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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index afdfd69..652d8d1 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -167,7 +167,7 @@ public class AlignViewport
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
       rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
+      centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
       autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
       padGaps = Cache.getDefault("PAD_GAPS", true);
@@ -456,9 +456,14 @@ public class AlignViewport
     boolean updatingConsensus = false;
 
     boolean updatingConservation = false;
+    /**
+     * centre columnar annotation labels in displayed alignment annotation
+     * TODO: add to jalviewXML and annotation display settings
+     */
+    boolean centreColumnLabels=false;
 
     /**
-     * DOCUMENT ME!
+     * trigger update of conservation annotation
      */
     public void updateConservation(final AlignmentPanel ap)
     {
@@ -472,7 +477,7 @@ public class AlignViewport
     }
 
     /**
-     * DOCUMENT ME!
+     * trigger update of consensus annotation
      */
     public void updateConsensus(final AlignmentPanel ap)
     {
@@ -513,7 +518,7 @@ public class AlignViewport
 
         try
         {
-          int aWidth = alignment.getWidth();
+          int aWidth = (alignment!=null) ? alignment.getWidth() : 0; // null pointer possibility here.
           if(aWidth<0)
         {
             return;
@@ -1893,4 +1898,13 @@ public class AlignViewport
       }
       return false;
     }
+    
+    public boolean getCentreColumnLabels()
+    {
+      return centreColumnLabels;
+    }
+    public void setCentreColumnLabels(boolean centrecolumnlabels)
+    {
+      centreColumnLabels =  centrecolumnlabels;
+    }
 }