JAL-1812 bind Groovy to Jalview rather than Desktop, remove reflection

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d1f3421..7701d3e 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;
@@ -466,6 +468,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       formatMenu.add(vsel);
     }
+    addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusGained(FocusEvent e)
+      {
+        Jalview.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;
 
   /*
@@ -1276,13 +1297,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI alignmentToExport = null;
     AlignExportSettingI settings = exportSettings;
     String[] omitHidden = null;
-    int[] alignmentStartEnd = new int[2];
 
     HiddenSequences hiddenSeqs = viewport.getAlignment()
             .getHiddenSequences();
 
     alignmentToExport = viewport.getAlignment();
-    alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
     if (settings == null)
@@ -1297,6 +1316,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       omitHidden = viewport.getViewAsString(false);
     }
 
+    int[] alignmentStartEnd = new int[2];
     if (hasHiddenSeqs && settings.isExportHiddenSequences())
     {
       alignmentToExport = hiddenSeqs.getFullAlignment();
@@ -1304,7 +1324,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       alignmentToExport = viewport.getAlignment();
-      alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+      alignmentStartEnd = viewport.getAlignment()
+              .getVisibleStartAndEndIndex(
+                      viewport
               .getColumnSelection().getHiddenColumns());
     }
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
@@ -1312,55 +1334,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return ed;
   }
 
-  public static int[] getStartEnd(int[] aligmentStartEnd,
-          List<int[]> hiddenCols)
-  {
-    int startPos = aligmentStartEnd[0];
-    int endPos = aligmentStartEnd[1];
-
-    int[] lowestRange = new int[] { -1, -1 };
-    int[] higestRange = new int[] { -1, -1 };
-
-    for (int[] hiddenCol : hiddenCols)
-    {
-      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
-      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
-    }
-
-    if (lowestRange[0] == -1 && lowestRange[1] == -1)
-    {
-      startPos = aligmentStartEnd[0];
-    }
-    else
-    {
-      startPos = lowestRange[1] + 1;
-    }
-
-    if (higestRange[0] == -1 && higestRange[1] == -1)
-    {
-      endPos = aligmentStartEnd[1];
-    }
-    else
-    {
-      endPos = higestRange[0] - 1;
-    }
-
-    // System.out.println("Export range : " + startPos + " - " + endPos);
-    return new int[] { startPos, endPos };
-  }
-
-  public static void main(String[] args)
-  {
-    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
-    hiddenCols.add(new int[] { 0, 0 });
-    hiddenCols.add(new int[] { 6, 9 });
-    hiddenCols.add(new int[] { 11, 12 });
-    hiddenCols.add(new int[] { 33, 33 });
-    hiddenCols.add(new int[] { 50, 50 });
-
-    int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
-    // System.out.println("Export range : " + x[0] + " - " + x[1]);
-  }
 
   /**
    * DOCUMENT ME!
@@ -3667,8 +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]);
 
@@ -4172,7 +4144,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         JMenuItem tm = new JMenuItem();
         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+        if (sm.isDNA() == viewport.getAlignment().isNucleotide()
+                || sm.isProtein() == !viewport.getAlignment()
+                        .isNucleotide())
         {
           String smn = MessageManager.getStringOrReturn(
                   "label.score_model_", sm.getName());
@@ -5419,7 +5393,7 @@ 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,
@@ -6136,6 +6110,38 @@ 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()
+  {
+    Jalview.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");
+    }
+  }
 }
 
 class PrintThread extends Thread