JAL-4034 Fix #2 show an icon and a button to press to initiate search

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 3eced2f..112d502 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
@@ -135,13 +136,15 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   @Override
   public void save_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 JalviewFileChooser - Save option
+
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     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);
@@ -150,8 +153,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       try
       {
-        PrintWriter out = new PrintWriter(new FileWriter(
-                chooser.getSelectedFile()));
+        PrintWriter out = new PrintWriter(
+                new FileWriter(chooser.getSelectedFile()));
 
         out.print(getText());
         out.close();
@@ -196,8 +199,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     try
     {
-      textarea.append((String) contents
-              .getTransferData(DataFlavor.stringFlavor));
+      textarea.append(
+              (String) contents.getTransferData(DataFlavor.stringFlavor));
     } catch (Exception ex)
     {
     }
@@ -228,8 +231,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
     if (format == null)
     {
-      System.err.println(MessageManager
-              .getString("label.couldnt_read_data"));
+      System.err
+              .println(MessageManager.getString("label.couldnt_read_data"));
       if (!Jalview.isHeadlessMode())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -253,16 +256,16 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.couldnt_read_pasted_text", new String[]
-              { ex.toString() }), MessageManager
-              .getString("label.error_parsing_text"),
+              { ex.toString() }),
+              MessageManager.getString("label.error_parsing_text"),
               JvOptionPane.WARNING_MESSAGE);
     }
 
     if (al != null && al.hasValidSequence())
     {
-      String title = MessageManager.formatMessage(
-              "label.input_cut_paste_params",
-              new String[] { format.getName() });
+      String title = MessageManager
+              .formatMessage("label.input_cut_paste_params", new String[]
+              { format.getName() });
       FeatureSettingsModelI proxyColourScheme = source
               .getFeatureColourScheme();
 
@@ -272,11 +275,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
        */
       if (viewport != null && viewport.getAlignment() != null)
       {
-        if (proxyColourScheme != null)
-        {
-          viewport.applyFeaturesStyle(proxyColourScheme);
-        }
         ((AlignViewport) viewport).addAlignment(al, title);
+        viewport.applyFeaturesStyle(proxyColourScheme);
       }
       else
       {
@@ -299,8 +299,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
           af.setMenusForViewport();
-          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
-                  colourSchemeName, al);
+          ColourSchemeI cs = ColourSchemeMapper
+                  .getJalviewColourScheme(colourSchemeName, al);
           if (cs != null)
           {
             af.changeColour(cs);
@@ -322,13 +322,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         af.currentFileFormat = format;
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText(MessageManager
+        af.setStatus(MessageManager
                 .getString("label.successfully_pasted_alignment_file"));
 
         try
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
-                  false));
+          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
         } catch (Exception ex)
         {
         }
@@ -336,8 +335,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
     else
     {
-      System.err.println(MessageManager
-              .getString("label.couldnt_read_data"));
+      System.err
+              .println(MessageManager.getString("label.couldnt_read_data"));
       if (!Jalview.isHeadlessMode())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,