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
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
|
// --------------------------------------------------------------------------
// 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: Alexandra Zerck $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/TARGETED/PrecursorIonSelectionPreprocessing.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(PrecursorIonSelectionPreprocessing, "$Id: PrecursorIonSelectionPreprocessing_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
PrecursorIonSelectionPreprocessing* ptr = 0;
PrecursorIonSelectionPreprocessing* nullPointer = 0;
START_SECTION(PrecursorIonSelectionPreprocessing())
ptr = new PrecursorIonSelectionPreprocessing();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PrecursorIonSelectionPreprocessing())
delete ptr;
END_SECTION
ptr = new PrecursorIonSelectionPreprocessing();
START_SECTION(PrecursorIonSelectionPreprocessing(const PrecursorIonSelectionPreprocessing &source))
PrecursorIonSelectionPreprocessing copy(*ptr);
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(PrecursorIonSelectionPreprocessing& operator=(const PrecursorIonSelectionPreprocessing &source))
PrecursorIonSelectionPreprocessing copy;
copy = *ptr;
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
Param param;
param.setValue("precursor_mass_tolerance",0.9);
param.setValue("precursor_mass_tolerance_unit","Da");
param.setValue("missed_cleavages",0);
std::string tmp_filename;
NEW_TMP_FILE(tmp_filename);
param.setValue("preprocessed_db_path",tmp_filename);
ptr->setParameters(param);
ptr->dbPreprocessing(OPENMS_GET_TEST_DATA_PATH("PrecursorIonSelectionPreprocessing_db.fasta"),true);
START_SECTION((const std::map<String,std::vector<DoubleReal> >& getProtMasses() const))
std::map<String,std::vector<DoubleReal> > prot_map = ptr->getProtMasses();
TEST_EQUAL(prot_map.size(), 3)
END_SECTION
START_SECTION((const std::vector<DoubleReal> & getMasses(String acc) const))
const std::vector<DoubleReal>& pep_masses= ptr->getMasses("P01008");
TEST_EQUAL(pep_masses.size(), 14)
TEST_REAL_SIMILAR(pep_masses[0],1356.68332791328)
const std::vector<DoubleReal>& pep_masses2= ptr->getMasses("P02787");
TEST_EQUAL(pep_masses2.size(), 19)
TEST_REAL_SIMILAR(pep_masses2[0],306.159984588623)
END_SECTION
START_SECTION(void dbPreprocessing(String db_path, bool save=true))
std::map<String,std::vector<DoubleReal> > prot_map = ptr->getProtMasses();
TEST_EQUAL(prot_map.size(), 3)
END_SECTION
START_SECTION(DoubleReal getWeight(DoubleReal mass))
DoubleReal w = ptr->getWeight(147.113);
TEST_REAL_SIMILAR(w,1)
END_SECTION
START_SECTION(void loadPreprocessing())
PrecursorIonSelectionPreprocessing ldb;
ldb.setParameters(param);
ldb.loadPreprocessing();
TEST_EQUAL(ldb.getProtMasses().size(),3)
DoubleReal w = ldb.getWeight(147.113);
TEST_REAL_SIMILAR(w,1)
std::vector<DoubleReal> pep_masses_l = ldb.getMasses("P01008");
std::vector<DoubleReal> pep_masses = ptr->getMasses("P01008");
TEST_EQUAL(pep_masses_l.size(),pep_masses.size())
TEST_REAL_SIMILAR(pep_masses_l[0],pep_masses[0])
END_SECTION
PrecursorIonSelectionPreprocessing rt_pt_pp;
rt_pt_pp.setParameters(param);
rt_pt_pp.dbPreprocessing(OPENMS_GET_TEST_DATA_PATH("PrecursorIonSelectionPreprocessing_db.fasta"),
OPENMS_GET_TEST_DATA_PATH("PrecursorIonSelectionPreprocessing_rt.model"),
OPENMS_GET_TEST_DATA_PATH("DetectabilitySimulation.svm"),false);
START_SECTION(void dbPreprocessing(String db_path,String rt_model_path,String dt_model_path,bool save=true))
