X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=acc71f306db90e9e4fc3930de20837b5535f79e5;hb=4513bd826c54623c14aa8946a51a2382f64e98f3;hp=cd5c79277e59d9d14f87ec18d8623c34922319d7;hpb=3f25214f0a8d25899d472a024e3b49d84fefc3a4;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index cd5c792..acc71f3 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -35,6 +35,7 @@ import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
@@ -66,6 +67,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   AlignViewportI viewport;
 
   FileParse source = null;
+
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -129,7 +131,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_text_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -233,8 +236,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.formatMessage(
-                        "label.couldnt_read_pasted_text", new String[]
-                        { ex.toString() }), MessageManager
+                        "label.couldnt_read_pasted_text",
+                        new String[] { ex.toString() }), MessageManager
                         .getString("label.error_parsing_text"),
                 JOptionPane.WARNING_MESSAGE);
       }
@@ -243,8 +246,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     if (al != null && al.hasValidSequence())
     {
       String title = MessageManager.formatMessage(
-              "label.input_cut_paste_params", new String[]
-              { format });
+              "label.input_cut_paste_params", new String[] { format });
       if (viewport != null)
       {
         ((AlignViewport) viewport).addAlignment(al, title);
@@ -261,14 +263,16 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
-          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          String colourSchemeName = ((ComplexAlignFile) source)
+                  .getGlobalColourScheme();
           FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                   .getDisplayedFeatures();
           af = new AlignFrame(al, hiddenSeqs, colSel,
-                  AlignFrame.DEFAULT_WIDTH,
-                  AlignFrame.DEFAULT_HEIGHT);
+                  AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
           af.changeColour(cs);
         }
         else
@@ -306,7 +310,6 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
   }
 
-
   /**
    * DOCUMENT ME!
    *