ProteoWizard
PeakelPickerTest.cpp
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1//
2// $Id$
3//
4//
5// Original author: Darren Kessner <darren@proteowizard.org>
6//
7// Copyright 2009 Center for Applied Molecular Medicine
8// University of Southern California, Los Angeles, CA
9//
10// Licensed under the Apache License, Version 2.0 (the "License");
11// you may not use this file except in compliance with the License.
12// You may obtain a copy of the License at
13//
14// http://www.apache.org/licenses/LICENSE-2.0
15//
16// Unless required by applicable law or agreed to in writing, software
17// distributed under the License is distributed on an "AS IS" BASIS,
18// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19// See the License for the specific language governing permissions and
20// limitations under the License.
21//
22
23
24#include "PeakelPicker.hpp"
27#include <cstring>
28
29
30using namespace pwiz::util;
31using namespace pwiz::analysis;
32using namespace pwiz::data::peakdata;
33
34
35ostream* os_ = 0;
36
37
38shared_ptr<PeakelField> createToyPeakelField()
39{
40 //
41 // 0 1 2
42 // |.....:.....|.....:.....|
43 // 10 x x o
44 // 20 x x o x
45 // 30 x x o x
46 // 40 x x o <-- feature z==3, noise Peakel at mono+.5
47 // 50
48 // 60 x x
49 // 70 x x x
50 // 80 x x x
51 // 90 x <-- feature z==2
52 //
53
54 shared_ptr<PeakelField> toy(new PeakelField);
55
56 PeakelPtr battery(new Peakel(Peak(0,10)));
57 battery->peaks.push_back(Peak(0, 20));
58 battery->peaks.push_back(Peak(0, 30));
59 battery->peaks.push_back(Peak(0, 40));
60 toy->insert(battery);
61
62 battery.reset(new Peakel(Peak(1./3 + 1e-6, 10)));
63 battery->peaks.push_back(Peak(1./3, 20));
64 battery->peaks.push_back(Peak(1./3, 30));
65 battery->peaks.push_back(Peak(1./3, 40));
66 toy->insert(battery);
67
68 battery.reset(new Peakel(Peak(.5, 10)));
69 battery->peaks.push_back(Peak(.5, 20));
70 battery->peaks.push_back(Peak(.5, 30));
71 battery->peaks.push_back(Peak(.5, 40));
72 toy->insert(battery);
73
74 battery.reset(new Peakel(Peak(2./3, 20)));
75 battery->peaks.push_back(Peak(2./3, 30));
76 toy->insert(battery);
77
78 battery.reset(new Peakel(Peak(1./3, 60)));
79 battery->peaks.push_back(Peak(1./3, 70));
80 battery->peaks.push_back(Peak(1./3, 80));
81 battery->peaks.push_back(Peak(1./3, 90));
82 toy->insert(battery);
83
84 battery.reset(new Peakel(Peak(1./3 + .5, 60)));
85 battery->peaks.push_back(Peak(1./3 + .5, 70));
86 battery->peaks.push_back(Peak(1./3 + .5, 80));
87 toy->insert(battery);
88
89 battery.reset(new Peakel(Peak(1./3 + 1, 70)));
90 battery->peaks.push_back(Peak(1./3 + 1, 80));
91 toy->insert(battery);
92
93 return toy;
94}
95
96
97void testToy()
98{
99 PeakelPicker_Basic::Config config; // TODO: specify parameters?
100
101 if (os_)
102 {
103 *os_ << "testToy()\n";
104 config.log = os_;
105 }
106
107 PeakelPicker_Basic peterPiper(config);
108
109 shared_ptr<PeakelField> peakels = createToyPeakelField();
110 unit_assert(peakels->size() == 7);
111
112 FeatureField peck;
113 peterPiper.pick(*peakels, peck);
114
115 unit_assert(peck.size() == 2);
116 unit_assert(peakels->size() == 1);
117
118 FeatureField::const_iterator it = peck.begin();
119 unit_assert((*it)->mz == 0);
120 unit_assert((*it)->charge == 3);
121 unit_assert_equal((*it)->retentionTime, 25, 20);
122
123 ++it;
124 unit_assert((*it)->mz == 1./3);
125 unit_assert((*it)->charge == 2);
126 unit_assert_equal((*it)->retentionTime, 75, 20);
127}
128
129
130void test()
131{
132 testToy();
133}
134
135
136int main(int argc, char* argv[])
137{
138 TEST_PROLOG(argc, argv)
139
140 try
141 {
142 if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
143 test();
144 }
145 catch (exception& e)
146 {
147 TEST_FAILED(e.what())
148 }
149 catch (...)
150 {
151 TEST_FAILED("Caught unknown exception.")
152 }
153
155}
156
int main(int argc, char *argv[])
void testToy()
shared_ptr< PeakelField > createToyPeakelField()
ostream * os_
void test()
virtual void pick(PeakelField &peakels, FeatureField &features) const
boost::shared_ptr< Peakel > PeakelPtr
Definition PeakData.hpp:242
MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT.
Definition MZRTField.hpp:95
represents some generic metadata about a peak detected in a signal
struct for an eluted peak (PEAK ELution)
Definition PeakData.hpp:212
#define unit_assert(x)
Definition unit.hpp:85
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define unit_assert_equal(x, y, epsilon)
Definition unit.hpp:99
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175