HiddenSequences now array, not hashtable

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ddb871e..7d02e14 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -280,9 +280,11 @@ public class AlignViewport
         {
           long t = System.currentTimeMillis();
 
+          int alWidth = alignment.getWidth();
+
           Conservation cons = new jalview.analysis.Conservation("All",
               jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alignment.getWidth() - 1);
+              alignment.getSequences(), 0, alWidth -1);
 
           cons.calculate();
           cons.verdict(false, ConsPercGaps);
@@ -295,7 +297,7 @@ public class AlignViewport
           System.out.println("Conservation took " + (System.currentTimeMillis() - t) +
                              "ms");
 
-          int alWidth = alignment.getWidth();
+
           String sequence = cons.getConsSequence().getSequence();
           float minR;
           float minG;
@@ -389,7 +391,7 @@ public class AlignViewport
 
         if(ap!=null)
         {
-          ap.annotationPanel.repaint();
+          ap.repaint();
         }
         updatingConservation = false;
       }
@@ -523,7 +525,7 @@ public class AlignViewport
 
         if (ap != null)
         {
-          ap.annotationPanel.repaint();
+          ap.repaint();
         }
 
 
@@ -1439,7 +1441,7 @@ public class AlignViewport
       // be done to remove redundancy.
       CigarArray aligview = getViewAsCigars(selectedOnly);
       if (aligview!=null) {
-        return new AlignmentView(aligview, 
+        return new AlignmentView(aligview,
             (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
       }
       return null;