X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3e3780a17a9ed10619944f282a40fe55e509a4c9;hb=8bcfd58a217316c956529258080b4a3b171fc14c;hp=67152f2655a89a7fa6118f1b0f09a95d0cf35b9e;hpb=1df694418a9563a3bab8b5421a77bc7c83f03f90;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 67152f2..3e3780a 100644
--- 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;
@@ -131,7 +132,6 @@ 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;
@@ -3641,8 +3641,7 @@ 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 +4714,10 @@ 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
@@ -5035,6 +5038,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               "text/uri-list;class=java.lang.String");
       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
+        Cache.log.debug("Drop handled as javaFileListFlavor");
         // Works on Windows and MacOSX
         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
         files = (java.util.List) t
@@ -5042,9 +5046,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       else if (t.isDataFlavorSupported(uriListFlavor))
       {
+        Cache.log.debug("Drop handled as uriListFlavor");
         // This is used by Unix drag system
         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
         String data = (String) t.getTransferData(uriListFlavor);
+        if (data == null)
+        {
+          Cache.log.debug("standard URIListFlavor (" + uriListFlavor
+                  + ") doesn't resolve. trying others.");
+          // try 'best' dataflavor
+          data = (String) t.getTransferData(DataFlavor
+                  .selectBestTextFlavor(t.getTransferDataFlavors()));
+          Cache.log.debug("Dataflavor "
+                  + DataFlavor.selectBestTextFlavor(t
+                          .getTransferDataFlavors()) + " returned " + data);
+        }
         files = new java.util.ArrayList(1);
         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
                 data, "\r\n"); st.hasMoreTokens();)
@@ -5069,6 +5085,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             files.add(file.toString());
           }
         }
+        if (files.size() < 1)
+        {
+          Cache.log
+                  .debug("Couldn't resolve drop data with 'best text'. Here are the supported flavors:");
+          if (data == null && Cache.log.isDebugEnabled())
+          {
+            for (DataFlavor fl : t.getTransferDataFlavors())
+            {
+              Cache.log.debug("Supported transfer dataflavor: "
+                      + fl.toString());
+              Object df = t.getTransferData(fl);
+              if (df != null)
+              {
+                Cache.log.debug("Retrieves: " + df);
+              }
+            }
+          }
+        }
       }
     } catch (Exception e)
     {
@@ -5395,7 +5429,7 @@ 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 +6156,12 @@ 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 +6178,31 @@ 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