JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- static String TestFiles[][] = {
- { "Test example annotation import/export", "examples/uniref50.fa",
- "examples/testdata/example_annot_file.jva" },
+ static String TestFiles[][] = { { "Test example annotation import/export",
+ "examples/uniref50.fa", "examples/testdata/example_annot_file.jva" },
{ "Test multiple combine annotation statements import/export",
"examples/uniref50.fa",
"examples/testdata/test_combine_annot.jva" },
- {
- "Test multiple combine annotation statements with sequence_ref import/export",
+ { "Test multiple combine annotation statements with sequence_ref import/export",
"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
- {
- "Test group only annotation file parsing results in parser indicating annotation was parsed",
+ { "Test group only annotation file parsing results in parser indicating annotation was parsed",
"examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
{ "Test hiding/showing of insertions on sequence_ref",
- "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
+ "examples/uniref50.fa",
+ "examples/testdata/uniref50_seqref.jva" } };
@Test(groups = { "Functional" })
public void exampleAnnotationFileIO() throws Exception
{
for (String[] testPair : TestFiles)
{
- testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
- testPair[2]));
+ testAnnotationFileIO(testPair[0], new File(testPair[1]),
+ new File(testPair[2]));
}
}
{
e.printStackTrace();
}
- Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
+ Assert.fail(
+ "Couln't read the alignment in file '" + f.toString() + "'");
return null;
}
* - label for IO class used to write and read back in the data from
* f
*/
- void testAnnotationFileIO(String testname, File f,
- File annotFile)
+ void testAnnotationFileIO(String testname, File f, File annotFile)
{
System.out.println("Test: " + testname + "\nReading annotation file '"
+ annotFile + "' onto : " + f);
{
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, cs, af,
DataSourceType.FILE));
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
al.getProperties(), null, al, v);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Null string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
anfileout != null);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Empty string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
anfileout.length() > "JALVIEW_ANNOTATION".length());
- System.out.println("Output annotation file:\n" + anfileout
- + "\n<<EOF\n");
+ System.out.println(
+ "Output annotation file:\n" + anfileout + "\n<<EOF\n");
AlignmentI al_new = readAlignmentFile(f);
- assertTrue(
- "Test "
- + testname
- + "\nregenerated annotation file did not annotate alignment.",
+ assertTrue("Test " + testname
+ + "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
DataSourceType.PASTE));
{
e.printStackTrace();
}
- Assert.fail("Test "
- + testname
+ Assert.fail("Test " + testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ annotFile + "'.");
}
-
- @Test(groups="Functional")
+
+ @Test(groups = "Functional")
public void testAnnotateAlignmentView()
{
long t1 = System.currentTimeMillis();
+ "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
+ "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
+ "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
- new AnnotationFile().annotateAlignmentView(af.getViewport(), annotationFile, DataSourceType.PASTE);
-
+ new AnnotationFile().annotateAlignmentView(af.getViewport(),
+ annotationFile, DataSourceType.PASTE);
+
AlignmentI al = af.getViewport().getAlignment();
List<SequenceGroup> groups = al.getGroups();
assertEquals(3, groups.size());
sg = groups.get(1);
assertEquals("Group2", sg.getName());
assertTrue(sg.contains(al.getSequenceAt(1)));
-
+
/*
* the bug fix: a second group of the same name is also given properties
*/