JAL-4034 add round corners to 3DB confirmation button with icon on a mac

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

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index bb26caa..fd75296 100644 (file)
--- 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
 {
@@ -344,7 +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);
@@ -415,14 +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))
@@ -513,7 +514,7 @@ public class AlignmentPanel extends Panel
       vpRanges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview);
+    paintAlignment(redrawOverview, false);
     return true;
   }
 
@@ -562,7 +563,7 @@ public class AlignmentPanel extends Panel
     apvscroll.addNotify();
     hscroll.addNotify();
     validate();
-    paintAlignment(true);
+    paintAlignment(true, false);
   }
 
   /**
@@ -669,14 +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;
@@ -913,7 +909,8 @@ 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());
@@ -921,13 +918,14 @@ 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();