+ HiddenColumns colSel = ((ComplexAlignFile) source)
+ .getHiddenColumns();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ af = new AlignFrame(al, hiddenSeqs, colSel,
+ alignFrame.viewport.applet,
+ "Cut & Paste input - " + format, false);
+ af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }