/*
- * 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.
*
*/
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.JPred301Client;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-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.Argument;
import compbio.metadata.WrongParameterException;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.JPred301Client;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
public class JpredJabaStructExportImport
{
public static String testseqs = "examples/uniref50.fa";
System.out.println("State of jpredws: " + jpredws);
if (jpredws == null)
- System.exit(0);
+ {
+ Assert.fail("jpredws is null");
+ }
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
if (!success)
{
jpredClient.cancelCurrentJob();
- fail("Jpred Client didn't run with hardwired default parameters.");
+ Assert.fail("Jpred Client didn't run with hardwired default parameters.");
}
} catch (InterruptedException x)
String aligfileout = new FormatAdapter().formatSequences("PFAM",
al.getSequencesArray());
- String anfileout = new AnnotationFile().printAnnotations(
- al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
+ String anfileout = new AnnotationFile()
+ .printAnnotationsForAlignment(al);
assertTrue(
"Test "
+ testname
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.");
}
- // @Test
+ @Test
public void testJpredwsSettingsRecovery()
{
- fail("not implemnented");
+ Assert.fail("not implemnented");
List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
.getRunnerConfig().getArguments())
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);