From f55ab79ffe7987b4efa091a28a393019c69adfbe Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 26 Jun 2020 17:21:55 +0100
Subject: [PATCH] =?utf8?q?JAL-3518=20fix=20highlighting=20in=20Jalview=20for?=
 =?utf8?q?=20selections=20in=20ChimeraX=20-=20needed=20to=20thread=20off=20t?=
 =?utf8?q?he=20subsequent=20POST=20back=20to=20ChimeraX=20so=20ChimeraX=20ca?=
 =?utf8?q?n=20first=20hangup=20its=20GET=20to=20Jalview=E2=80=99s=20Rest=20A?=
 =?utf8?q?PI?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 .../ext/rbvi/chimera/JalviewChimeraBinding.java    |   69 ++++++++++++--------
 1 file changed, 40 insertions(+), 29 deletions(-)

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 16aca58..549636b 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -444,40 +444,51 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * Ask Chimera for its current selection
      */
     StructureCommandI command = getCommandGenerator().getSelectedResidues();
-    List<String> chimeraReply = executeCommand(command, true);
-    List<String> selectedResidues = new ArrayList<>();
-    if (chimeraReply != null)
+    
+    Runnable action = new Runnable()
     {
-      /*
-       * expect 0, 1 or more lines of the format either
-       * Chimera:
-       * residue id #0:43.A type GLY
-       * ChimeraX:
-       * residue id /A:89 name THR index 88
-       * We are only interested in the atomspec (third token of the reply)
-       */
-      for (String inputLine : chimeraReply)
+      @Override
+      public void run()
       {
-        String[] inputLineParts = inputLine.split("\\s+");
-        if (inputLineParts.length >= 5)
+        List<String> chimeraReply = executeCommand(command, true);
+        
+        List<String> selectedResidues = new ArrayList<>();
+        if (chimeraReply != null)
         {
-          selectedResidues.add(inputLineParts[2]);
+          /*
+           * expect 0, 1 or more lines of the format either
+           * Chimera:
+           * residue id #0:43.A type GLY
+           * ChimeraX:
+           * residue id /A:89 name THR index 88
+           * We are only interested in the atomspec (third token of the reply)
+           */
+          for (String inputLine : chimeraReply)
+          {
+            String[] inputLineParts = inputLine.split("\\s+");
+            if (inputLineParts.length >= 5)
+            {
+              selectedResidues.add(inputLineParts[2]);
+            }
+          }
         }
-      }
-    }
-
-    /*
-     * Parse model number, residue and chain for each selected position,
-     * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
-     */
-    List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
-            selectedResidues);
 
-    /*
-     * Broadcast the selection (which may be empty, if the user just cleared all
-     * selections)
-     */
-    getSsm().mouseOverStructure(atomSpecs);
+        /*
+         * Parse model number, residue and chain for each selected position,
+         * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
+         */
+        List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+                selectedResidues);
+
+        /*
+         * Broadcast the selection (which may be empty, if the user just cleared all
+         * selections)
+         */
+        getSsm().mouseOverStructure(atomSpecs);
+        
+      }
+    };
+    new Thread(action).start();
   }
 
   /**
-- 
1.7.10.2