@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 testDNAtoRNA() {
BiojavaSequence seq = null;
try {
seq = biojava.loadSequence(TestData.getPathToDNAFastaSequence());
} catch (IOException e1) {
LogUtils.debugTrace(logger, e1);
fail(e1.getMessage());
} catch (Exception e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
}
assertNotNull(seq);
assertTrue(seq instanceof BiojavaDNASequence);
BiojavaDNASequence dnaSeq = (BiojavaDNASequence) seq;
try {
assertEquals("GATTACA", seq.getPlainSequence().trim().toUpperCase());
BiojavaRNASequence rnaSeq;
rnaSeq = biojava.DNAtoRNA(dnaSeq);
assertEquals("GAUUACA", rnaSeq.getPlainSequence().trim().toUpperCase());
} catch (IOException e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
} catch (Exception e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
}
}
/*
@Test
public void testRNAtoDNA() {
BiojavaSequence seq = biojava.createSequence("GAUUACA");
assertNotNull(seq);
assertTrue(seq instanceof BiojavaRNASequence);
BiojavaRNASequence rnaSeq = (BiojavaRNASequence) seq;
try {
//Check correctly read
assertEquals( "GAUUACA", rnaSeq.getPlainSequence().trim().toUpperCase() );
BiojavaDNASequence dnaSeq = biojava.RNAtoDNA(rnaSeq);
//Check correctly converted
assertEquals( "GATTACA", dnaSeq.getPlainSequence().trim().toUpperCase() );
} catch (IOException e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
} catch (Exception e) {
LogUtils.debugTrace(logger, e);
fail(e.getMessage());
}
}
*/
@Test
public void testLoadFastaSequenceCollection() throws BioclipseException, IOException {
BiojavaSequenceList sequenceCollection = null;
sequenceCollection = biojava.loadSequences(TestData.getPathToMultipleSequences());
assertNotNull(sequenceCollection);
assertEquals(2, sequenceCollection.size());
// Check individual sequences
BiojavaSequence seq1 = sequenceCollection.get(0);
BiojavaSequence seq2 = sequenceCollection.get(1);
try {
assertEquals(341, seq1.getPlainSequence().length());
assertEquals(342, seq2.getPlainSequence().length());
} catch (IOException 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());
}
}