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/*
* =====================================================================================
*
* Filename: FASTAReader_gtest.cpp
*
* Description: Test common/FASTAReader.h
*
* Version: 1.0
* Created: 10/29/2012 05:18:52 PM
* Revision: none
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <gtest/gtest.h>
#include <pbdata/testdata.h>
#include <pbdata/FASTAReader.hpp>
class FASTAReaderTest : public ::testing::Test
{
public:
void SetUp()
{
std::string filename(fastaFile1);
reader.Initialize(filename);
}
void TearDown()
{
reader.Close();
seq.Free();
}
FASTAReader reader;
FASTASequence seq;
};
TEST_F(FASTAReaderTest, GetNext)
{
reader.GetNext(seq);
EXPECT_EQ(strcmp(seq.title, "read1"), 0);
EXPECT_EQ(seq.length, 100u);
std::string expected_seq(
"AAAAAGGGGGCCCCCACGGCAGCCAGATTTAAATTGAGGGCCCCCCCTTT"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
EXPECT_EQ(strcmp((char*)seq.seq, expected_seq.c_str()), 0);
reader.GetNext(seq);
EXPECT_EQ(std::strcmp(seq.title, "read2"), 0);
EXPECT_EQ(seq.length, 99u);
}
TEST_F(FASTAReaderTest, ReadAllSequences)
{
std::vector<FASTASequence> seqs;
reader.ReadAllSequences(seqs);
EXPECT_EQ(seqs.size(), 12u);
EXPECT_EQ(std::strcmp(seqs[11].title, "read2x"), 0);
std::string expected_seq(
"AAAAAGGGGGCCCACGGCAGCCAGATTTAAATTGAGGGCAACCCCCCTTT"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
EXPECT_EQ(strcmp((char*)seqs[11].seq, expected_seq.c_str()), 0);
}
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