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
|
// --------------------------------------------------------------------------
// 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: Nico Pfeifer $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/FORMAT/PepXMLFileMascot.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(PepXMLFileMascot, "$Id: PepXMLFileMascot_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
PepXMLFileMascot* ptr = 0;
PepXMLFileMascot* nullPointer = 0;
PepXMLFileMascot file;
START_SECTION(PepXMLFileMascot())
ptr = new PepXMLFileMascot();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PepXMLFileMascot())
delete ptr;
END_SECTION
START_SECTION(void load(const String& filename, std::map<String, std::vector<AASequence> >& peptides))
std::map<String, std::vector<AASequence> > peptides;
std::map<String, std::vector<AASequence> >::iterator it;
std::vector<AASequence> temp_sequences;
String filename = OPENMS_GET_TEST_DATA_PATH("PepXMLFileMascot_test.pepXML");
file.load(filename, peptides);
it = peptides.begin();
TEST_EQUAL(peptides.size(), 3)
TEST_EQUAL(it->first, "402.42_14_3688.53")
temp_sequences = it->second;
TEST_EQUAL(temp_sequences.size(), 4)
TEST_EQUAL(temp_sequences[0].toUnmodifiedString(), "LAPSAAEDGAFR")
TEST_EQUAL(temp_sequences[0].toString(), "LAPSAAEDGAFR")
TEST_EQUAL(temp_sequences[1].toUnmodifiedString(), "GQPLGQLEAHR")
TEST_EQUAL(temp_sequences[1].toString(), "GQPLGQLEAHR")
TEST_EQUAL(temp_sequences[2].toUnmodifiedString(), "SPAPLVPVRLR")
TEST_EQUAL(temp_sequences[2].toString(), "SPAPLVPVRLR")
TEST_EQUAL(temp_sequences[3].toUnmodifiedString(), "QPYLHPSFSK")
TEST_EQUAL(temp_sequences[3].toString(), "Q(Deamidated)PYLHPSFSK")
++it;
TEST_EQUAL(it->first, "404.875_14_333.442")
temp_sequences = it->second;
TEST_EQUAL(temp_sequences.size(), 7)
TEST_EQUAL(temp_sequences[0].toUnmodifiedString(), "AQAVAAEIRER")
TEST_EQUAL(temp_sequences[0].toString(), "AQAVAAEIRER")
TEST_EQUAL(temp_sequences[1].toUnmodifiedString(), "AALNAADIVTVR")
TEST_EQUAL(temp_sequences[1].toString(), "AALNAADIVTVR")
TEST_EQUAL(temp_sequences[2].toUnmodifiedString(), "AEPAAELALEAK")
TEST_EQUAL(temp_sequences[2].toString(), "AEPAAELALEAK")
TEST_EQUAL(temp_sequences[3].toUnmodifiedString(), "LANAASPAITQR")
TEST_EQUAL(temp_sequences[3].toString(), "LANAASPAITQ(Deamidated)R")
TEST_EQUAL(temp_sequences[4].toUnmodifiedString(), "SGHSAVLLQDGK")
TEST_EQUAL(temp_sequences[4].toString(), "SGHSAVLLQ(Deamidated)DGK")
TEST_EQUAL(temp_sequences[5].toUnmodifiedString(), "AGAGIANVQAAIR")
TEST_EQUAL(temp_sequences[5].toString(), "AGAGIAN(Deamidated)VQ(Deamidated)AAIR")
TEST_EQUAL(temp_sequences[6].toUnmodifiedString(), "VTAPAARSAALGK")
TEST_EQUAL(temp_sequences[6].toString(), "VTAPAARSAALGK")
++it;
TEST_EQUAL(it->first, "411.766_14_3724.98")
temp_sequences = it->second;
TEST_EQUAL(temp_sequences.size(), 7)
TEST_EQUAL(temp_sequences[0].toUnmodifiedString(), "LLAWMGRTER")
TEST_EQUAL(temp_sequences[0].toString(), "LLAWMGRTER")
TEST_EQUAL(temp_sequences[1].toUnmodifiedString(), "VLALYRAAQAR")
TEST_EQUAL(temp_sequences[1].toString(), "VLALYRAAQ(Deamidated)AR")
TEST_EQUAL(temp_sequences[2].toUnmodifiedString(), "RTLLMSLTGLK")
TEST_EQUAL(temp_sequences[2].toString(), "RTLLMSLTGLK")
TEST_EQUAL(temp_sequences[3].toUnmodifiedString(), "LLGLSRFGLQK")
TEST_EQUAL(temp_sequences[3].toString(), "LLGLSRFGLQ(Deamidated)K")
TEST_EQUAL(temp_sequences[4].toUnmodifiedString(), "MGGIALLDEIGK")
TEST_EQUAL(temp_sequences[4].toString(), "M(Oxidation)GGIALLDEIGK")
TEST_EQUAL(temp_sequences[5].toUnmodifiedString(), "DQMDNALRIR")
TEST_EQUAL(temp_sequences[5].toString(), "DQMDN(Deamidated)ALRIR")
TEST_EQUAL(temp_sequences[6].toUnmodifiedString(), "QTLAGRMVVQK")
TEST_EQUAL(temp_sequences[6].toString(), "Q(Deamidated)TLAGRMVVQ(Deamidated)K")
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
