Minor change, in getHostId4Ifx one of the error messages was being written to out, now to err

In latest commit method insertIdsToKeyMaster wasn't yet complying with the new way of dealing with key
Now modified insertIdsToKeyMaster accordingly. Now we create a ClusterConnection object to call the createNewKeyMasterTable method.

New method createNewKeyMasterTbl
To create a new keyMaster table in the key_master database for a certain table
Will also insert a new record in dbs_keys for the new table.
If a record for it already existed it will print an error and continue as the error is harmless.

Got rid of keyColumn
Now key is directly the keyColumn name, e.g. key is asu_id not asu
This makes things less confusing and simpler.
We've done this following last commit of DataDistribution to also change the ways we deal with key/keyColumn.
Note that now the checkKeyCounts and checkDifferingKeys are using to get the keyTable name a ClusterConnection object and the new ClusterConnection method getTableOnNode

2 important changes:
Fixed important bug on the constructor that gets the key passed (the bug was there since a lot of revisions ago and always passed since that constructor was not used in other classes)
Got rid of keyColumn, was useless. Now key is directly the keyColumn name which is more logical and makes everything simpler
- changed all calls to keyColumn to key
- got rid of keyColumn field and setKeyColumn
- changed completely the methods setKeyTable to get the table name from the dbs_keys on key_master db
- introduced new method getTableOnNode. Gets the name of the table where splitted data is stored for this db and key

New method getIdSetsFromNodes, equivalent to splitIdsIntoSets but rather a posteriori, when tables are already distributed in cluster's nodes
Modified method getAllIds4KeyAndTable, now taking host as parameter too, more general
Changed the comments a lot for all those 3 methods. There are many catches to be taken in account, the comments explain them quite well

KEYMASTERDB had value for testing, change that back.

Added method insertIdsToKeyMaster
Added call to the new insertIdsToKeyMaster in splitTableToCluster method

Added another clusterExecuteQuery method to take a HashMap of queries rather than only one.
To be used in cases where the queries to be sent to nodes are different for each node (like in load/dump methods of this class)
Right now strictly serial must paralelize it as with the other clusterExecuteQuery

Modified methods getAllIdxAndClients and getAllIdxFromMaster.
They return now:
- getAllIdxAndClients: an int[]
- getAllIdxFromMaster: a HashMap<Integer,String>
Got rid of having ResultSets returned which is very messy and dangerous.

Made MASTER final static variable also public. It is in use by other classes.

Initial commit of DataDistribution.java into aglappe repository
Copied from repository scripts-jose rev 69
If want to have a look at previous history must do it from repository scripts-jose, there was no way of copying with history between different repositories

Added method getCreateIndex4Table

Fixed bug in getAllIndexes4Table, the SELECT needed a DISTINCT

Got rid of method dbExists. Was useless and not working.

Added method setSqlMode, to set sql_mode server variable

Added method dbExists to check whether database exists in server, used in constructor that passes a dbName
Moved all the private methods to the beginning of methods section

Changed comments in constructors
Changed in method readConnectionFile:
- variable to count mandatory parameters to paramCount
- number of mandatory parameters now 4, dbname is also mandatory

Now executeSQL method throws exception instead of catching it. Thought it was better than the calling class deals with these exceptions.

Added getConnectionObject
Added printDbSizeInfo and 2 getRange methods from utils4DB
Made private the loadMySQLDriver and readConnectionFile methods

execUpdateQuery method added and code in comments was removed

Initial commit.
Class to create a connection to mysql db with basic functionality.
Cann take parameters for connection as argument in constructor or from connection file (passing the filename to the constructor)
Using code from both DBConnection (henning) and mySQLConnect (ioannis)

initial import

Fixed a bug with setKeyDb method, was not actually working:
 as well as setting the MASTERDB string needed to change connection to master database to point to new db!
From now on take care if setKeyDb is used in another class. It will open another master connection, thus master connection won't be always the same during the run of the program

Changed error message printed in getHostId4Idx

Added setKeyDb method, to be used in testing, i.e. with this method we can change from another class the default MASTERDB database.

More flexibility in coloring, popDefaults/setDefaults methods plus comments

Refresh method added plus refresh added before saving image

Added cgo functionality/examples in Graph2Pml and testGraph2Pml

PyMol class: adding refresh in saveImage methods

Graph2Pymol class now functional
testGraph2Pymol class now functional with comments also
PyMol class:python strings methods and removeList, concatList, refresh methods added
Machine class: indentation

In PyMol class, objectNameQuotes class variable is replaced by the method parameter called variable. Graph2Pml is modified accrodingly.

Added executeSql method

Adding Graph2Pml and testGraph2Pml classes (non functional code!)

getRange methods now return double array instead of Float array. Previous code is into comments.

Adding Msdsd2Pdb and PyMol classes

Adding comments

Added getAllIdxAndClients method:
gets all ids and client_names for a certain key

Some changes in error messages to be more clear.

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