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JAL-2629 current hmmer commands are now executed in threads
[jalview.git]
/
test
/
jalview
/
io
/
AnnotationFileIOTest.java
diff --git
a/test/jalview/io/AnnotationFileIOTest.java
b/test/jalview/io/AnnotationFileIOTest.java
index
18e008e
..
6a00cde
100644
(file)
--- a/
test/jalview/io/AnnotationFileIOTest.java
+++ b/
test/jalview/io/AnnotationFileIOTest.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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,20
+20,32
@@
*/
package jalview.io;
*/
package jalview.io;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.gui.JvOptionPane;
+import jalview.io.AnnotationFile.ViewDef;
import java.io.File;
import java.io.File;
+import java.util.Hashtable;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class AnnotationFileIOTest
{
public class AnnotationFileIOTest
{
- static String TestFiles[][] =
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
{
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ static String TestFiles[][] = {
{ "Test example annotation import/export", "examples/uniref50.fa",
"examples/testdata/example_annot_file.jva" },
{ "Test multiple combine annotation statements import/export",
{ "Test example annotation import/export", "examples/uniref50.fa",
"examples/testdata/example_annot_file.jva" },
{ "Test multiple combine annotation statements import/export",
@@
-44,9
+56,11
@@
public class AnnotationFileIOTest
"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
{
"Test group only annotation file parsing results in parser indicating annotation was parsed",
"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
{
"Test group only annotation file parsing results in parser indicating annotation was parsed",
- "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } };
+ "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
+ { "Test hiding/showing of insertions on sequence_ref",
+ "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
- @Test
+ @Test(groups = { "Functional" })
public void exampleAnnotationFileIO() throws Exception
{
for (String[] testPair : TestFiles)
public void exampleAnnotationFileIO() throws Exception
{
for (String[] testPair : TestFiles)
@@
-56,7
+70,7
@@
public class AnnotationFileIOTest
}
}
}
}
- public static AlignmentI readAlignmentFile(File f)
+ AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
@@
-64,14
+78,13
@@
public class AnnotationFileIOTest
{
FormatAdapter rf = new FormatAdapter();
{
FormatAdapter rf = new FormatAdapter();
- AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
- new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+ AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+ new IdentifyFile().identify(ff, DataSourceType.FILE));
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(
- al.getSequenceAt(i).createDatasetSequence());
+ al.getSequenceAt(i).createDatasetSequence();
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
@@
-79,7
+92,7
@@
public class AnnotationFileIOTest
{
e.printStackTrace();
}
{
e.printStackTrace();
}
- fail("Couln't read the alignment in file '" + f.toString() + "'");
+ Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
return null;
}
return null;
}
@@
-93,7
+106,7
@@
public class AnnotationFileIOTest
* - label for IO class used to write and read back in the data from
* f
*/
* - label for IO class used to write and read back in the data from
* f
*/
- public static void testAnnotationFileIO(String testname, File f,
+ void testAnnotationFileIO(String testname, File f,
File annotFile)
{
System.out.println("Test: " + testname + "\nReading annotation file '"
File annotFile)
{
System.out.println("Test: " + testname + "\nReading annotation file '"
@@
-102,17
+115,21
@@
public class AnnotationFileIOTest
try
{
AlignmentI al = readAlignmentFile(f);
try
{
AlignmentI al = readAlignmentFile(f);
-
+ HiddenColumns cs = new HiddenColumns();
assertTrue(
"Test "
+ testname
+ "\nAlignment was not annotated - annotation file not imported.",
assertTrue(
"Test "
+ testname
+ "\nAlignment was not annotated - annotation file not imported.",
- new AnnotationFile().readAnnotationFile(al, af,
- FormatAdapter.FILE));
+ new AnnotationFile().readAnnotationFile(al, cs, af,
+ DataSourceType.FILE));
+ AnnotationFile aff = new AnnotationFile();
+ // ViewDef is not used by Jalview
+ ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
+ new Hashtable());
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
+ al.getProperties(), null, al, v);
assertTrue(
"Test "
+ testname
assertTrue(
"Test "
+ testname
@@
-133,16
+150,17
@@
public class AnnotationFileIOTest
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
- FormatAdapter.PASTE));
+ DataSourceType.PASTE));
// test for consistency in io
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
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 for '"
+ annotFile + "'.");
+ testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ annotFile + "'.");