[Jmol-commits] SF.net SVN: jmol:[16780] trunk/Jmol

[<ha...@us...>]

Revision: 16780
          http://jmol.svn.sourceforge.net/jmol/?rev=16780&view=rev
Author:   hansonr
Date:     2012-02-12 18:31:02 +0000 (Sun, 12 Feb 2012)
Log Message:
-----------
JSpecView fixes

Modified Paths:
--------------
    trunk/Jmol/appletweb/jspecview.jar
    trunk/Jmol/jars/jspecview.jar
    trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
    trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java

Modified: trunk/Jmol/appletweb/jspecview.jar
===================================================================
(Binary files differ)

Modified: trunk/Jmol/jars/jspecview.jar
===================================================================
(Binary files differ)

Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java	2012-02-11 21:55:53 UTC (rev 16779)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java	2012-02-12 18:31:02 UTC (rev 16780)
@@ -331,6 +331,8 @@
       if (n > 0)
         appendLoadNote((String) atomSetCollection.getAtomSetAuxiliaryInfo(0, "name"));
     }
+    for (int i = atomSetCollection.getAtomSetCount(); --i >= 0;)
+      atomSetCollection.setAtomSetNumber(i, i + 1);
   }
 
   private String allTypes;

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2012-02-11 21:55:53 UTC (rev 16779)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2012-02-12 18:31:02 UTC (rev 16780)
@@ -1628,17 +1628,20 @@
   }
 
   /**
-  * Sets the number for the current AtomSet
-  *
-  * @param atomSetNumber The number for the current AtomSet.
-  */
+   * Sets the number for the current AtomSet
+   * 
+   * @param atomSetNumber
+   *        The number for the current AtomSet.
+   */
   public void setAtomSetNumber(int atomSetNumber) {
-    if (isTrajectory)
-      atomSetNumbers[currentAtomSetIndex + trajectoryStepCount] = atomSetNumber;
-    else
-      atomSetNumbers[currentAtomSetIndex] = atomSetNumber;
+    setAtomSetNumber(currentAtomSetIndex
+        + (isTrajectory ? trajectoryStepCount : 0), atomSetNumber);
   }
   
+  public void setAtomSetNumber(int index, int atomSetNumber) {
+    atomSetNumbers[index] = atomSetNumber;
+  }
+  
   /**
    * Sets a property for the current AtomSet
    * used specifically for creating directories and plots of frequencies and 

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