/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.jabaws;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.AutoCalcSetting;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
import java.awt.Component;
import java.util.ArrayList;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
import compbio.metadata.WrongParameterException;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
public class RNAStructExportImport
{
- public static String testseqs = "examples/unfolded_RF00031.aln";
+ public static String testseqs = "examples/RF00031_folded.stk";
public static Jws2Discoverer disc;
if (rnaalifoldws == null)
{
- System.exit(0);
+ Assert.fail("no web service");
}
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
+ // remove any existing annotation
+ List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation rna : af.getViewport().getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (rna.isRNA())
+ {
+ aal.add(rna);
+ }
+ }
+ for (AlignmentAnnotation rna : aal)
+ {
+ af.getViewport().getAlignment().deleteAnnotation(rna);
+ }
+ af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel
+ // public?
}
@AfterClass
}
@Test
+ public void testRNAAliFoldValidStructure()
+ {
+
+ alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+
+ af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ } while (af.getViewport().getCalcManager().isWorking());
+
+ AlignmentI orig_alig = af.getViewport().getAlignment();
+ for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+ {
+ if (alifoldClient.involves(aa))
+ {
+ if (aa.isRNA())
+ {
+ assertTrue(
+ "Did not create valid structure from RNAALiFold prediction",
+ aa.isValidStruc());
+ }
+ }
+ }
+ }
+
+ @Test
public void testRNAStructExport()
{
FormatAdapter.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
return;
} catch (Exception e)
{
e.printStackTrace();
}
- fail("Test "
+ Assert.fail("Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
rg.setValue("292");
} catch (WrongParameterException q)
{
- fail("Couldn't set the temperature parameter "
+ Assert.fail("Couldn't set the temperature parameter "
+ q.getStackTrace());
}
opts.add(rg);