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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
test
/
jalview
/
ws
/
jabaws
/
DisorderAnnotExportImport.java
diff --git
a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index
58aa019
..
35d5ccd
100644
(file)
--- a/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,10
+20,8
@@
*/
package jalview.ws.jabaws;
*/
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 jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-34,10
+32,15
@@
import jalview.ws.jws2.AADisorderClient;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
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;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+@Test(groups = { "Network" })
public class DisorderAnnotExportImport
{
public static String testseqs = "examples/uniref50.fa";
public class DisorderAnnotExportImport
{
public static String testseqs = "examples/uniref50.fa";
@@
-50,7
+53,7
@@
public class DisorderAnnotExportImport
public static jalview.gui.AlignFrame af = null;
public static jalview.gui.AlignFrame af = null;
- @BeforeClass
+ @BeforeClass(inheritGroups = true)
public static void setUpBeforeClass() throws Exception
{
public static void setUpBeforeClass() throws Exception
{
@@
-71,13
+74,14
@@
public class DisorderAnnotExportImport
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
if (af != null)
{
af.setVisible(false);
af.dispose();
public static void tearDownAfterClass() throws Exception
{
if (af != null)
{
af.setVisible(false);
af.dispose();
+ af = null;
}
}
}
}
@@
-100,16
+104,17
@@
public class DisorderAnnotExportImport
;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
;
} 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<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+ for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
{
if (aa.autoCalculated)
{
toremove.add(aa);
}
}
{
if (aa.autoCalculated)
{
toremove.add(aa);
}
}
- for (AlignmentAnnotation aa:toremove)
+ for (AlignmentAnnotation aa : toremove)
{
orig_alig.deleteAnnotation(aa);
}
{
orig_alig.deleteAnnotation(aa);
}
@@
-123,9
+128,8
@@
public class DisorderAnnotExportImport
{
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
@@
-150,13
+154,13
@@
public class DisorderAnnotExportImport
FormatAdapter.PASTE));
// test for consistency in io
FormatAdapter.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
return;
} catch (Exception e)
{
e.printStackTrace();
}
return;
} catch (Exception e)
{
e.printStackTrace();
}
- fail("Test "
+ Assert.fail("Test "
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}