+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.*;
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
-
-
+
jalview.bin.Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
-
+
for (Jws2Instance svc : disc.getServices())
{
-
+
if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
{
rnaalifoldws = svc;
}
}
-
+
System.out.println("State of rnaalifoldws: " + rnaalifoldws);
-
- if (rnaalifoldws == null) System.exit(0);
-
+
+ if (rnaalifoldws == null)
+ System.exit(0);
+
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-
+
af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
-
+
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
-
+
}
@AfterClass
@Test
public void testRNAStructExport()
{
-
-
+
alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
-
+
af.getViewport().getCalcManager().startWorker(alifoldClient);
-
-
+
do
{
try
}
;
} while (af.getViewport().getCalcManager().isWorking());
-
-
+
AlignmentI orig_alig = af.getViewport().getAlignment();
-
+
testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
{
try
{
- // what format would be appropriate for RNAalifold annotations?
+ // what format would be appropriate for RNAalifold annotations?
String aligfileout = new FormatAdapter().formatSequences("PFAM",
al.getSequencesArray());
-
-
+
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
al.getProperties());
}
}
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,
+ "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())
+ 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));
}
}
}
git://source.jalview.org / jalview.git / blobdiff