X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=0f83843a3e41ac42cd8e632856b7d27dad25df3b;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=463c6c3caf142d2902255d92528a6e67cec73510;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 463c6c3..0f83843 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -162,15 +162,18 @@ 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 +181,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     nfr.transferSettings(seqPanel.seqCanvas.fr);
     return nfr;
   }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -449,37 +453,37 @@ 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)
+      {
         /*
-         * Else results are already visible - no need to scroll
+         * 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);
+      }
+      /*
+       * Else results are already visible - no need to scroll
+       */
     }
     else
     {
@@ -953,6 +957,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (updateOverview)
     {
+      // TODO: determine if this paintAlignment changed structure colours
       jalview.structure.StructureSelectionManager
               .getStructureSelectionManager(av.applet)
               .sequenceColoursChanged(this);