off by one for sequence associated annotation

[jalview.git] / src / jalview / ws / jws2 / AADisorderClient.java

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index f3f8ae3..e971746 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -118,7 +118,10 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
     amap.put("Short", new HashMap<String, Object>());
     amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5});
     amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5});
-
+    annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
+            amap = new HashMap<String, Map<String, Object>>());
+    amap.put("JRonn", new HashMap<String, Object>());
+    amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5});
   }
 
   @Override
@@ -137,7 +140,7 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
       /**
        * grouping for any annotation rows created
        */
-      int graphGroup = 1, iGraphGroup = 1;
+      int graphGroup = 1;
       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
       {
         for (AlignmentAnnotation ala : alignViewport.getAlignment()
@@ -212,7 +215,7 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
             AlignmentAnnotation annot = createAnnotationRowsForScores(
                     ourAnnot, service.serviceType + " (" + scr.getMethod()
                             + ")", service.getServiceTypeURI()+"/"+ scr.getMethod(), aseq,
-                    base, scr);
+                    base+1, scr);
             annot.graph = AlignmentAnnotation.LINE_GRAPH;
             annot.visible = (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(INVISIBLE) == null);
             double[] thrsh=(annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null) ? null : (double[]) annotTypeMap.get(scr.getMethod()).get(THRESHOLD);