+/*
+ * 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 java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Vector;
-
-import jalview.api.AlignCalcManagerI;
-import jalview.datamodel.AlignmentAnnotation;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
+import jalview.gui.Jalview2XML;
import jalview.io.AnnotationFile;
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.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
-public class RNAStructExportImport
+import compbio.metadata.WrongParameterException;
+
+public class RNAStructExportImport
{
public static String testseqs = "examples/unfolded_RF00031.aln";
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
-
-
- System.out.println("test1");
jalview.bin.Cache.initLogger();
- disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
-
- System.out.println("test2");
-
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
+
for (Jws2Instance svc : disc.getServices())
{
-
- System.out.println("Service type: " + svc.serviceType);
-
+
if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
{
rnaalifoldws = svc;
}
}
-
+
System.out.println("State of rnaalifoldws: " + rnaalifoldws);
-
- if (rnaalifoldws == null) System.exit(0);
-
- System.out.println("test3");
-
+
+ if (rnaalifoldws == null)
+ {
+ System.exit(0);
+ }
+
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-
- // Following this method a long way we find some (probably important!)
- // code that I have just commented out!
+
af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
-
+
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
-
- System.out.println("test5");
-
+
}
@AfterClass
}
}
- /**
- * test for patches to JAL-1294
- */
@Test
public void testRNAStructExport()
{
+
alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
-
- System.out.println("Service action text:\n" + alifoldClient.getServiceActionText());
-
-
- System.out.println("START FOLDING");
+
af.getViewport().getCalcManager().startWorker(alifoldClient);
-
-
+
do
{
try
}
;
} while (af.getViewport().getCalcManager().isWorking());
-
- System.out.println("END FOLDING");
-
- // ALL FOR TESTING
- AlignCalcManagerI test = af.getViewport().getCalcManager();
- RNAalifoldClient testWorker = ((RNAalifoldClient)test.getRegisteredWorkersOfClass(RNAalifoldClient.class).get(0));
- testWorker.updateResultAnnotation(true);
- System.out.println("Annotation from RNAalifoldclient");
- for (Annotation ann : testWorker.ourAnnots.get(0).annotations) {
- System.out.print(ann.toString()+"|");
- }
- System.out.println();
-
-
- // Why are the AlignViewport.alignment and the RNAalifoldClient alignment
- // Annotations different
+
AlignmentI orig_alig = af.getViewport().getAlignment();
-
- System.out.println("orig_alig has class: " + orig_alig.getClass());
-
- // some time before here but after the RNAalifoldClient Update method
- // the alignment annotation is replaced....
-
- System.out.println("orig_alig annotation:\n");
- for (AlignmentAnnotation an : orig_alig.getAlignmentAnnotation()) {
- for (Annotation ann : an.annotations) {
- System.out.print(ann.toString()+"|");
- }
- System.out.println();
- }
-
-
+
testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
{
try
{
- String aligfileout = new FormatAdapter().formatSequences("CLUSTAL",
+ // what format would be appropriate for RNAalifold annotations?
+ String aligfileout = new FormatAdapter().formatSequences("PFAM",
al.getSequencesArray());
-
- // test
-// System.out.println("aligfileout:\n" + aligfileout);
-
- String anfileout = new AnnotationFile().printAnnotations(
- al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
+
+ String anfileout = new AnnotationFile()
+ .printAnnotationsForAlignment(al);
assertTrue(
"Test "
+ testname
System.out.println("Output annotation file:\n" + anfileout
+ "\n<<EOF\n");
+ // again what format would be appropriate?
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
- FormatAdapter.PASTE, "CLUSTAL");
+ FormatAdapter.PASTE, "PFAM");
assertTrue(
"Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
+ @Test
+ 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())
+ {
+ if (rg.getDescription().contains("emperature"))
+ {
+ try
+ {
+ rg.setValue("292");
+ } catch (WrongParameterException q)
+ {
+ fail("Couldn't set the temperature parameter "
+ + q.getStackTrace());
+ }
+ opts.add(rg);
+ }
+ if (rg.getDescription().contains("max"))
+ {
+ opts.add(rg);
+ }
+ }
+ alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+
+ af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ } while (af.getViewport().getCalcManager().isWorking());
+ 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)
+ {
+ 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()))
+ {
+ i.doClick();
+ break;
+ }
+ }
+ }
+ while (af.getViewport().isCalcInProgress())
+ {
+ 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));
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff