expectedSeqs.put(seq.getName(), seq);
}
- // create and add sequence groups
- ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ // create and add a sequence group
+ List<SequenceI> grpSeqs = new ArrayList<SequenceI>();
grpSeqs.add(seqs[1]);
grpSeqs.add(seqs[2]);
grpSeqs.add(seqs[3]);
grpSeqs.add(seqs[4]);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs,
+ "JGroup:1883305585",
null, true, true, false, 21, 29);
ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
"zappo", seqGrp);
"Zappo colour scheme expected!");
}
- @Test(groups = { "Functional" })
/**
- * Test for bug JAL-2489, NPE when exporting BioJSON with global colour scheme set as 'None'
+ * Test for bug JAL-2489, NPE when exporting BioJSON with global colour
+ * scheme, and a group colour scheme, set as 'None'
*/
- public void testBioJSONRoundTripWithGlobalColourSchemeSetAsNone()
+ @Test(groups = { "Functional" })
+ public void testBioJSONRoundTripWithColourSchemeNone()
{
AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
bioJsonFile.getHiddenSequences(),
bioJsonFile.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- // Change colour scheme to 'None' and perform round trip
+
+ /*
+ * Create a group on the alignment;
+ * Change global and group colour scheme to 'None' and perform round trip
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(_alignment.getSequenceAt(0), false);
+ sg.setColourScheme(null);
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
ResidueColourScheme.NONE, _alignment);
alignFrame.changeColour(cs);
// System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
return matched;
}
+
+ /**
+ * Test group roundtrip with null (None) group colour scheme
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testGrpParsed_colourNone() throws IOException
+ {
+ AlignmentI copy = new Alignment(testAlignment);
+ SequenceGroup sg = testAlignment.getGroups().get(0);
+ SequenceGroup copySg = new SequenceGroup(new ArrayList<SequenceI>(),
+ sg.getName(),
+ null, sg.getDisplayBoxes(), sg.getDisplayText(),
+ sg.getColourText(), sg.getStartRes(), sg.getEndRes());
+ for (SequenceI seq : sg.getSequences())
+ {
+ int seqIndex = testAlignment.findIndex(seq);
+ copySg.addSequence(copy.getSequenceAt(seqIndex), false);
+ }
+ copy.addGroup(copySg);
+
+ AlignFrame af = new AlignFrame(copy, copy.getWidth(), copy.getHeight());
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter(
+ af.alignPanel);
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
+ copy, false);
+ formatAdapter = new AppletFormatAdapter();
+ AlignmentI newAlignment = formatAdapter.readFile(jsonOutput,
+ DataSourceType.PASTE, FileFormat.Json);
+
+ Assert.assertNotNull(newAlignment.getGroups());
+ for (SequenceGroup seqGrp : newAlignment.getGroups())
+ {
+ SequenceGroup expectedGrp = expectedGrps.get(seqGrp.getName());
+ AssertJUnit.assertTrue(
+ "Failed SequenceGroup Test for >>> " + seqGrp.getName(),
+ isGroupMatched(expectedGrp, seqGrp));
+ passedCount++;
+ }
+ AssertJUnit.assertEquals("Some SequenceGroups did not pass the test",
+ TEST_GRP_HEIGHT, passedCount);
+ }
}