TEST_EQUAL(rt_pt_pp.getProtMasses().size(),3);
DoubleReal w = rt_pt_pp.getWeight(147.113);
TEST_REAL_SIMILAR(w,1)
TEST_REAL_SIMILAR(rt_pt_pp.getRT("P01008",1),831.46429)
TEST_REAL_SIMILAR(rt_pt_pp.getPT("P01008",1),0.0402)
END_SECTION
START_SECTION(DoubleReal getRT(String prot_id,Size peptide_index))
TEST_REAL_SIMILAR(rt_pt_pp.getRT("P01008",1),831.46429)
END_SECTION
START_SECTION(DoubleReal getPT(String prot_id,Size peptide_index))
TEST_REAL_SIMILAR(rt_pt_pp.getPT("P01008",1),0.0402)
END_SECTION
START_SECTION((const std::map<String, std::vector<DoubleReal> >& getProteinRTMap() const))
const std::map<String, std::vector<DoubleReal> >& rt_map = rt_pt_pp.getProteinRTMap();
TEST_REAL_SIMILAR(rt_map.find("P01008")->second[1],831.46429)
TEST_EQUAL(rt_map.size(),3);
END_SECTION
START_SECTION((const std::map<String, std::vector<DoubleReal> >& getProteinPTMap() const))
const std::map<String, std::vector<DoubleReal> >& pt_map = rt_pt_pp.getProteinPTMap();
TEST_REAL_SIMILAR(pt_map.find("P01008")->second[1],0.0402)
TEST_EQUAL(pt_map.size(),3);
END_SECTION
START_SECTION((const std::map<String, std::vector<String> >& getProteinPeptideSequenceMap() const))
const std::map<String, std::vector<String> >& map = rt_pt_pp.getProteinPeptideSequenceMap();
TEST_EQUAL(map.size(),0);
END_SECTION
START_SECTION((void setFixedModifications(StringList & modifications)))
{
StringList list = StringList::create("Carbamidomethylation (C)");
ptr->setFixedModifications(list);
const std::map<char, std::vector<String> > & map = ptr->getFixedModifications();
TEST_EQUAL(map.size(),1)
TEST_EQUAL(map.begin()->first,'C')
TEST_EQUAL(map.begin()->second[0],"Carbamidomethylation")
}
END_SECTION
START_SECTION((const std::map<char, std::vector<String> > & getFixedModifications()))
{
StringList list = StringList::create("Oxidation (M)");
ptr->setFixedModifications(list);
const std::map<char, std::vector<String> > & map = ptr->getFixedModifications();
TEST_EQUAL(map.size(),1)
TEST_EQUAL(map.begin()->first,'M')
TEST_EQUAL(map.begin()->second[0],"Oxidation")
}
END_SECTION
START_SECTION((void setGaussianParameters(DoubleReal mu, DoubleReal sigma)))
{
ptr->setGaussianParameters(-3.,10.);
TEST_REAL_SIMILAR(ptr->getGaussMu(),-3.)
TEST_REAL_SIMILAR(ptr->getGaussSigma(),10.)
}
END_SECTION
START_SECTION((DoubleReal getGaussMu()))
{
ptr->setGaussianParameters(-10.,10.);
TEST_REAL_SIMILAR(ptr->getGaussMu(),-10.)
}
END_SECTION
START_SECTION((DoubleReal getGaussSigma()))
{
ptr->setGaussianParameters(-10.,15.);
TEST_REAL_SIMILAR(ptr->getGaussSigma(),15.)
}
END_SECTION
std::vector< ConvexHull2D > hulls(2);
hulls[0].addPoint(DPosition<2>(810.0,1.0));
hulls[0].addPoint(DPosition<2>(810.0,2.0));
hulls[1].addPoint(DPosition<2>(854.5,1.0));
hulls[1].addPoint(DPosition<2>(854.5,4.0));
START_SECTION((DoubleReal getRTProbability(String prot_id, Size peptide_index, Feature &feature)))
{
Feature f;
f.setRT(831.46);
f.setConvexHulls(hulls);
param.setValue("rt_settings:min_rt",800.);
param.setValue("rt_settings:max_rt",900.);
param.setValue("rt_settings:rt_step_size",10.);
rt_pt_pp.setParameters(param);
rt_pt_pp.setGaussianParameters(0.,1.);
TEST_REAL_SIMILAR(rt_pt_pp.getRTProbability("P01008",1,f),0.9973)
}
END_SECTION
START_SECTION((DoubleReal getRTProbability(DoubleReal pred_rt, Feature &feature)))
{
Feature f;
f.setRT(831.46);
f.setConvexHulls(hulls);
TEST_REAL_SIMILAR(rt_pt_pp.getRTProbability(831.46429,f),0.9973)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
