From 9f91642f99bc1a3f01d7c97a7a109d4694a88049 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Fri, 13 Oct 2023 17:45:17 +0100
Subject: [PATCH] =?utf8?q?JAL-4295=20concatenate=20all=20mouseover=20highlig?=
 =?utf8?q?hts=20into=20one=20call=20to=20jmolScript=20-=20so=20we=20don=E2=80?=
 =?utf8?q?=99t=20need=20to=20invoke=20scriptWait=20and=20risk=20blocking=20U?=
 =?utf8?q?I?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |   33 +++++++++++++++++---------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 870db65..dc18369 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -267,16 +267,30 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
-      boolean useScriptWait = atoms.size() > 1;
       if (resetLastRes.length() > 0)
       {
-        jmolScript(resetLastRes.toString(), useScriptWait);
+        jmolScript(resetLastRes.toString());
         resetLastRes.setLength(0);
       }
+      StringBuilder highlightCommands=null;
       for (AtomSpec atom : atoms)
       {
-        highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
-                atom.getChain(), atom.getPdbFile(), useScriptWait);
+        StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+                atom.getChain(), atom.getPdbFile());
+        if (thisAtom!=null) {
+          if (highlightCommands==null)
+          {
+            highlightCommands=thisAtom;                  
+          } else {
+            highlightCommands.append(thisAtom);
+          }
+        }
+      }
+      if (highlightCommands!=null)
+      {
+        jmolHistory(false);
+        jmolScript(highlightCommands.toString());
+        jmolHistory(true);
       }
       // Highlight distances between atoms with a 'measure' command - not yet
       // working
@@ -306,17 +320,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   // jmol/ssm only
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile, boolean useScriptWait)
+  private StringBuilder highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     String modelId = getModelIdForFile(pdbfile);
     if (modelId.isEmpty())
     {
-      return;
+      return null;
     }
 
-    jmolHistory(false, useScriptWait);
-
     StringBuilder selection = new StringBuilder(32);
     StringBuilder cmd = new StringBuilder(64);
     selection.append("select ").append(String.valueOf(pdbResNum));
@@ -333,8 +345,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     resetLastRes.append(selection).append(";wireframe 0;").append(selection)
             .append(" and not hetero; spacefill 0;");
 
-    jmolScript(cmd.toString(), useScriptWait);
-    jmolHistory(true, useScriptWait);
+    return cmd;
   }
 
   private boolean debug = true;
-- 
1.7.10.2