merge from develop

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ad7e75c..e29a0e2 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -362,8 +362,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
       // DEBUG
+//       System.err.println(this.av.viewName + " Seq : " + seqIndex
+//       + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -373,7 +374,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
-        end = Math.min(end + offset, seq.getEnd() - 1);
+        end = end + offset - 1;
       }
       if (start < 0)
       {
@@ -402,6 +403,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       seqIndex = Math.max(0, seqIndex - verticalOffset);
 
+      // System.out.println("start=" + start + ", end=" + end + ", startv="
+      // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+      // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
@@ -668,14 +672,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Adjust row/column scrollers to show a visible position in the alignment.
    * 
    * @param x
-   *          visible column to scroll to DOCUMENT ME!
+   *          visible column to scroll to
    * @param y
    *          visible row to scroll to
    * 
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll to "+x+","+y);
+    // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -1609,7 +1613,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public AlignmentI getAlignment()
   {
-    return av.getAlignment();
+    return av == null ? null : av.getAlignment();
   }