********>Bugfix 7
Author: Jianyin Shao
Date: 06/05/2008

Programs: ptraj

Description: The bug in PtrajClusteringGetAttributeArrayCount() of cluster.c may 
point to an empty pointer, therefore could cause a runtime error. 
The other bug in mask.c will falsely issue a warning for "*" for empty mask, this 
bug will not cause any error.

Fix: This patch acctually affects multiple files. So, run it from the $AMBERHOME
     directory, with:
     $ patch -p0 -N -r patch_rejects < bugfix.6

------------------------------------------------------------------------------
diff -Naur oldamber/src/ptraj/cluster.c newamber/src/ptraj/cluster.c
--- src/ptraj/cluster.c       2008-02-22 10:52:34.000000000 -0700
+++ src/ptraj/cluster.c       2008-06-05 15:13:21.000000000 -0600
@@ -6513,7 +6513,7 @@
   Cluster* NewCluster;
   int PointInCluster;
   int ClusterCount = This->ClusterCount;
-  int AttributeCount = PtrajClusteringGetAttributeArrayCount(This);
+  int AttributeCount = PtrajClusteringGetAttributeCount(This);
   int i, j, k, diff;
   int* AttributeDifference;

@@ -6806,8 +6806,8 @@
       ClusterFindBestP2C( (PtrajCluster *) Node->Cluster);
       Node = Node->pNext;  
     }
     
-    PtrajClusteringSOMExtractDifference( (PtrajClustering *) This, SOMNodes); /* print out significant differences in attributes between clusters. */
+    if (prnlev >6) PtrajClusteringSOMExtractDifference( (PtrajClustering *) This, SOMNodes); /* print out significant differences in attributes between clusters. */
 }
 
 /*
diff -Naur oldamber/src/ptraj/cluster.c newamber/src/ptraj/mask.c
--- src/ptraj/mask.c       2008-02-22 10:52:34.000000000 -0700
+++ src/ptraj/mask.c       2008-06-05 15:13:21.000000000 -0600
@@ -397,8 +397,8 @@
       flag = 1;
       n++;
     } else if ( *p == ']' ) {
-      if ( n < 3 )
-        printf("Warning: empty token?\n");
+      if ( n < 3 && *(p-1) != '*' )
+        printf("Warning: \'%c\' empty token?\n", *(p-1));
       flag = 0;
       n = 0;
     } else {

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Temporary workarounds: none