JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 6a621ff..199c4e5 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -49,6 +49,7 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.awt.image.BufferedImage;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
@@ -122,8 +123,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   boolean mouseDragging = false;
 
-  boolean MAC = false;
-
   // for editing cursor
   int cursorX = 0;
 
@@ -141,9 +140,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
-
-    MAC = jalview.util.Platform.isAMac();
-
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -445,8 +441,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     StringBuilder collatedInput = new StringBuilder(64);
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
-    // TODO: refactor and save av.getColumnSelection for efficiency
-    List<Integer> selected = viscols.getSelected();
+
+    /*
+     * the selection list (read-only view) is in selection order, not
+     * column order; make a copy so we can sort it
+     */
+    List<Integer> selected = new ArrayList<Integer>(viscols.getSelected());
     Collections.sort(selected);
     for (int index : selected)
     {
@@ -458,8 +458,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       String tlabel = null;
       if (anots[index] != null)
       { // LML added stem code
-        if (type.equals(HELIX) || type.equals(SHEET)
-                || type.equals(STEM) || type.equals(LABEL))
+        if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+                || type.equals(LABEL))
         {
           tlabel = anots[index].description;
           if (tlabel == null || tlabel.length() < 1)
@@ -507,6 +507,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int height = 0;
     activeRow = -1;
 
+    final int y = evt.getY();
     for (int i = 0; i < aa.length; i++)
     {
       if (aa[i].visible)
@@ -514,7 +515,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         height += aa[i].height;
       }
 
-      if (evt.getY() < height)
+      if (y < height)
       {
         if (aa[i].editable)
         {
@@ -524,58 +525,71 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           // Stretch Graph
           graphStretch = i;
-          graphStretchY = evt.getY();
+          graphStretchY = y;
         }
 
         break;
       }
     }
 
+    /*
+     * isPopupTrigger fires in mousePressed on Mac,
+     * not until mouseRelease on Windows
+     */
     if (evt.isPopupTrigger() && activeRow != -1)
     {
-      if (av.getColumnSelection() == null
-              || av.getColumnSelection().isEmpty())
-      {
-        return;
-      }
+      showPopupMenu(y, evt.getX());
+      return;
+    }
 
-      JPopupMenu pop = new JPopupMenu(
-              MessageManager.getString("label.structure_type"));
-      JMenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide())
-      {
-        item = new JMenuItem(STEM);
-        item.addActionListener(this);
-        pop.add(item);
-      }
-      else
-      {
-        item = new JMenuItem(HELIX);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(SHEET);
-        item.addActionListener(this);
-        pop.add(item);
-      }
-      item = new JMenuItem(LABEL);
+    ap.getScalePanel().mousePressed(evt);
+  }
+
+  /**
+   * Construct and display a context menu at the right-click position
+   * 
+   * @param y
+   * @param x
+   */
+  void showPopupMenu(final int y, int x)
+  {
+    if (av.getColumnSelection() == null
+            || av.getColumnSelection().isEmpty())
+    {
+      return;
+    }
+
+    JPopupMenu pop = new JPopupMenu(
+            MessageManager.getString("label.structure_type"));
+    JMenuItem item;
+    /*
+     * Just display the needed structure options
+     */
+    if (av.getAlignment().isNucleotide())
+    {
+      item = new JMenuItem(STEM);
       item.addActionListener(this);
       pop.add(item);
-      item = new JMenuItem(COLOUR);
+    }
+    else
+    {
+      item = new JMenuItem(HELIX);
       item.addActionListener(this);
       pop.add(item);
-      item = new JMenuItem(REMOVE);
+      item = new JMenuItem(SHEET);
       item.addActionListener(this);
       pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
-
-      return;
     }
-
-    ap.getScalePanel().mousePressed(evt);
-
+    item = new JMenuItem(LABEL);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(COLOUR);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(REMOVE);
+    item.addActionListener(this);
+    pop.add(item);
+    pop.show(this, x, y);
   }
 
   /**
@@ -591,6 +605,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     graphStretchY = -1;
     mouseDragging = false;
     ap.getScalePanel().mouseReleased(evt);
+
+    /*
+     * isPopupTrigger is set in mouseReleased on Windows
+     * (in mousePressed on Mac)
+     */
+    if (evt.isPopupTrigger() && activeRow != -1)
+    {
+      showPopupMenu(evt.getY(), evt.getX());
+    }
+
   }
 
   /**
@@ -790,8 +814,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         text.append(", ")
                 .append(MessageManager.getString("label.sequence"))
-                .append(" ")
-                .append(seqIndex + 1);
+                .append(" ").append(seqIndex + 1);
         char residue = seqref.getCharAt(column);
         if (!Comparison.isGap(residue))
         {
@@ -1110,4 +1133,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return null;
     }
   }
+
+  /**
+   * Try to ensure any references held are nulled
+   */
+  public void dispose()
+  {
+    av = null;
+    ap = null;
+    image = null;
+    fadedImage = null;
+    gg = null;
+    _mwl = null;
+
+    /*
+     * I created the renderer so I will dispose of it
+     */
+    if (renderer != null)
+    {
+      renderer.dispose();
+    }
+  }
 }