import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
af = new AlignFrame(al, hiddenSeqs, colSel,
alignFrame.viewport.applet, "Cut & Paste input - "
+ format, false);
af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
- af.changeColour(cs);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
}
else
{