import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
- scheme, true, true, false, 21, 29);
+ null, true, true, false, 21, 29);
+ ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+ "zappo", seqGrp);
+ seqGrp.cs = scheme;
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,
+ actualGrp.getStartRes());
System.out.println(expectedGrp.getEndRes() + " | "
+ actualGrp.getEndRes());
+ actualGrp.getStartRes());
System.out.println(expectedGrp.getEndRes() + " | "
+ actualGrp.getEndRes());
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()