Clean up a bit and added some more comments

Refactor some method names to be more consistent.
Changed some fields to be final (and uppercase them)
Added comments for the most importat methods
Made the createStatment(idx) method private, this should only be used internally. Would be dangerous to use it from anothe class.

Changed all error printing in catches to STDERR instead of STDOUT

New exec method taking only a String argument wasn't working. Fixed the bug.

Added exec method to take only a string as argument.

introduced generics, so class will compile in Java 5, not sure though whether the functionality is the same as before, will need more testing

changed server port to standard

prevent overlong commands from being sent to the server

initial import

fixed bug for very long command strings (> 255 characters)

moved executables (classes with main function) to root directory

Fixed important bug:
- now closing nCon connection before opening a new one in the setHost method.
- this is important. Before lots of connection were left opened after having used the ClusterConnection object

Fixed bug in getIdxSet method. Wasn't reading properly the index_matrix table into the array. Was starting from columnn 1 which actually is the serial column. Now starting from column 2.

New method int[][] getIdxSet. 
- Returns a 2-dimensional array with all indices for a certain key.
- Each column j corresponds to client_id j+1
- Each row i is a set of idx values for each of the client_ids. If there is no idx for a certain client_id then the value is 0.

Grouped all the setIdxColumn and setMasterTable into setKey.
Also rationalised a bit the constructors by calling one from the other.

Added package tools.

Initial commit of the ClusterConnection class + small test class to test it out.

removed ununsed imports and variables

Adding SystemCmd class

removed some debug code

Corrected some bad mistake

Initial commit of the remote-pymol-from-java stuff

Adding R class

Moved everything to subdir tools, so that we keep the tools name for the package. Also changed the package name in the files to tools. To work with it please check out only file:///.../svn/tools/trunk/tools