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 e439696..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;
@@ -112,7 +113,6 @@ 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;
@@ -131,7 +131,6 @@ import java.awt.print.PageFormat;
 import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
 import java.io.File;
-import java.lang.reflect.Method;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -922,7 +921,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 
     showProducts.setEnabled(canShowProducts());
-    setGroovyEnabled(Desktop.instance.getGroovyConsole() != null);
+    setGroovyEnabled(Desktop.getGroovyConsole() != null);
 
     updateEditMenuBar();
   }
@@ -3641,8 +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]);
 
@@ -4715,6 +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
@@ -5027,49 +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();
@@ -5395,7 +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,
@@ -6122,19 +6086,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void runGroovy_actionPerformed()
   {
     Desktop.setCurrentAlignFrame(this);
-    Object console = Desktop.instance.getGroovyConsole();
+    groovy.ui.Console console = Desktop.getGroovyConsole();
     if (console != null)
     {
-      /*
-       * use reflection here to avoid compile-time dependency
-       * on Groovy libraries
-       */
       try
       {
-        Class<?> gcClass = getClass().getClassLoader().loadClass(
-                "groovy.ui.Console");
-        Method runScript = gcClass.getMethod("runScript");
-        runScript.invoke(console);
+        console.runScript();
       } catch (Exception ex)
       {
         System.err.println((ex.toString()));
@@ -6151,6 +6108,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       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