JAL-1552 refactor shared dataflavor hander

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 28ff0a1..401ccb7 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -74,6 +74,7 @@ import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.gff.SequenceOntologyI;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -112,13 +113,14 @@ import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.DataFlavor;
 import java.awt.datatransfer.StringSelection;
 import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
 import java.awt.dnd.DropTargetDragEvent;
 import java.awt.dnd.DropTargetDropEvent;
 import java.awt.dnd.DropTargetEvent;
 import java.awt.dnd.DropTargetListener;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyAdapter;
@@ -466,6 +468,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       formatMenu.add(vsel);
     }
+    addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusGained(FocusEvent e)
+      {
+        Desktop.setCurrentAlignFrame(AlignFrame.this);
+      }
+    });
 
   }
 
@@ -911,10 +921,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 
     showProducts.setEnabled(canShowProducts());
+    setGroovyEnabled(Desktop.getGroovyConsole() != null);
 
     updateEditMenuBar();
   }
 
+  /**
+   * Set the enabled state of the 'Run Groovy' option in the Calculate menu
+   * 
+   * @param b
+   */
+  public void setGroovyEnabled(boolean b)
+  {
+    runGroovy.setEnabled(b);
+  }
+
   private IProgressIndicator progressBar;
 
   /*
@@ -3619,8 +3640,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isControlDown()
-                    || SwingUtilities.isRightMouseButton(evt))
+            if (evt.isPopupTrigger())
             {
               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
@@ -4693,6 +4713,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
                     DEFAULT_HEIGHT);
+            if (Cache.getDefault("HIDE_INTRONS", true))
+            {
+              newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+            }
             String newtitle = String.format("%s %s %s",
                     MessageManager.getString(dna ? "label.proteins"
                             : "label.nucleotides"), MessageManager
@@ -5005,49 +5029,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void drop(DropTargetDropEvent evt)
   {
     Transferable t = evt.getTransferable();
-    java.util.List files = null;
+    java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
 
     try
     {
-      DataFlavor uriListFlavor = new DataFlavor(
-              "text/uri-list;class=java.lang.String");
-      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
-      {
-        // Works on Windows and MacOSX
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        files = (java.util.List) t
-                .getTransferData(DataFlavor.javaFileListFlavor);
-      }
-      else if (t.isDataFlavorSupported(uriListFlavor))
-      {
-        // This is used by Unix drag system
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        String data = (String) t.getTransferData(uriListFlavor);
-        files = new java.util.ArrayList(1);
-        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
-                data, "\r\n"); st.hasMoreTokens();)
-        {
-          String s = st.nextToken();
-          if (s.startsWith("#"))
-          {
-            // the line is a comment (as per the RFC 2483)
-            continue;
-          }
-
-          java.net.URI uri = new java.net.URI(s);
-          // check to see if we can handle this kind of URI
-          if (uri.getScheme().toLowerCase().startsWith("http"))
-          {
-            files.add(uri.toString());
-          }
-          else
-          {
-            // otherwise preserve old behaviour: catch all for file objects
-            java.io.File file = new java.io.File(uri);
-            files.add(file.toString());
-          }
-        }
-      }
+      Desktop.transferFromDropTarget(files, protocols, evt, t);
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -5373,7 +5359,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
-    if (SwingUtilities.isRightMouseButton(e))
+    if (e.isPopupTrigger())
     {
       String msg = MessageManager.getString("label.enter_view_name");
       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
@@ -6090,6 +6076,63 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
   }
+
+  /**
+   * Try to run a script in the Groovy console, having first ensured that this
+   * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
+   * be targeted at this alignment.
+   */
+  @Override
+  protected void runGroovy_actionPerformed()
+  {
+    Desktop.setCurrentAlignFrame(this);
+    groovy.ui.Console console = Desktop.getGroovyConsole();
+    if (console != null)
+    {
+      try
+      {
+        console.runScript();
+      } catch (Exception ex)
+      {
+        System.err.println((ex.toString()));
+        JOptionPane
+                .showInternalMessageDialog(Desktop.desktop, MessageManager
+                        .getString("label.couldnt_run_groovy_script"),
+                        MessageManager
+                                .getString("label.groovy_support_failed"),
+                        JOptionPane.ERROR_MESSAGE);
+      }
+    }
+    else
+    {
+      System.err.println("Can't run Groovy script as console not found");
+    }
+  }
+
+  /**
+   * Hides columns containing (or not containing) a specified feature, provided
+   * that would not leave all columns hidden
+   * 
+   * @param featureType
+   * @param columnsContaining
+   * @return
+   */
+  public boolean hideFeatureColumns(String featureType,
+          boolean columnsContaining)
+  {
+    boolean notForHiding = avc.markColumnsContainingFeatures(
+            columnsContaining, false, false, featureType);
+    if (notForHiding)
+    {
+      if (avc.markColumnsContainingFeatures(!columnsContaining, false,
+              false, featureType))
+      {
+        getViewport().hideSelectedColumns();
+        return true;
+      }
+    }
+    return false;
+  }
 }
 
 class PrintThread extends Thread