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

[jalview.git] / src / jalview / appletgui / AlignmentPanel.java

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index fd6652b..813ab84 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -68,7 +68,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  public void finalize()
+  @Override
+  public void finalize() throws Throwable
   {
     alignFrame = null;
     av = null;
@@ -80,6 +81,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     annotationPanel = null;
     annotationPanelHolder = null;
     annotationSpaceFillerHolder = null;
+    super.finalize();
   }
 
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
@@ -121,6 +123,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     addComponentListener(new ComponentAdapter()
     {
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         setScrollValues(av.getStartRes(), av.getStartSeq());
@@ -146,6 +149,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     final AlignmentPanel ap = this;
     av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
     {
+      @Override
       public void propertyChange(java.beans.PropertyChangeEvent evt)
       {
         if (evt.getPropertyName().equals("alignment"))
@@ -162,15 +166,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     return av;
   }
+
   public SequenceRenderer getSequenceRenderer()
   {
     return seqPanel.seqCanvas.sr;
   }
+
   @Override
   public jalview.api.FeatureRenderer getFeatureRenderer()
   {
     return seqPanel.seqCanvas.fr;
   }
+
   @Override
   public jalview.api.FeatureRenderer cloneFeatureRenderer()
   {
@@ -178,6 +185,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     nfr.transferSettings(seqPanel.seqCanvas.fr);
     return nfr;
   }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -449,37 +457,37 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       // setScrollValues(start, seqIndex);
       // }
       // logic copied from jalview.gui.AlignmentPanel:
-        if ((startv = av.getStartRes()) >= start)
-        {
-          /*
-           * Scroll left to make start of search results visible
-           */
-          setScrollValues(start - 1, seqIndex);
-        }
-        else if ((endv = av.getEndRes()) <= end)
-        {
-          /*
-           * Scroll right to make end of search results visible
-           */
-          setScrollValues(startv + 1 + end - endv, seqIndex);
-        }
-        else if ((starts = av.getStartSeq()) > seqIndex)
-        {
-          /*
-           * Scroll up to make start of search results visible
-           */
-          setScrollValues(av.getStartRes(), seqIndex);
-        }
-        else if ((ends = av.getEndSeq()) <= seqIndex)
-        {
-          /*
-           * Scroll down to make end of search results visible
-           */
-          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
-        }
+      if ((startv = av.getStartRes()) >= start)
+      {
+        /*
+         * Scroll left to make start of search results visible
+         */
+        setScrollValues(start - 1, seqIndex);
+      }
+      else if ((endv = av.getEndRes()) <= end)
+      {
+        /*
+         * Scroll right to make end of search results visible
+         */
+        setScrollValues(startv + 1 + end - endv, seqIndex);
+      }
+      else if ((starts = av.getStartSeq()) > seqIndex)
+      {
+        /*
+         * Scroll up to make start of search results visible
+         */
+        setScrollValues(av.getStartRes(), seqIndex);
+      }
+      else if ((ends = av.getEndSeq()) <= seqIndex)
+      {
         /*
-         * Else results are already visible - no need to scroll
+         * Scroll down to make end of search results visible
          */
+        setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+      }
+      /*
+       * Else results are already visible - no need to scroll
+       */
     }
     else
     {
@@ -534,6 +542,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    * automatically adjust annotation panel height for new annotation whilst
    * ensuring the alignment is still visible.
    */
+  @Override
   public void adjustAnnotationHeight()
   {
     // TODO: display vertical annotation scrollbar if necessary
@@ -766,6 +775,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = av.getStartRes();
@@ -943,6 +953,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   /**
    * Repaint the alignment and annotations, and, optionally, any overview window
    */
+  @Override
   public void paintAlignment(boolean updateOverview)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
@@ -965,11 +976,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     invalidate();