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
|
//
// testsequence.cpp
// Mothur
//
// Created by Sarah Westcott on 3/23/15.
// Copyright (c) 2015 Schloss Lab. All rights reserved.
//
#include "testsequence.h"
#include "dataset.h"
/**************************************************************************************************/
TestSequence::TestSequence() { //setup
m = MothurOut::getInstance();
TestDataSet data;
vector<string> filenames = data.getSubsetFNGFiles();
fastafile = filenames[0];
}
/**************************************************************************************************/
TestSequence::~TestSequence() {}//teardown
/**************************************************************************************************/
TEST(Test_Container_Sequence, SequenceConstructors) {
Sequence seq("testSeq", "ATGCGTCATC");
EXPECT_EQ(seq.getAligned(), "ATGCGTCATC");
EXPECT_EQ(seq.getName(), "testSeq");
EXPECT_EQ(seq.getUnaligned(), "ATGCGTCATC");
Sequence seq1;
EXPECT_EQ(seq1.getAligned(), "");
EXPECT_EQ(seq1.getName(), "");
EXPECT_EQ(seq1.getUnaligned(), "");
}
TEST(Test_Container_Sequence, setGets) {
Sequence seq; seq.setName("mothurSeq");
EXPECT_EQ("mothurSeq", seq.getName());
seq.setAligned("A--TGC-G-TCA--TC");
EXPECT_EQ("A--TGC-G-TCA--TC", seq.getAligned());
seq.setUnaligned("A--TGC-G-TCA--TC");
EXPECT_EQ("ATGCGTCATC", seq.getUnaligned());
seq.reverseComplement();
EXPECT_EQ("GATGACGCAT", seq.getUnaligned());
seq.setComment("This is my sequence comment. It can contain anything I want including numbers and symbols & % -- 234");
EXPECT_EQ("This is my sequence comment. It can contain anything I want including numbers and symbols & % -- 234", seq.getComment());
Sequence seq2("testSeq", "ATNNGTCATC");
EXPECT_EQ("testSeq\tATNNGTCATC", seq2.getInlineSeq());
EXPECT_EQ(2, seq2.getNumNs());
EXPECT_EQ(0, seq.getNumNs());
Sequence seq3("testSeq", "ATGCGTCATC");
EXPECT_EQ(10, seq3.getNumBases());
EXPECT_EQ(1, seq3.getStartPos());
EXPECT_EQ(10, seq3.getEndPos());
Sequence seq4("testSeq", "..A--TGC-G-TCA--TC..");
EXPECT_EQ(3, seq4.getStartPos());
EXPECT_EQ(18, seq4.getEndPos());
seq3.trim(5);
EXPECT_EQ("ATGCG", seq3.getAligned());
seq4.trim(5);
EXPECT_EQ("ATGCG", seq4.getAligned());
seq4.padToPos(3);
EXPECT_EQ("..GCG", seq4.getAligned());
seq4.padFromPos(3);
EXPECT_EQ("..G..", seq4.getAligned());
seq.setAligned("ATGCG");
seq.filterToPos(2);
EXPECT_EQ("..GCG", seq.getAligned());
seq.setAligned("ATGCG");
seq.filterFromPos(2);
EXPECT_EQ("AT...", seq.getAligned());
seq.setAligned("..GCG");
seq.filterFromPos(2);
EXPECT_EQ(".....", seq.getAligned());
seq.setAligned("..A--TGC-G-TCA--TC..");
EXPECT_EQ(20, seq.getAlignLength());
EXPECT_EQ(0, seq.getAmbigBases());
seq.setAligned("..A--MGC-G-TCA--TC..");
EXPECT_EQ(1, seq.getAmbigBases());
seq.removeAmbigBases();
EXPECT_EQ(0, seq.getAmbigBases());
EXPECT_EQ("..A---GC-G-TCA--TC..", seq.getAligned());
EXPECT_EQ(1, seq.getLongHomoPolymer());
seq.setAligned("..A--AAA-G-TCA--TC..");
EXPECT_EQ(4, seq.getLongHomoPolymer());
EXPECT_EQ("0000231031", seq.convert2ints());
}
/**************************************************************************************************/
|
