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
|
/*
* =====================================================================================
*
* Filename: FASTASequence_gtest.cpp
*
* Description: Test pbdata/FASTASequence.hpp
*
* Version: 1.0
* Created: 10/29/2012 05:19:13 PM
* Revision: none
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <climits>
#include <fstream>
#include <iostream>
#include <gtest/gtest.h>
#include <pbdata/FASTASequence.hpp>
class FASTASequenceTest : public ::testing::Test
{
public:
virtual void SetUp() {}
virtual void TearDown()
{
fastaOne.Free();
fastaTwo.Free();
fastaThree.Free();
}
FASTASequence fastaOne;
FASTASequence fastaTwo;
FASTASequence fastaThree;
std::streambuf* sbuf;
std::ofstream ofs;
};
//Test FASTASequence
TEST_F(FASTASequenceTest, ALLFUNC)
{
// Test constructor
EXPECT_TRUE(fastaOne.title == NULL);
EXPECT_TRUE(fastaOne.titleLength == 0);
EXPECT_TRUE(fastaOne.seq == NULL);
EXPECT_TRUE(fastaOne.length == 0);
EXPECT_FALSE(fastaOne.deleteOnExit);
EXPECT_EQ(fastaOne.GetStorageSize(), 0);
DNASequence dna;
Nucleotide thisNuc[] = "ATGCATGCTC";
dna.seq = thisNuc;
dna.length = 10;
int titleLength = 22;
std::string title("fasta_seq_one comments");
fastaOne.title = new char[titleLength];
memcpy(fastaOne.title, title.c_str(), titleLength);
fastaOne.titleLength = titleLength;
EXPECT_EQ(fastaOne.GetName(), std::string("fasta_seq_one"));
fastaOne.seq = thisNuc;
fastaOne.length = 10;
// use ShallowCopy carefully, since title may double free
// fastaTwo.ShallowCopy(fastaOne);
// EXPECT_EQ(fastaTwo.seq, fastaOne.seq);
// EXPECT_EQ(fastaTwo.title, fastaOne.title);
// Test AppendToTitle
fastaOne.AppendToTitle(std::string("XXX"));
EXPECT_EQ(fastaOne.titleLength, 26);
std::string newTitle = "fasta_seq_one commentsXXX";
EXPECT_STREQ(fastaOne.title, newTitle.c_str());
// Test ReverseComplementSelf()
fastaOne.ReverseComplementSelf();
std::string rcSeq = "GAGCATGCAT";
for (size_t i = 0; i < rcSeq.size(); i++) {
EXPECT_EQ(fastaOne.seq[i], rcSeq[i]);
}
// Test operator =
fastaTwo = fastaOne;
EXPECT_NE(fastaOne.title, fastaTwo.title);
EXPECT_EQ(fastaOne.titleLength, fastaTwo.titleLength);
EXPECT_STREQ(fastaOne.title, fastaTwo.title);
EXPECT_NE(fastaOne.seq, fastaTwo.seq);
for (size_t i = 0; i < fastaOne.length; i++) {
EXPECT_EQ(fastaOne.seq[i], fastaTwo.seq[i]);
}
// Test MakeRC(rhs&)
fastaOne.MakeRC(fastaThree);
// Test PrintSeq
std::stringstream ss;
fastaThree.PrintSeq(ss);
std::string thisTitle, thisComment, thisSeq;
ss >> thisTitle;
ss >> thisComment;
ss >> thisSeq;
EXPECT_EQ(thisTitle, ">fasta_seq_one");
EXPECT_EQ(thisComment, "commentsXXX");
EXPECT_EQ(thisSeq, "ATGCATGCTC");
}
TEST_F(FASTASequenceTest, CopyFromString)
{
std::string name = "read_name";
std::string seq = "ATGGGCGC";
fastaOne.Copy(name, seq);
EXPECT_EQ(fastaOne.title, name);
EXPECT_EQ(fastaOne.length, seq.size());
EXPECT_EQ(fastaOne.deleteOnExit, true);
for (size_t i = 0; i < fastaOne.length; i++) {
EXPECT_EQ(fastaOne.seq[i], seq[i]);
}
// Copy sequence from another string.
std::string seq2 = "GGTTGTG";
fastaOne.Copy(seq2);
// Name not changed.
EXPECT_EQ(fastaOne.title, name);
EXPECT_EQ(fastaOne.length, seq2.size());
EXPECT_EQ(fastaOne.deleteOnExit, true);
for (size_t i = 0; i < fastaOne.length; i++) {
EXPECT_EQ(fastaOne.seq[i], seq2[i]);
}
}
TEST_F(FASTASequenceTest, ReverseComplementSelf)
{
const std::string name = "fasta-seq-name";
const std::string s = "TTAAGG";
const std::string r = "CCTTAA";
fastaOne.Copy(name, s);
EXPECT_EQ(fastaOne.title, name);
EXPECT_EQ(fastaOne.ReverseComplementSelf().ToString(), r);
EXPECT_EQ(fastaOne.title, name);
EXPECT_EQ(fastaOne.ReverseComplementSelf().ToString(), s);
FASTASequence fastaTwo;
fastaTwo.ReferenceSubstring(fastaOne, 1, 3);
fastaTwo.CopyTitle(fastaOne.title);
EXPECT_EQ(fastaTwo.deleteOnExit, false);
EXPECT_EQ(fastaTwo.title, name);
EXPECT_EQ(fastaTwo.ToString(), "TAA");
EXPECT_EQ(fastaTwo.ReverseComplementSelf().ToString(), "TTA");
EXPECT_EQ(fastaTwo.title, name);
EXPECT_EQ(fastaTwo.deleteOnExit, true);
}
|
