+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
+ alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ alignFrame.getViewport().setShowSequenceFeatures(
+ showSeqFeatures);
+ alignFrame.getViewport().setFeaturesDisplayed(fd);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }