JAL-1812 JAL-2068 add Run Groovy Script to AlignFrame Calculate menu

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 05505a4..bc6def9 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1292,3 +1292,6 @@ status.cancelled_image_export_operation = Cancelled {0} export operation.
 info.error_creating_file = Error creating {0} file.
 exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File
 info.error_creating_file = Error creating {0} file.
+label.run_groovy = Run Groovy console script
+label.run_groovy_tip = Run the script in the Groovy console over this alignment
+label.couldnt_run_groovy_script = Failed to run Groovy script

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 28ff0a1..e439696 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -119,6 +119,8 @@ 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;
@@ -129,6 +131,7 @@ 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;
@@ -466,6 +469,14 @@ 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 +922,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 
     showProducts.setEnabled(canShowProducts());
+    setGroovyEnabled(Desktop.instance.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;
 
   /*
@@ -6090,6 +6112,45 @@ 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);
+    Object console = Desktop.instance.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);
+      } 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");
+    }
+  }
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 27f60ea..ba7f255 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2507,9 +2507,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
               new Class[] { String.class, Object.class });
       java.lang.reflect.Method run = gcClass.getMethod("run");
-      Object gc = gccons.newInstance();
-      setvar.invoke(gc, new Object[] { "Jalview", this });
-      run.invoke(gc);
+      groovyConsole = gccons.newInstance();
+      setvar.invoke(groovyConsole, new Object[] { "Jalview", this });
+      run.invoke(groovyConsole);
+      /*
+       * and rebuild alignframe menus to enable 'Run Groovy'
+       */
+
+      AlignFrame[] alignFrames = getAlignFrames();
+      if (alignFrames != null)
+      {
+        for (AlignFrame af : alignFrames)
+        {
+          af.setGroovyEnabled(true);
+        }
+      }
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
@@ -2917,6 +2929,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   private java.util.concurrent.Semaphore block = new Semaphore(0);
 
+  /*
+   * groovy.ui.Console object - if Groovy jars are present and the 
+   * user has activated the Groovy console. Use via reflection to
+   * avoid compile-time dependency on Groovy libraries.
+   */
+  private static Object groovyConsole;
+
   /**
    * add another dialog thread to the queue
    * 
@@ -3145,4 +3164,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     Desktop.currentAlignFrame = currentAlignFrame;
   }
 
+  public Object getGroovyConsole()
+  {
+    return groovyConsole;
+  }
+
 }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 205b9c6..1eb558e 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -179,6 +179,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu showProducts = new JMenu();
 
+  protected JMenuItem runGroovy = new JMenuItem();
+
   protected JMenuItem rnahelicesColour = new JMenuItem();
 
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
@@ -1726,6 +1728,17 @@ public class GAlignFrame extends JInternalFrame
     // for show products actions see AlignFrame.canShowProducts
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
+    runGroovy.setText(MessageManager.getString("label.run_groovy"));
+    runGroovy.setToolTipText(MessageManager.getString("label.run_groovy_tip"));
+    runGroovy.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        runGroovy_actionPerformed();
+      }
+    });
+
     JMenuItem openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
@@ -2160,6 +2173,7 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
     fileMenu.add(reload);
@@ -2178,6 +2192,9 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
+
+    pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
     editMenu.add(undoMenuItem);
     editMenu.add(redoMenuItem);
     editMenu.add(cut);
@@ -2198,6 +2215,13 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
 
+    showMenu.add(showAllColumns);
+    showMenu.add(showAllSeqs);
+    showMenu.add(showAllhidden);
+    hideMenu.add(hideSelColumns);
+    hideMenu.add(hideSelSequences);
+    hideMenu.add(hideAllSelection);
+    hideMenu.add(hideAllButSelection);
     viewMenu.add(newView);
     viewMenu.add(expandViews);
     viewMenu.add(gatherViews);
@@ -2268,6 +2292,12 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
     colourMenu.add(rnahelicesColour);
+
+    sort.add(sortIDMenuItem);
+    sort.add(sortLengthMenuItem);
+    sort.add(sortGroupMenuItem);
+    sort.add(sortPairwiseMenuItem);
+    sort.add(sortByTreeMenu);
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
@@ -2281,17 +2311,14 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(autoCalculate);
     calculateMenu.add(sortByTree);
     calculateMenu.addSeparator();
+    calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
+    calculateMenu.addSeparator();
+    calculateMenu.add(runGroovy);
+
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    pasteMenu.add(pasteNew);
-    pasteMenu.add(pasteThis);
-    sort.add(sortIDMenuItem);
-    sort.add(sortLengthMenuItem);
-    sort.add(sortGroupMenuItem);
-    sort.add(sortPairwiseMenuItem);
-    sort.add(sortByTreeMenu);
     exportImageMenu.add(htmlMenuItem);
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
@@ -2303,13 +2330,6 @@ public class GAlignFrame extends JInternalFrame
     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
     statusPanel.add(statusBar, null);
     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-    showMenu.add(showAllColumns);
-    showMenu.add(showAllSeqs);
-    showMenu.add(showAllhidden);
-    hideMenu.add(hideSelColumns);
-    hideMenu.add(hideSelSequences);
-    hideMenu.add(hideAllSelection);
-    hideMenu.add(hideAllButSelection);
 
     formatMenu.add(font);
     formatMenu.addSeparator();
@@ -2337,7 +2357,6 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
     selectMenu.add(annotationColumn);
-    calculateMenu.add(expandAlignment);
     // TODO - determine if the listenToViewSelections button is needed : see bug
     // JAL-574
     // selectMenu.addSeparator();
@@ -2355,6 +2374,14 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
+   * Try to run script in a Groovy console, having first ensured that this
+   * alignframe is set as currentAlignFrame in Desktop
+   */
+  protected void runGroovy_actionPerformed()
+  {
+
+  }
+  /**
    * Adds the given action listener and key accelerator to the given menu item.
    * Also saves in a lookup table to support lookup of action by key stroke.
    *