total annotation score is a double for maximum precision.

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index df82b5f..ffdbb1b 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -159,13 +159,15 @@ public class JalviewLite
   {
     try
     {
-      Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
-
-      jmolAvailable = true;
+      if (!System.getProperty("java.version").startsWith("1.1"))
+      {
+        Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+        jmolAvailable = true;
+      }
     }
     catch (java.lang.ClassNotFoundException ex)
     {
-      System.out.println("Jmol not found - Using MCview for structures");
+      System.out.println("Jmol not available - Using MCview for structures");
     }
 
     int r = 255;
@@ -549,6 +551,10 @@ public class JalviewLite
 
           pdb.setFile(param);
 
+          for(int i=0; i<seqs.length; i++)
+          {
+            ((Sequence)seqs[i]).addPDBId(pdb);
+          }
 
           if (jmolAvailable)
             new jalview.appletgui.AppletJmol(pdb,