X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=e944720f0107a2d8520a4c1fb5cdd56773515b1f;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=c5320f1f7594457bb4e3fa9906b765464d1af43e;hpb=8002d3a28b1e21a9d89a24e4c81cf9397ecea0db;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index c5320f1..e944720 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -103,13 +103,13 @@ 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;
             }