X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=2a8a00ffbe3873507e8daa3e3cbce0e311e9113c;hb=d065bc916cb63af83cdab7319f5177a855724aba;hp=e944720f0107a2d8520a4c1fb5cdd56773515b1f;hpb=0a93d297a3c64c93eab0253fd2019edd33bd3571;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index e944720..2a8a00f 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -59,7 +59,7 @@ 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].getLength();
     int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
     if ((delMap != null && delMap.length > width)
             || (delMap == null && gapmap.length != width))
@@ -68,8 +68,7 @@ public class JnetAnnotationMaker
               MessageManager
                       .formatMessage(
                               "exception.number_of_residues_in_query_sequence_differ_from_prediction",
-                              new String[]
-                              {
+                              new String[] {
                                   (delMap == null ? "" : MessageManager
                                           .getString("label.mapped")),
                                   al.getSequenceAt(firstSeq).getName(),
@@ -193,13 +192,13 @@ public class JnetAnnotationMaker
           if (id.equals("JNETCONF"))
           {
             annot = new AlignmentAnnotation(preds[i].getName(),
-                    "JNet Output", annotations, 0f, 10f,
+                    "JPred Output", annotations, 0f, 10f,
                     AlignmentAnnotation.BAR_GRAPH);
           }
           else
           {
             annot = new AlignmentAnnotation(preds[i].getName(),
-                    "JNet Output", annotations);
+                    "JPred Output", annotations);
           }
 
           if (seqRef != null)