update author list in license for (JAL-826)

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index abb170f..011f24e 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -27,6 +27,7 @@ import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasListener;
+import jalview.structure.VamsasSource;
 
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
@@ -61,7 +62,7 @@ import uk.ac.vamsas.objects.core.Seg;
  * @author jimp
  * 
  */
-public class VamsasApplication implements SelectionSource
+public class VamsasApplication implements SelectionSource,VamsasSource
 {
   IClient vclient = null;
 
@@ -222,14 +223,12 @@ public class VamsasApplication implements SelectionSource
     } catch (Error e)
     {
       Cache.log
-              .warn(
-                      "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+              .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
                       e);
     } catch (Exception e)
     {
       Cache.log
-              .warn(
-                      "Probable VAMSAS client incompatibility - carrying on regardless",
+              .warn("Probable VAMSAS client incompatibility - carrying on regardless",
                       e);
     }
   }
@@ -241,8 +240,8 @@ public class VamsasApplication implements SelectionSource
    */
   private ClientHandle getJalviewHandle()
   {
-    return new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache
-            .getProperty("VERSION"));
+    return new ClientHandle("jalview.bin.Jalview",
+            jalview.bin.Cache.getProperty("VERSION"));
   }
 
   /**
@@ -305,8 +304,7 @@ public class VamsasApplication implements SelectionSource
     } catch (Exception e)
     {
       Cache.log
-              .warn(
-                      "Exception whilst refreshing jalview windows after a vamsas document update.",
+              .warn("Exception whilst refreshing jalview windows after a vamsas document update.",
                       e);
     }
   }
@@ -758,8 +756,8 @@ public class VamsasApplication implements SelectionSource
       {
         final IPickManager pm = vclient.getPickManager();
         final StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager();
-        final SelectionSource me = this;
+                .getStructureSelectionManager(Desktop.instance);
+        final VamsasApplication me = this;
         pm.registerMessageHandler(new IMessageHandler()
         {
           String last = null;
@@ -791,8 +789,8 @@ public class VamsasApplication implements SelectionSource
                 // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
                 // bound to "+jvobj+" at "+mm.getPosition());
                 // position is character position in aligned sequence
-                ssm.mouseOverVamsasSequence((SequenceI) jvobj, mm
-                        .getPosition());
+                ssm.mouseOverVamsasSequence((SequenceI) jvobj,
+                        mm.getPosition(), me);
               }
             }
             if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage)
@@ -960,7 +958,7 @@ public class VamsasApplication implements SelectionSource
 
           int i = -1;
 
-          public void mouseOver(SequenceI seq, int index)
+          public void mouseOver(SequenceI seq, int index, VamsasSource source)
           {
             if (jv2vobj == null)
               return;
@@ -1064,8 +1062,8 @@ public class VamsasApplication implements SelectionSource
                   }
                   else
                   {
-                    int[] intervals = colsel.getVisibleContigs(seqsel
-                            .getStartRes(), seqsel.getEndRes() + 1);
+                    int[] intervals = colsel.getVisibleContigs(
+                            seqsel.getStartRes(), seqsel.getEndRes() + 1);
                     for (int iv = 0; iv < intervals.length; iv += 2)
                     {
                       Seg s = new Seg();