@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;
}
/**
* This method is called when 'Finish' button is pressed in the wizard. We will create an
* operation and run it using wizard as execution context.
*/
public boolean performFinish() {
try {
Options opts = new Options(new String[0]);
opts.setDefaultURL(serverPage.getSelectedServer() + "/services/NMRShiftDB");
Service service = new Service();
Call call = (Call) service.createCall();
call.setOperationName("doSearch");
call.setTargetEndpointAddress(new URL(opts.getURL()));
DocumentBuilder builder;
builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
SOAPBodyElement[] input = new SOAPBodyElement[1];
Document doc = builder.newDocument();
Element cdataElem;
cdataElem = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "doSearch");
Element reqElem;
reqElem = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "searchstring");
/*DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Node node = db.parse(new ByteArrayInputStream(new Convertor(true,"").cdkAtomContainerToCMLMolecule(ac).toXML().getBytes()));*/
Node node =
DOMConverter.convert(
new nu.xom.Document(new Convertor(true, "").cdkAtomContainerToCMLMolecule(ac)),
builder.getDOMImplementation())
.getFirstChild();
reqElem.appendChild(doc.importNode(node, true));
Element reqElem2;
reqElem2 = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "searchtype");
Node node2;
node2 = doc.createTextNode("--");
reqElem2.appendChild(node2);
Element reqElem3;
reqElem3 = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "searchfield");
Node node3;
node3 = doc.createTextNode(NmrshiftdbUtils.replaceSpaces(serverPage.selectedOption()));
reqElem3.appendChild(node3);
cdataElem.appendChild(reqElem);
cdataElem.appendChild(reqElem2);
cdataElem.appendChild(reqElem3);
input[0] = new SOAPBodyElement(cdataElem);
Vector elems = (Vector) call.invoke(input);
SOAPBodyElement elem = (SOAPBodyElement) elems.get(0);
Element e = elem.getAsDOM();
CMLBuilder cmlbuilder = new CMLBuilder();
CMLElement cmlElement = (CMLElement) cmlbuilder.parseString(XMLUtils.ElementToString(e));
if (cmlElement.getChildCount() > 0) {
IFolder folder = NmrshiftdbUtils.createVirtualFolder();
for (int i = 0; i < cmlElement.getChildCount(); i++) {
net.bioclipse.specmol.Activator.getDefault()
.getJavaSpecmolManager()
.saveSpecmol(
new JumboSpecmol((CMLCml) cmlElement.getChildCMLElements().get(i)),
folder.getFile(
((CMLMolecule)
cmlElement
.getChildCMLElements()
.get(i)
.getChildCMLElement("molecule", 0))
.getId()
+ "."
+ SpectrumEditor.CML_TYPE));
}
} else {
MessageDialog.openInformation(
PlatformUI.getWorkbench().getActiveWorkbenchWindow().getShell(),
"No results",
"No spectra in NMRShiftDB for this structure!");
}
} catch (Exception ex) {
LogUtils.handleException(ex, logger);
}
return true;
}
