import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();
- private ColumnSelection expectedColSel = new ColumnSelection();
+ private HiddenColumns expectedColSel = new HiddenColumns();
private SequenceI[] expectedHiddenSeqs = new SequenceI[1];
null, true, true, false, 21, 29);
ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
"zappo", seqGrp);
- seqGrp.cs = scheme;
+ seqGrp.cs.setColourScheme(scheme);
seqGrp.setShowNonconserved(false);
seqGrp.setDescription(null);
TEST_SEQ_HEIGHT = expectedSeqs.size();
TEST_GRP_HEIGHT = expectedGrps.size();
TEST_ANOT_HEIGHT = expectedAnnots.size();
- TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size();
+ TEST_CS_HEIGHT = expectedColSel.getHiddenRegions().size();
AlignExportSettingI exportSettings = new AlignExportSettingI()
{
try
{
alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
- AppletFormatAdapter.FILE, JSONFile.FILE_DESC);
+ DataSourceType.FILE, FileFormat.Json);
jf = (JSONFile) formatAdapter.getAlignFile();
AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
- jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ jf.getHiddenColumns(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
String colourSchemeName = jf.getGlobalColourScheme();
af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
- String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC,
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
af.alignPanel.getAlignment(), false);
formatAdapter = new AppletFormatAdapter();
testAlignment = formatAdapter.readFile(jsonOutput,
- AppletFormatAdapter.PASTE, JSONFile.FILE_DESC);
+ DataSourceType.PASTE, FileFormat.Json);
testJsonFile = (JSONFile) formatAdapter.getAlignFile();
// System.out.println(jsonOutput);
} catch (IOException e)
@Test(groups = { "Functional" })
public void hiddenColsTest()
{
- ColumnSelection cs = testJsonFile.getColumnSelection();
+ HiddenColumns cs = testJsonFile.getHiddenColumns();
Assert.assertNotNull(cs);
- Assert.assertNotNull(cs.getHiddenColumns());
- List<int[]> hiddenCols = cs.getHiddenColumns();
+ Assert.assertNotNull(cs.getHiddenRegions());
+ List<int[]> hiddenCols = cs.getHiddenRegions();
Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
Assert.assertEquals(hiddenCols.get(0), expectedColSel
- .getHiddenColumns().get(0),
+ .getHiddenRegions().get(0),
"Mismatched hidden columns!");
}