X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=c0e59a49b9e126143e217c0f8c4818df09b752ae;hb=57ea736ced3c474a9e8e8bc2de1a15a220384e93;hp=f5a8e1c946139b97a3a2d3a07ec36bd2d81adc8d;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index f5a8e1c..c0e59a4 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -24,6 +24,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -35,6 +36,7 @@ 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;
 
@@ -71,6 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   {
     SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         textarea.requestFocus();
@@ -123,6 +126,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     textarea.append(text);
   }
 
+  @Override
   public void save_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -159,6 +163,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void copyItem_actionPerformed(ActionEvent e)
   {
     textarea.getSelectedText();
@@ -172,6 +177,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void pasteMenu_actionPerformed(ActionEvent e)
   {
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -197,6 +203,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void ok_actionPerformed(ActionEvent e)
   {
     String text = getText();
@@ -205,7 +212,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       return;
     }
 
-    String format = new IdentifyFile().Identify(text, "Paste");
+    String format = new IdentifyFile().identify(text, "Paste");
     if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
     {
       System.err.println(MessageManager
@@ -246,7 +253,11 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       String title = MessageManager.formatMessage(
               "label.input_cut_paste_params", new String[] { format });
-      if (viewport != null)
+      /*
+       * if the view panel was closed its alignment is nulled
+       * and this is an orphaned cut and paste window
+       */
+      if (viewport != null && viewport.getAlignment() != null)
       {
         ((AlignViewport) viewport).addAlignment(al, title);
       }
@@ -262,19 +273,29 @@ 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);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
-          af.changeColour(cs);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
+          if (cs != null)
+          {
+            af.changeColour(cs);
+          }
         }
         else
         {
           af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
                   AlignFrame.DEFAULT_HEIGHT);
+          if (source instanceof FeaturesSourceI)
+          {
+            af.getViewport().setShowSequenceFeatures(true);
+          }
         }
 
         af.currentFileFormat = format;
@@ -312,6 +333,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void cancel_actionPerformed(ActionEvent e)
   {
     try
@@ -322,6 +344,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
   }
 
+  @Override
   public void textarea_mousePressed(MouseEvent e)
   {
     if (SwingUtilities.isRightMouseButton(e))
@@ -332,6 +355,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
               MessageManager.getString("action.copy"));
       item.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           copyItem_actionPerformed(e);
@@ -341,6 +365,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       item = new JMenuItem(MessageManager.getString("action.paste"));
       item.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           pasteMenu_actionPerformed(e);