From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 11 May 2015 09:44:16 +0000 (+0100)
Subject: Merge branch 'features/JAL-1641_JSON_' into develop
X-Git-Tag: Release_2_10_0~682^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2a42323bc7b92e39c676fc46768f28d032f2f686;hp=a40bbc57a85658544e2e5d7cc2a7596b762566dc;p=jalview.git

Merge branch 'features/JAL-1641_JSON_' into develop
---

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;
             }