should be sorted now
// TEST_EQUAL(seq_to_value.size(), 2);
// TEST_EQUAL(seq_to_value["ABC"], -0.25);
// TEST_EQUAL(seq_to_value["DEF"], -1);
// }
// END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
