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Merge remote-tracking branch 'origin/develop' into
[jalview.git]
/
test
/
jalview
/
ws
/
jabaws
/
JpredJabaStructExportImport.java
diff --git
a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index
30317f7
..
0743581
100644
(file)
--- a/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@
-77,6
+77,13
@@
public class JpredJabaStructExportImport
}
}
}
}
+ System.out.println("State of jpredws: " + jpredws);
+
+ if (jpredws == null)
+ {
+ System.exit(0);
+ }
+
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
@@
-105,8
+112,6
@@
public class JpredJabaStructExportImport
af.getViewport().getSelectionGroup().getSequenceAt(0),
false);
af.hideSelSequences_actionPerformed(null);
af.getViewport().getSelectionGroup().getSequenceAt(0),
false);
af.hideSelSequences_actionPerformed(null);
-
- assertNotNull(jpredws);
jpredClient = new JPred301Client(jpredws, af, null, null);
assertTrue(
jpredClient = new JPred301Client(jpredws, af, null, null);
assertTrue(
@@
-152,7
+157,7
@@
public class JpredJabaStructExportImport
@Test
public void testJPredStructExport()
{
@Test
public void testJPredStructExport()
{
- assertNotNull(jpredws);
+
jpredClient = new JPred301Client(jpredws, af, null, null);
af.getViewport().getCalcManager().startWorker(jpredClient);
jpredClient = new JPred301Client(jpredws, af, null, null);
af.getViewport().getCalcManager().startWorker(jpredClient);
@@
-182,9
+187,8
@@
public class JpredJabaStructExportImport
String aligfileout = new FormatAdapter().formatSequences("PFAM",
al.getSequencesArray());
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
assertTrue(
"Test "
+ testname
@@
-246,8
+250,6
@@
public class JpredJabaStructExportImport
opts.add(rg);
}
}
opts.add(rg);
}
}
-
- assertNotNull(jpredws);
jpredClient = new JPred301Client(jpredws, af, null, opts);
af.getViewport().getCalcManager().startWorker(jpredClient);
jpredClient = new JPred301Client(jpredws, af, null, opts);
af.getViewport().getCalcManager().startWorker(jpredClient);
@@
-268,10
+270,10
@@
public class JpredJabaStructExportImport
// write out parameters
jalview.gui.AlignFrame nalf = null;
assertTrue("Couldn't write out the Jar file",
// 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,
"testJPredWS_param.jar", "trial parameter writeout"));
assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
"testJPredWS_param.jar", "trial parameter writeout"));
assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
- false).LoadJalviewAlign("testJpredWS_param.jar")) != null);
+ false).loadJalviewAlign("testJpredWS_param.jar")) != null);
if (nalf != null)
{
AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
if (nalf != null)
{
AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(