X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=a529fae5e827d81ddca27ea721b725ec4656e34e;hb=d1cf4609268fb7fbae0716b6e699a130eea02647;hp=903d9b7c53faed57f0b58f2490c44f61758de5d2;hpb=931c66e5efd8c066326b6db713b4db498657ebe6;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 903d9b7..a529fae 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -45,7 +45,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsModelI;
 import jalview.api.SequenceRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AppJmol;
@@ -83,6 +83,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public Viewer jmolViewer;
 
+  private boolean globalUseScriptWait = false;
+
   public JalviewJmolBinding(StructureSelectionManager ssm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           DataSourceType protocol)
@@ -122,9 +124,22 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   private String jmolScript(String script)
   {
-    Cache.log.debug(">>Jmol>> " + script);
-    String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
-    Cache.log.debug("<<Jmol<< " + s);
+    return jmolScript(script, false);
+  }
+
+  private String jmolScript(String script, boolean useScriptWait)
+  {
+    Console.debug(">>Jmol>> " + script);
+    String s;
+    if (globalUseScriptWait || useScriptWait)
+    {
+      s = jmolViewer.scriptWait(script);
+    }
+    else
+    {
+      s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+    }
+    Console.debug("<<Jmol<< " + s);
 
     return s;
   }
@@ -254,22 +269,30 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
+      // we set the globalUseScriptWait (and reset to previous value) only if
+      // we're going to use it here
+      boolean useScriptWait = atoms.size() > 1;
+      boolean prevUseScriptWait = false;
+      if (useScriptWait)
+        prevUseScriptWait = setGlobalUseScriptWait(useScriptWait);
       if (resetLastRes.length() > 0)
       {
-        jmolScript(resetLastRes.toString());
+        jmolScript(resetLastRes.toString(), useScriptWait);
         resetLastRes.setLength(0);
       }
       for (AtomSpec atom : atoms)
       {
         highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
-                atom.getChain(), atom.getPdbFile());
+                atom.getChain(), atom.getPdbFile(), useScriptWait);
       }
+      if (useScriptWait)
+        setGlobalUseScriptWait(prevUseScriptWait);
     }
   }
 
   // jmol/ssm only
   public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
+          String pdbfile, boolean useScriptWait)
   {
     String modelId = getModelIdForFile(pdbfile);
     if (modelId.isEmpty())
@@ -295,7 +318,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     resetLastRes.append(selection).append(";wireframe 0;").append(selection)
             .append(" and not hetero; spacefill 0;");
 
-    jmolScript(cmd.toString());
+    jmolScript(cmd.toString(), useScriptWait);
     jmolHistory(true);
   }
 
@@ -1052,4 +1075,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     return "http://wiki.jmol.org"; // BH 2018
   }
+
+  private boolean setGlobalUseScriptWait(boolean b)
+  {
+    boolean prev = globalUseScriptWait;
+    globalUseScriptWait = b;
+    return prev;
+  }
 }