import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.AfterTest;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.AfterTest;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
null, true, true, false, 21, 29);
ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
"zappo", seqGrp);
null, true, true, false, 21, 29);
ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
"zappo", seqGrp);
jf = (JSONFile) formatAdapter.getAlignFile();
AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
jf = (JSONFile) formatAdapter.getAlignFile();
AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
- af.changeColour(jf.getColourScheme());
+ String colourSchemeName = jf.getGlobalColourScheme();
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, alignment);
+ af.changeColour(cs);
af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
af.alignPanel.getAlignment(), false);
formatAdapter = new AppletFormatAdapter();
testAlignment = formatAdapter.readFile(jsonOutput,
af.alignPanel.getAlignment(), false);
formatAdapter = new AppletFormatAdapter();
testAlignment = formatAdapter.readFile(jsonOutput,
Assert.assertNotNull(cs.getHiddenColumns());
List<int[]> hiddenCols = cs.getHiddenColumns();
Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
Assert.assertNotNull(cs.getHiddenColumns());
List<int[]> hiddenCols = cs.getHiddenColumns();
Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
- Assert.assertEquals(hiddenCols, expectedColSel.getHiddenColumns(),
+ Assert.assertEquals(hiddenCols.get(0), expectedColSel
+ .getHiddenColumns().get(0),
{
Assert.assertNotNull(testJsonFile.getHiddenSequences(),
"Hidden sequence Expected but found Null");
{
Assert.assertNotNull(testJsonFile.getHiddenSequences(),
"Hidden sequence Expected but found Null");