X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=199c4e599a9ff1e5cc0cf83a272f668e993b91b1;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=60c95472f5d9063c65b684ca20b76e773f3d215a;hpb=e2227e5cbd0772e74c24f9e5420a8427fae5ddac;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 60c9547..199c4e5 100755
--- 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)
@@ -532,6 +532,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
 
+    /*
+     * isPopupTrigger fires in mousePressed on Mac,
+     * not until mouseRelease on Windows
+     */
     if (evt.isPopupTrigger() && activeRow != -1)
     {
       showPopupMenu(y, evt.getX());
@@ -539,7 +543,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
 
     ap.getScalePanel().mousePressed(evt);
-
   }
 
   /**
@@ -603,6 +606,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     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());
@@ -807,8 +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))
         {
@@ -1127,4 +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();
+    }
+  }
 }