/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.io.AnnotationFile;
import javax.swing.JMenuItem;
import org.junit.AfterClass;
+import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
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);
+ 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())
+ {
+ Assert.assertTrue("Did not create valid structure from RNAALiFold prediction", aa.isValidStruc());
+ }
+ }
+ }
+ }
+
+ @Test
public void testRNAStructExport()
{
// write out parameters
jalview.gui.AlignFrame nalf = null;
assertTrue("Couldn't write out the Jar file",
- new Jalview2XML(false).SaveAlignment(af,
+ new Jalview2XML(false).saveAlignment(af,
"testRnalifold_param.jar", "trial parameter writeout"));
assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
- false).LoadJalviewAlign("testRnalifold_param.jar")) != null);
+ false).loadJalviewAlign("testRnalifold_param.jar")) != null);
if (nalf != null)
{
AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(