/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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
{
}
AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
- boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
+ boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein, dna);
if (!mapped)
{
return false;
}
/*
+ * 'align' the added alignment to match the current one
+ */
+ al.alignAs(thisAlignment);
+
+ /*
* Open SplitFrame with DNA above and protein below, including the alignment
* from textbox and a copy of the original.
*/