X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=9bf1a666d14473ab5d127c1b2d39f3703a51429f;hb=ba1f9fee25b87bdac0c535019252b787939a8f80;hp=8e333ba2c15e8e1615e383062a0dfbcb8d385f13;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 8e333ba..9bf1a66 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -46,6 +46,7 @@ import java.awt.event.ComponentEvent;
 import java.beans.PropertyChangeEvent;
 import java.util.List;
 
+@SuppressWarnings("serial")
 public class AlignmentPanel extends Panel
         implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI
 {
@@ -73,23 +74,6 @@ public class AlignmentPanel extends Panel
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  @Override
-  public void finalize() throws Throwable
-  {
-    alignFrame = null;
-    av = null;
-    vpRanges = null;
-    seqPanel = null;
-    seqPanelHolder = null;
-    sequenceHolderPanel = null;
-    scalePanel = null;
-    scalePanelHolder = null;
-    annotationPanel = null;
-    annotationPanelHolder = null;
-    annotationSpaceFillerHolder = null;
-    super.finalize();
-  }
-
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     try
@@ -361,7 +345,7 @@ public class AlignmentPanel extends Panel
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     // do we need to scroll the panel?
-    if (results != null && results.getSize() > 0)
+    if (results != null && results.getCount() > 0)
     {
       AlignmentI alignment = av.getAlignment();
       int seqIndex = alignment.findIndex(results);
@@ -379,7 +363,7 @@ public class AlignmentPanel extends Panel
       {
         if (JalviewLite.debug)
         {// DEBUG
-          System.out.println(
+          jalview.bin.Console.outPrintln(
                   "DEBUG: scroll didn't happen - results not within alignment : "
                           + seq.getStart() + "," + seq.getEnd());
         }
@@ -389,7 +373,7 @@ public class AlignmentPanel extends Panel
       {
         // DEBUG
         /*
-         * System.out.println("DEBUG: scroll: start=" + r[0] +
+         * jalview.bin.Console.outPrintln("DEBUG: scroll: start=" + r[0] +
          * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
          * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
          * " hextent=" + hextent);
@@ -432,14 +416,14 @@ public class AlignmentPanel extends Panel
   public boolean scrollTo(int ostart, int end, int seqIndex,
           boolean scrollToNearest, boolean redrawOverview)
   {
-    int startv, endv, starts, ends, width;
+    int startv, endv, starts, ends;// , width;
 
     int start = -1;
     if (av.hasHiddenColumns())
     {
       AlignmentI al = av.getAlignment();
-      start = al.getHiddenColumns().findColumnPosition(ostart);
-      end = al.getHiddenColumns().findColumnPosition(end);
+      start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+      end = al.getHiddenColumns().absoluteToVisibleColumn(end);
       if (start == end)
       {
         if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
@@ -530,7 +514,7 @@ public class AlignmentPanel extends Panel
       vpRanges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview);
+    paintAlignment(redrawOverview, false);
     return true;
   }
 
@@ -571,7 +555,7 @@ public class AlignmentPanel extends Panel
     // this is called after loading new annotation onto alignment
     if (alignFrame.getSize().height == 0)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "adjustAnnotationHeight frame size zero NEEDS FIXING");
     }
     fontChanged();
@@ -579,7 +563,7 @@ public class AlignmentPanel extends Panel
     apvscroll.addNotify();
     hscroll.addNotify();
     validate();
-    paintAlignment(true);
+    paintAlignment(true, false);
   }
 
   /**
@@ -686,14 +670,9 @@ public class AlignmentPanel extends Panel
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        width = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(width);
-      }
       if (x < 0)
       {
         x = 0;
@@ -714,7 +693,8 @@ public class AlignmentPanel extends Panel
 
       if ((hextent + x) > width)
       {
-        System.err.println("hextent was " + hextent + " and x was " + x);
+        jalview.bin.Console
+                .errPrintln("hextent was " + hextent + " and x was " + x);
 
         x = width - hextent;
       }
@@ -731,7 +711,7 @@ public class AlignmentPanel extends Panel
 
       if (x < 0)
       {
-        System.err.println("x was " + x);
+        jalview.bin.Console.errPrintln("x was " + x);
         x = 0;
       }
 
@@ -930,7 +910,8 @@ public class AlignmentPanel extends Panel
    * Repaint the alignment and annotations, and, optionally, any overview window
    */
   @Override
-  public void paintAlignment(boolean updateOverview)
+  public void paintAlignment(boolean updateOverview,
+          boolean updateStructures)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
@@ -938,13 +919,14 @@ public class AlignmentPanel extends Panel
             av.getSortAnnotationsBy());
     repaint();
 
-    if (updateOverview)
+    if (updateStructures)
     {
-      // TODO: determine if this paintAlignment changed structure colours
       jalview.structure.StructureSelectionManager
               .getStructureSelectionManager(av.applet)
               .sequenceColoursChanged(this);
-
+    }
+    if (updateOverview)
+    {
       if (overviewPanel != null)
       {
         overviewPanel.updateOverviewImage();
@@ -1130,7 +1112,7 @@ public class AlignmentPanel extends Panel
   public void raiseOOMWarning(String string, OutOfMemoryError error)
   {
     // TODO: JAL-960
-    System.err.println("Out of memory whilst '" + string + "'");
+    jalview.bin.Console.errPrintln("Out of memory whilst '" + string + "'");
     error.printStackTrace();
   }