ProteoWizard
PeptideID_flatTest.cpp
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1//
2// $Id$
3//
4//
5// Original author: Robert Burke <robert.burke@cshs.org>
6//
7// Copyright 2008 Spielberg Family Center for Applied Proteomics
8// Cedars-Sinai Medical Center, Los Angeles, California 90048
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
24#include <cstring>
25
26#include "PeptideID_flat.hpp"
29
30using namespace pwiz::util;
31using namespace pwiz::peptideid;
32using namespace pwiz::minimxml::SAXParser;
33
34ostream* os_;
35
36const char* sampleFlat =
37 "1\t1000.0\t1000.0\t0.9\tABC\n"
38 "2\t2000\t500.0\t0.7\tDEF\n";
39
40const char* sampleMSI =
41"scan time mz mass intensity charge chargeStates kl background median peaks scanFirst scanLast scanCount\n"
42"1 2.248 878.889 1755.7633 61.847733 2 1 0.05977635 0.9152653 1.0536207 5 693 721 1\n"
43"1 2.248 752.86017 1503.7076 41.52021 2 1 0.10636939 1.6415321 0.8086928 5 693 715 1\n"
44"1 2.248 933.4445 932.4372 33.840942 1 1 0.2521489 5.717129 2.8336976 2 695 707 1\n"
45"4 7.116 801.4013 800.3538 18.389582 1 1 0.6249515 1.6089915 1.3883085 3 698 713 1\n";
46
47
49{
50 istringstream data (sampleFlat);
51
52 PeptideID_flat ppFlat(&data, shared_ptr<FlatRecordBuilder>(new FlatRecordBuilder));
53
54 PeptideID::Location loc("1", 1000., 0);
55 PeptideID::Record bf = ppFlat.record(loc);
56
57 unit_assert(bf.nativeID == "1");
58 unit_assert(bf.sequence == "ABC");
59 unit_assert_equal(bf.normalizedScore, 0.9, 1e-14);
60}
61
63{
64 istringstream data (sampleMSI);
65
66 PeptideID_flat ppFlat(&data, shared_ptr<FlatRecordBuilder>(new MSInspectRecordBuilder()));
67
68 PeptideID::Location loc("1", 2.248, 878.889);
69 PeptideID::Record bf = ppFlat.record(loc);
70
71 unit_assert(bf.nativeID == "1");
72 unit_assert(bf.sequence == "");
73 unit_assert_equal(bf.normalizedScore, 0.05977635, 1e-14);
74}
75
76//void testFilename()
77//{
78// ifstream data ("test.txt");
79//
80// PeptideID_flat<> ppFlat(&data);
81//
82//
83// PeptideID::Location loc("1", 0, 0.9);
84// PeptideID::Record bf = ppFlat.record(loc);
85//
86// unit_assert(bf.nativeID == "1");
87// unit_assert(bf.sequence == "ABC");
88// unit_assert_equal(bf.normalizedScore, 0.9, 1e-14);
89//}
90
91int main(int argc, char* argv[])
92{
93 TEST_PROLOG(argc, argv)
94
95 try
96 {
97 if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
100 //testFilename();
101 //testDone();
102 //testBadXML();
103 //testNested();
104 }
105 catch (exception& e)
106 {
107 TEST_FAILED(e.what())
108 }
109 catch (...)
110 {
111 TEST_FAILED("Caught unknown exception.")
112 }
113
115}
const char * sampleMSI
int main(int argc, char *argv[])
const char * sampleFlat
void testMSInspectIStream()
void testIStream()
ostream * os_
This class allows access to peptides listed in a flat tab delimited text file.
virtual Record record(const Location &location) const
Returns the Record object associated with the given nativeID.
An extended SAX interface for custom XML stream parsing.
Definition SAXParser.hpp:54
#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