@Test
public void testLoadFastaSequences() {
BiojavaSequence seq = null;
try {
// Test read Protein as fasta
seq = biojava.loadSequence(TestData.getPathToAAFastaSequence());
assertNotNull(seq);
assertEquals("SEQUENCE", seq.getPlainSequence().trim().toUpperCase());
// Test read DNA as fasta
seq = biojava.loadSequence(TestData.getPathToDNAFastaSequence());
assertNotNull(seq);
assertEquals("GATTACA", seq.getPlainSequence().trim().toUpperCase());
/*
//Test read RNA as fasta
seq = biojava.loadSequence( TestData.getPathToRNAFastaSequence() );
assertNotNull( seq );
assertEquals( "GAUUACA", seq.getPlainSequence().trim().toUpperCase() );
*/
} catch (IOException e) {
fail(e.getMessage());
} catch (Exception e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
}
}
@Test
public void testToFasta() {
BiojavaSequence seq = null;
try {
seq = biojava.loadSequence(TestData.getPathToAAFastaSequence());
// seq = biojava.loadSequence( TestData.getPathToFosbFastaSequence() );
} catch (IOException e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
} catch (Exception e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
}
assertNotNull(seq);
// assertEquals( "Sequence", seq.getName());
try {
assertEquals("SEQUENCE", seq.getPlainSequence().trim());
} catch (IOException e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
}
}
