X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FSecondaryStructureDistanceModel.java;h=0aac7fac83a739ca4146d7f997c30b39bf1f1fd1;hb=f1b00517fe5f888f3213d70270e27a83dffe1695;hp=7fcee35fcc55650655866356c3e728f9bb76b989;hpb=77d73c1194625fe12c6e3f3431b37459e5592d8a;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
index 7fcee35..0aac7fa 100644
--- a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
@@ -255,14 +255,19 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel
 	  int seqPosition = seq.findPosition(columnPosition);
 	  AlignmentAnnotation[] aa = seq.getRefSeq().getAnnotation("Secondary Structure");
 	  if (aa != null) {
+	    if (aa[0].getAnnotationForPosition(seqPosition) != null) {
 	      Annotation a = aa[0].getAnnotationForPosition(seqPosition);
 	      ss = a.secondaryStructure;
 	      if (ss == ' ') {
-	          ss = 'C'; // In JalView, 'C' is represented as ' ' 
-	      }
-	      if (ss != '\0') { // Check if ss is not the default null character
-	          secondaryStructure.add(String.valueOf(ss));
+	        ss = 'C'; // In JalView, 'C' is represented as ' ' 
 	      }
+	    }
+	    else {
+	      ss = 'C';
+	    }
+	    if (ss != '\0') { // Check if ss is not the default null character
+	      secondaryStructure.add(String.valueOf(ss));
+	    }
 	  }
 	  return secondaryStructure;
   }