+ if (source instanceof ComplexAlignFile)
+ {
+ HiddenColumns colSel = ((ComplexAlignFile) source)
+ .getHiddenColumns();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
+ alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.getViewport().setFeaturesDisplayed(fd);
+ alignFrame.getViewport().setShowSequenceFeatures(
+ ((ComplexAlignFile) source).isShowSeqFeatures());
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }
+ }
+ else
+ {
+ alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (source instanceof FeaturesSourceI)
+ {
+ alignFrame.getViewport().setShowSequenceFeatures(true);
+ }
+ }
+ // add metadata and update ui
+ if (!(protocol == DataSourceType.PASTE))
+ {