X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fws%2Fjabaws%2FDisorderAnnotExportImport.java;h=c1847229cf2e2480da460f222af11310adae2009;hb=3412b273e964fb1a9d22564b04a5f0c827ec2461;hp=bd743e0e1f786c23615e8931a8c79ed30721b9b7;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index bd743e0..c184722 100644
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -1,28 +1,31 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* 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.List;
-
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.Assert;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.io.AnnotationFile;
@@ -32,9 +35,8 @@ import jalview.ws.jws2.AADisorderClient;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.util.ArrayList;
+import java.util.List;
public class DisorderAnnotExportImport
{
@@ -98,16 +100,17 @@ public class DisorderAnnotExportImport
;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
- // NOTE: Consensus annotation row cannot be exported and reimported faithfully - so we remove them
+ // NOTE: Consensus annotation row cannot be exported and reimported
+ // faithfully - so we remove them
List toremove = new ArrayList();
- for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+ for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
{
if (aa.autoCalculated)
{
toremove.add(aa);
}
}
- for (AlignmentAnnotation aa:toremove)
+ for (AlignmentAnnotation aa : toremove)
{
orig_alig.deleteAnnotation(aa);
}
@@ -121,9 +124,8 @@ public class DisorderAnnotExportImport
{
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
@@ -148,13 +150,13 @@ public class DisorderAnnotExportImport
FormatAdapter.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
return;
} catch (Exception e)
{
e.printStackTrace();
}
- fail("Test "
+ Assert.fail("Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}