X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=b334a5c59cb271768b7fd667cabd524f6a228ebf;hb=8247c538f13da72c218ef52714ac9ca4acf564d3;hp=577e8742652c1414e7edceedbbc0aaca94b7e460;hpb=a5481d6e853a962af603f4a21b171ba6fc9c200d;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 577e874..b334a5c 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -42,14 +42,14 @@ public class JnetAnnotationMaker
     // in the future we could search for the query
     // sequence in the alignment before calling this function.
     SequenceI seqRef = al.getSequenceAt(firstSeq);
-    int width = preds[0].getSequence().length();
+    int width = preds[0].getSequence().length;
     int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
-    if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width)) 
+    if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width))
     {
       throw (new Exception(
           "Number of residues in "+(delMap==null ? "" : " mapped ")+"supposed query sequence ('" +
           al.getSequenceAt(firstSeq).getName() + "'\n" +
-          al.getSequenceAt(firstSeq).getSequence() +
+          al.getSequenceAt(firstSeq).getSequenceAsString() +
           ")\ndiffer from number of prediction sites in prediction (" + width +
           ")"));
     }
@@ -127,7 +127,7 @@ public class JnetAnnotationMaker
             for (int j = 0; j < width; j++)
             {
             annotations[gapmap[delMap[j]]] = new Annotation(preds[i].getCharAt(
-                j) + "", "", ' ', 0);            
+                j) + "", "", ' ', 0);
             }
           }
         }
@@ -178,4 +178,4 @@ public class JnetAnnotationMaker
      */
 
   }
-}
\ No newline at end of file
+}