From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 7 Jul 2013 12:08:52 +0000 (+0100)
Subject: JAL-1345 - set nSeconds arg for http://chemapps.stolaf.edu/jmol/docs/#compare accordi... 
X-Git-Tag: Jalview_2_9~229^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ac74307dcabaf35928007b2aecdf9a40f4dac65f;p=jalview.git

JAL-1345 - set nSeconds arg for chemapps.stolaf.edu/jmol/docs/#compare according to total number of superpositions
---

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 458a178..f31272a 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -357,8 +357,21 @@ public abstract class JalviewJmolBinding implements StructureListener,
       return;
     }
     StringBuffer selectioncom = new StringBuffer();
-    
-
+    // In principle - nSeconds specifies the speed of animation for each
+    // superposition - but is seems to behave weirdly, so we don't specify it.
+    String nSeconds = " ";
+    if (files.length > 10)
+    {
+      nSeconds = " 0.00001 ";
+    }
+    else
+    {
+      nSeconds = " " + (2.0 / files.length) + " ";
+      // if (nSeconds).substring(0,5)+" ";
+    }
+    // see JAL-1345 - should really automatically turn off the animation for
+    // large numbers of structures, but Jmol doesn't seem to allow that.
+    nSeconds = " ";
     // union of all aligned positions are collected together.
     for (int a = 0; a < _alignment.length; a++)
     {
@@ -553,7 +566,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         command.append(chainNames[pdbfnum]);
         command.append(") against reference (");
         command.append(chainNames[refStructure]);
-        command.append(")\";\ncompare ");
+        command.append(")\";\ncompare "+nSeconds);
         command.append("{");
         command.append(1 + pdbfnum);
         command.append(".1} {");