From 2aa69a7cbf3d401b0c4cbff140ad5e3b316634b5 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 5 Jan 2011 16:05:47 +0000
Subject: [PATCH] ensure group props are recalculated before alignment
 displayed

---
 src/jalview/ws/rest/RestJobThread.java |   14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index 581af9a..39f26ae 100644
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -11,6 +11,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.PaintRefresher;
 import jalview.gui.WebserviceInfo;
 import jalview.io.NewickFile;
 import jalview.io.packed.JalviewDataset;
@@ -50,7 +51,7 @@ public class RestJobThread extends AWSThread
     SUBMIT, POLL
   }
 
-  protected RestClient restClient;;
+  protected RestClient restClient;
 
   public RestJobThread(RestClient restClient)
   {
@@ -786,7 +787,6 @@ public class RestJobThread extends AWSThread
                 if (sg.getName() != null)
                 {
                   exsg = groupNames.get(sg.getName());
-                  recovered = true;
                 }
                 if (exsg == null)
                 {
@@ -795,6 +795,8 @@ public class RestJobThread extends AWSThread
                   visgrps.add(exsg);
                   exsg.setStartRes(sg.getStartRes() + contigs[ncnt]);
                   exsg.setEndRes(sg.getEndRes() + contigs[ncnt]);
+                } else {
+                  recovered = true;
                 }
                 // now replace any references from the result set with
                 // corresponding refs from alignment input set.
@@ -923,6 +925,13 @@ public class RestJobThread extends AWSThread
                   visan.sequenceRef = sqass;
                   visAlAn.add(visan);
                 }
+                if (contigs[ncnt]+alan[nrj][an].annotations.length>visan.annotations.length)
+                {
+                  // increase width of annotation row
+                  Annotation[] newannv = new Annotation[contigs[ncnt]+alan[nrj][an].annotations.length];
+                  System.arraycopy(visan.annotations, 0, newannv, 0, visan.annotations.length);
+                  visan.annotations=newannv;
+                }
                 // now copy local annotation data into correct position
                 System.arraycopy(alan[nrj][an].annotations, 0,
                         visan.annotations, contigs[ncnt],
@@ -985,6 +994,7 @@ public class RestJobThread extends AWSThread
         destcs = destColsel.get(als);
         destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
+        PaintRefresher.Refresh(destaf, destaf.getViewport().getSequenceSetId());
         // todo transfer any feature settings and colouring
         /*
          * destaf.getFeatureRenderer().transferSettings(this.featureSettings);
-- 
1.7.10.2