X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=1ee83930309ac5fef6711f9a428c803a9c6828b6;hb=4513bd826c54623c14aa8946a51a2382f64e98f3;hp=4590c54bd518f5437a45699592562971a7b4f9ec;hpb=39439812058a1c48ccec89eb80fb139888519d46;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 4590c54..1ee8393 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -33,6 +33,7 @@ import jalview.io.FileParse;
 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;
@@ -259,11 +260,14 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
                   .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);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
           af.changeColour(cs);
         }
         else