@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; }