+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jabaws;
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
-import java.awt.Component;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-
-import jalview.api.AlignCalcManagerI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AADisorderClient;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.dm.JabaOption;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.AutoCalcSetting;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.awt.Component;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+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;
+/*
+ * All methods in this class are set to the Network group because setUpBeforeClass will fail
+ * if there is no network.
+ */
+@Test(singleThreaded = true)
public class RNAStructExportImport
{
- public static String testseqs = "examples/unfolded_RF00031.aln";
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
+
+ public static String testseqs = "examples/RF00031_folded.stk";
public static Jws2Discoverer disc;
public static jalview.gui.AlignFrame af = null;
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.initLogger();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
- jalview.bin.Cache.initLogger();
- disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+ while (disc.isRunning())
+ {
+ // don't get services until discoverer has finished
+ Thread.sleep(100);
+ }
for (Jws2Instance svc : disc.getServices())
{
System.out.println("State of rnaalifoldws: " + rnaalifoldws);
if (rnaalifoldws == null)
- System.exit(0);
+ {
+ Assert.fail("no web service");
+ }
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
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
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
if (af != null)
{
af.setVisible(false);
af.dispose();
+ File f = new File(JAR_FILE_NAME);
+ if (f.exists())
+ {
+ f.delete();
+ }
}
}
- @Test
- public void testRNAStructExport()
+ @Test(groups = { "Network" })
+ public void testRNAAliFoldValidStructure()
{
alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
} 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());
+ }
+ }
+ }
+ }
- testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+ @Test(groups = { "Network" })
+ public void testRNAStructExport()
+ {
+
+ 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();
+ // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
+ // annotation is mistakenly recognised as an RNA annotation row when read in
+ // as an annotation file.
+ verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
- public static void testAnnotationFileIO(String testname, AlignmentI al)
+ static void verifyAnnotationFileIO(String testname, AlignmentI al)
{
try
{
// what format would be appropriate for RNAalifold annotations?
- String aligfileout = new FormatAdapter().formatSequences("PFAM",
- al.getSequencesArray());
+ String aligfileout = FileFormat.Pfam.getWriter(null).print(
+ al.getSequencesArray(), true);
- String anfileout = new AnnotationFile().printAnnotations(
- al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
- assertTrue(
+ String anfileout = new AnnotationFile()
+ .printAnnotationsForAlignment(al);
+ assertNotNull(
"Test "
+ testname
+ "\nAlignment annotation file was not regenerated. Null string",
- anfileout != null);
+ anfileout);
assertTrue(
"Test "
+ testname
// again what format would be appropriate?
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
- FormatAdapter.PASTE, "PFAM");
+ DataSourceType.PASTE, FileFormat.Pfam);
assertTrue(
"Test "
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
- FormatAdapter.PASTE));
+ DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ 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(groups = { "Network" })
public void testRnaalifoldSettingsRecovery()
{
- List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
- for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
- .getRunnerConfig().getArguments())
+ List<Argument> opts = new ArrayList<Argument>();
+ for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+ .getArguments())
{
if (rg.getDescription().contains("emperature"))
{
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);
}
}
alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
-
+
af.getViewport().getCalcManager().startWorker(alifoldClient);
-
+
do
{
try
}
;
} while (af.getViewport().getCalcManager().isWorking());
- AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
+ AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
+ alifoldClient.getCalcId());
String oldsettings = oldacs.getWsParamFile();
// write out parameters
- jalview.gui.AlignFrame nalf=null;
- assertTrue("Couldn't write out the Jar file",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);
- if (nalf!=null)
+ jalview.gui.AlignFrame nalf = null;
+ assertTrue("Couldn't write out the Jar file",
+ new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME,
+ "trial parameter writeout"));
+ assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
+ false).loadJalviewAlign(JAR_FILE_NAME)) != null);
+ if (nalf != null)
{
- AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
- assertTrue("Calc ID settings not recovered from viewport stash", acs.equals(oldacs));
- assertTrue("Serialised Calc ID settings not identical to those recovered from viewport stash", acs.getWsParamFile().equals(oldsettings));
- JMenu nmenu=new JMenu();
- new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, rnaalifoldws, af);
- assertTrue("Couldn't get menu entry for service",nmenu.getItemCount()>0);
- for (Component itm: nmenu.getMenuComponents())
+ AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
+ alifoldClient.getCalcId());
+ assertTrue("Calc ID settings not recovered from viewport stash",
+ acs.equals(oldacs));
+ assertTrue(
+ "Serialised Calc ID settings not identical to those recovered from viewport stash",
+ acs.getWsParamFile().equals(oldsettings));
+ JMenu nmenu = new JMenu();
+ new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
+ rnaalifoldws, af);
+ assertTrue("Couldn't get menu entry for service",
+ nmenu.getItemCount() > 0);
+ for (Component itm : nmenu.getMenuComponents())
{
if (itm instanceof JMenuItem)
{
JMenuItem i = (JMenuItem) itm;
- if (i.getText().equals(rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
- {
+ if (i.getText().equals(
+ rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
+ {
i.doClick();
break;
- }
+ }
}
}
while (af.getViewport().isCalcInProgress())
{
- try { Thread.sleep(200);
- } catch (Exception x) {};
+ try
+ {
+ Thread.sleep(200);
+ } catch (Exception x)
+ {
+ }
+ ;
}
- AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
- assertTrue("Calc ID settings after recalculation has not been recovered.", acs2.getWsParamFile().equals(oldsettings));
+ AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
+ alifoldClient.getCalcId());
+ assertTrue(
+ "Calc ID settings after recalculation has not been recovered.",
+ acs2.getWsParamFile().equals(oldsettings));
}
}
}