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/*
* =====================================================================================
*
* 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 "FASTASequence.hpp"
#include "gtest/gtest.h"
#include <climits>
#include <iostream>
#include <fstream>
using namespace std;
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;
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;
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(), 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(string("XXX"));
EXPECT_EQ(fastaOne.titleLength, 26);
string newTitle = "fasta_seq_one commentsXXX";
EXPECT_STREQ(fastaOne.title, newTitle.c_str());
// Test ReverseComplementSelf()
fastaOne.ReverseComplementSelf();
string rcSeq = "GAGCATGCAT";
for (int 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 (int i = 0; i < fastaOne.length; i++) {
EXPECT_EQ(fastaOne.seq[i], fastaTwo.seq[i]);
}
// Test MakeRC(rhs&)
fastaOne.MakeRC(fastaThree);
// Test PrintSeq
stringstream ss;
fastaThree.PrintSeq(ss);
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) {
string name = "read_name";
string seq = "ATGGGCGC";
fastaOne.Copy(name, seq);
EXPECT_EQ(fastaOne.title, name);
EXPECT_EQ(fastaOne.length, seq.size());
EXPECT_EQ(fastaOne.deleteOnExit, true);
for(int i = 0; i < fastaOne.length; i++) {
EXPECT_EQ(fastaOne.seq[i], seq[i]);
}
// Copy sequence from another string.
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(int i = 0; i < fastaOne.length; i++) {
EXPECT_EQ(fastaOne.seq[i], seq2[i]);
}
}
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