private Alignment alignment;
- private HashMap<String, SequenceI> expectedSeqs = new HashMap<String, SequenceI>();
+ private HashMap<String, SequenceI> expectedSeqs = new HashMap<>();
- private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<String, AlignmentAnnotation>();
+ private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<>();
- private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();
+ private HashMap<String, SequenceGroup> expectedGrps = new HashMap<>();
private HiddenColumns expectedColSel = new HiddenColumns();
}
// create and add a sequence group
- List<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ List<SequenceI> grpSeqs = new ArrayList<>();
grpSeqs.add(seqs[1]);
grpSeqs.add(seqs[2]);
grpSeqs.add(seqs[3]);
TEST_SEQ_HEIGHT = expectedSeqs.size();
TEST_GRP_HEIGHT = expectedGrps.size();
TEST_ANOT_HEIGHT = expectedAnnots.size();
- TEST_CS_HEIGHT = expectedColSel.getHiddenRegions().size();
+ TEST_CS_HEIGHT = expectedColSel.getHiddenColumnsCopy().size();
exportSettings = new AlignExportSettingI()
{
{
HiddenColumns cs = testJsonFile.getHiddenColumns();
Assert.assertNotNull(cs);
- Assert.assertNotNull(cs.getHiddenRegions());
- List<int[]> hiddenCols = cs.getHiddenRegions();
+ Assert.assertNotNull(cs.getHiddenColumnsCopy());
+ List<int[]> hiddenCols = cs.getHiddenColumnsCopy();
Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
Assert.assertEquals(hiddenCols.get(0), expectedColSel
- .getHiddenRegions().get(0),
+ .getHiddenColumnsCopy().get(0),
"Mismatched hidden columns!");
}