@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 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 testDNAtoProtein() {
BiojavaSequence seq = null;
seq = biojava.createSequence("CTCCTCGCGAAACGATACGAT");
assertNotNull(seq);
assertTrue(seq instanceof BiojavaDNASequence);
BiojavaDNASequence dnaSeq = (BiojavaDNASequence) seq;
try {
BiojavaAASequence rnaSeq = biojava.DNAToProtein(dnaSeq);
assertEquals("LLAKRYD", 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 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());
}
}
/*
@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());
}
}
public void runTest(
String testID,
IMolecule mol,
IReturner<List<? extends ITestResult>> returner,
IProgressMonitor monitor)
throws BioclipseException {
ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
IDSTest test = getTest(testID);
List<? extends ITestResult> ret = null;
try {
// Preprocess the molecule
ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
// Clone the mol
IAtomContainer clonedAC = null;
try {
clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
} catch (CloneNotSupportedException e) {
logger.error("Could not clone mol: " + cdkmol);
return;
}
ICDKMolecule clonedMol = new CDKMolecule(clonedAC);
ret = test.runWarningTest(clonedMol, monitor);
} catch (Exception e) {
// in case of error...
LogUtils.debugTrace(logger, e);
ITestResult er = new SimpleResult("Error: " + e.getMessage(), ITestResult.ERROR);
er.setDetailedMessage(e.getMessage());
List<ITestResult> trlist = new ArrayList<ITestResult>();
trlist.add(er);
monitor.done();
returner.completeReturn(trlist);
return;
}
monitor.done();
returner.completeReturn(ret);
}
public static ChoiceGenerator getGeneratorsFromExtensionPoint() {
ChoiceGenerator choiseGenerator = new ChoiceGenerator();
IExtensionRegistry registry = Platform.getExtensionRegistry();
IExtensionPoint generatorExtensionPoint = registry.getExtensionPoint(EP_GENERATOR);
if (generatorExtensionPoint != null) {
IExtension[] generatorExtensions = generatorExtensionPoint.getExtensions();
for (IExtension extension : generatorExtensions) {
for (IConfigurationElement element : extension.getConfigurationElements()) {
try {
final IGenerator generator = (IGenerator) element.createExecutableExtension("class");
choiseGenerator.add(generator);
} catch (CoreException e) {
LogUtils.debugTrace(Logger.getLogger(ChoiceGenerator.class), e);
}
}
}
}
return choiseGenerator;
}