X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=d5593e38ba1c92de0b224433949d3effa987c042;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=c5320f1f7594457bb4e3fa9906b765464d1af43e;hpb=8002d3a28b1e21a9d89a24e4c81cf9397ecea0db;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index c5320f1..d5593e3 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -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(),
@@ -103,13 +102,13 @@ public class JnetAnnotationMaker
           for (int spos = 0; spos < width; spos++)
           {
             int sposw = (delMap == null) ? gapmap[spos]
-                    : delMap[gapmap[spos]];
+                    : gapmap[delMap[spos]];
             if (firstsol)
             {
               sol[sposw] = new Annotation(0f);
             }
             if (preds[i].getCharAt(spos) == 'B'
-                    && (sol[spos].value == 0f || sol[spos].value < amnt))
+                    && (sol[sposw].value == 0f || sol[sposw].value < amnt))
             {
               sol[sposw].value = amnt;
             }