JAL-2446 merged to spike branch

[jalview.git] / src / jalview / gui / CutAndPasteTransfer.java

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 8b21058..3eced2f 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -28,9 +28,9 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -52,9 +52,11 @@ import java.awt.datatransfer.Transferable;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
 
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 
@@ -71,7 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewportI viewport;
 
-  AlignmentFileI source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer()
   {
@@ -148,8 +150,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       try
       {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-                new java.io.FileWriter(chooser.getSelectedFile()));
+        PrintWriter out = new PrintWriter(new FileWriter(
+                chooser.getSelectedFile()));
 
         out.print(getText());
         out.close();
@@ -230,10 +232,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
               .getString("label.couldnt_read_data"));
       if (!Jalview.isHeadlessMode())
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                AppletFormatAdapter.SUPPORTED_FORMATS,
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                AppletFormatAdapter.getSupportedFormats(),
                 MessageManager.getString("label.couldnt_read_data"),
-                JOptionPane.WARNING_MESSAGE);
+                JvOptionPane.WARNING_MESSAGE);
       }
       return;
     }
@@ -247,20 +249,20 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       al = fa.readFile(getText(), DataSourceType.PASTE, format);
       source = fa.getAlignFile();
 
-    } catch (java.io.IOException ex)
+    } catch (IOException ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.couldnt_read_pasted_text", new String[]
               { ex.toString() }), MessageManager
               .getString("label.error_parsing_text"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
     }
 
     if (al != null && al.hasValidSequence())
     {
       String title = MessageManager.formatMessage(
               "label.input_cut_paste_params",
-              new String[] { format.toString() });
+              new String[] { format.getName() });
       FeatureSettingsModelI proxyColourScheme = source
               .getFeatureColourScheme();
 
@@ -282,8 +284,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         AlignFrame af;
         if (source instanceof ComplexAlignFile)
         {
-          ColumnSelection colSel = ((ComplexAlignFile) source)
-                  .getColumnSelection();
+          HiddenColumns hidden = ((ComplexAlignFile) source)
+                  .getHiddenColumns();
           SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
@@ -292,10 +294,11 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   .getGlobalColourScheme();
           FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                   .getDisplayedFeatures();
-          af = new AlignFrame(al, hiddenSeqs, colSel,
+          af = new AlignFrame(al, hiddenSeqs, hidden,
                   AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
+          af.setMenusForViewport();
           ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
                   colourSchemeName, al);
           if (cs != null)
@@ -337,10 +340,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
               .getString("label.couldnt_read_data"));
       if (!Jalview.isHeadlessMode())
       {
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                AppletFormatAdapter.SUPPORTED_FORMATS,
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                AppletFormatAdapter.getSupportedFormats(),
                 MessageManager.getString("label.couldnt_read_data"),
-                JOptionPane.WARNING_MESSAGE);
+                JvOptionPane.WARNING_MESSAGE);
       }
     }
   }
@@ -365,6 +368,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   @Override
   public void textarea_mousePressed(MouseEvent e)
   {
+    /*
+     * isPopupTrigger is checked in mousePressed on Mac,
+     * in mouseReleased on Windows
+     */
     if (e.isPopupTrigger())
     {
       JPopupMenu popup = new JPopupMenu(