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Revision 188 - Directory Listing
Modified Mon Jun 11 14:05:50 2007 UTC (10 years, 5 months ago) by duarte
Copied from: trunk revision 187
Tagging version 0.5 for release of CM2PyMol version 0.5
Revision 187 - Directory Listing
Modified Mon Jun 11 14:04:54 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Changed to version 0.5
Revision 186 - Directory Listing
Modified Thu Jun 7 10:42:13 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning
Revision 185 - Directory Listing
Modified Thu Jun 7 09:14:46 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString
Revision 184 - Directory Listing
Modified Wed Jun 6 10:02:24 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
New class GenericContact. To store a generic contact, i.e. a pair of residue types
Revision 183 - Directory Listing
Modified Tue Jun 5 14:32:04 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Fixed bug: calculateEntropy was wrong when a pi was 0
Revision 182 - Directory Listing
Modified Tue Jun 5 13:41:05 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
FIXED BUG: the switch statement was missing the breaks
This was causing strange behaviour in counts NodeBackground getSize methods and also was making them being too slow
Revision 181 - Directory Listing
Modified Tue Jun 5 12:27:49 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
New class NbhProbDistribution
In NodeNbh implemented a few static classes to convert between different motifs and to match motifs using differing criteria

Revision 180 - Directory Listing
Modified Fri Jun 1 15:17:40 2007 UTC (10 years, 5 months ago) by lappe
Original Path: trunk

Revision 179 - Directory Listing
Modified Thu May 31 09:41:41 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them
NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh
New method getResidueType
Revision 178 - Directory Listing
Modified Tue May 29 08:01:46 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact
Revision 177 - Directory Listing
Modified Mon May 28 09:55:06 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Made public getUserName
Revision 176 - Directory Listing
Modified Mon May 28 09:53:00 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
New static method getUserName and new constructor with only server and db
Revision 175 - Directory Listing
Modified Fri May 25 17:31:58 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList
New class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
New method getRange in Contact
Revision 174 - Directory Listing
Modified Fri May 25 15:07:55 2007 UTC (10 years, 5 months ago) by lappe
Original Path: trunk
original version to be saved ... 
Revision 173 - Directory Listing
Modified Fri May 25 15:07:32 2007 UTC (10 years, 5 months ago) by lappe
Original Path: trunk
running version summing delta Rank
still to implement sum(deltza) for entropy etc. 
Revision 172 - Directory Listing
Modified Fri May 25 13:41:19 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Got rid of some unnecessary warnings
Revision 171 - Directory Listing
Modified Fri May 25 13:15:19 2007 UTC (10 years, 5 months ago) by lappe
Original Path: trunk
version of iterateNBHood for the uppercase background info 
pdb_reps_graph_4_2 for briefer output & calculation 
Revision 170 - Directory Listing
Modified Fri May 25 10:01:44 2007 UTC (10 years, 5 months ago) by lappe
Original Path: trunk
Running version, takes graph_id and resnr as input 
Revision 169 - Directory Listing
Modified Thu May 24 16:20:12 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk

Revision 168 - Directory Listing
Modified Thu May 24 16:19:48 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk

Revision 167 - Directory Listing
Modified Thu May 24 16:19:21 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk

Revision 166 - Directory Listing
Modified Thu May 24 16:19:00 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk
First version of exchange routine contact vs. CN - non functional 
Revision 165 - Directory Listing
Modified Thu May 24 15:43:13 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
New functionality: added methods to get node/edge neighbours
Revision 163 - Directory Listing
Modified Thu May 24 10:52:24 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
added Manifest
Revision 162 - Directory Listing
Modified Thu May 24 10:46:39 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Updated test class for Pdb/Graph objects
Revision 161 - Directory Listing
Modified Thu May 24 10:12:41 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
made Graph.directed public
Revision 160 - Directory Listing
Modified Thu May 24 09:52:22 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk
tab-Formatted output added
Revision 159 - Directory Listing
Modified Thu May 24 09:37:25 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Moved ContactMap and EdgeState out of this repository. 
Extra functionality of ContactMap now in Graph:
- new member variables fullLength, obsLength, numContacts. New method getIntMatrix
- removed getCM method
Revision 158 - Directory Listing
Modified Tue May 22 15:37:15 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database
Revision 157 - Directory Listing
Modified Tue May 22 12:04:43 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!
Revision 156 - Directory Listing
Modified Tue May 22 10:40:04 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Now passing also chaincode from Pdb object to Graph object in get_graph
Revision 155 - Directory Listing
Modified Tue May 22 10:13:03 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file
Revision 154 - Directory Listing
Modified Fri May 18 09:32:28 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality
Revision 153 - Directory Listing
Modified Wed May 16 17:22:08 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
NEW FUNCTIONALITY: Reading from pdb file given chain code or model serial fully implemented
Changed the chain that is dumped in dump2pdbfile directly to the Pdb.chain field i.e. internal chain identifier
Loads of new comments, including java doc for all constructors
Revision 152 - Directory Listing
Modified Wed May 16 14:12:50 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
FIXED 2 BUGS. NEW FEATURE reading graph from db given graph_id
Bugs:
- nodes TreeMap in read_graph_from_file contained one letter res codes, now three letter codes
- in getCM was passing residues as a TreeMap of nums to three letter residue types, now passing one letter residue types
New constructor for getting graph from db given graph_id, new method to go with that get_db_graph_info

Revision 151 - Directory Listing
Modified Wed May 16 14:05:48 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk
working version for each single nbring residue 
Revision 150 - Directory Listing
Modified Wed May 16 14:05:08 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk
- functional
Revision 149 - Directory Listing
Modified Wed May 16 14:04:54 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk
min-info - functional
Revision 148 - Directory Listing
Modified Wed May 16 13:59:25 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk
list of infogain per neighbouring residue 
- still buggy w.r.t. x elimination 
Revision 147 - Directory Listing
Modified Wed May 16 12:34:49 2007 UTC (10 years, 6 months ago) by lappe
Original Path: trunk
Max.Info Gain still with problems if only negative (loss) of info 
Revision 146 - Directory Listing
Modified Tue May 15 13:51:17 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Made cutoff and ct public
Revision 145 - Directory Listing
Modified Tue May 15 13:28:24 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Made some fields public: sequence, accode, chaincode, model
Revision 144 - Directory Listing
Modified Tue May 15 12:13:31 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
NEW FEATURE: Read and write graphs from file fully implemented.

Refactored read_contacts_from_file to read_graph_from_file. Now can read other fields as well as contacts. Also gets nodes if sequence present
New method write_graph_to_file

Revision 143 - Directory Listing
Modified Tue May 15 10:06:47 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
FIXED BUG: last commit didn't fix bug correctly:
Changed the ContactMap constructor to put into residueNums and residueTypes nums from 1 to maximum of residues.keySet()

Made public accode and chain fields in Graph
Revision 142 - Directory Listing
Modified Tue May 15 08:33:44 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
FIXED BUG: getCM wasn't working well when reading from db and there were unobserved residues

Now setting the sequence to blank when reading from db. Also when reading from file (still nodes reading is not implemented)
In ContactMap constructor different handling when sequence is blank
Revision 141 - Directory Listing
Modified Mon May 14 15:51:54 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)
Revision 140 - Directory Listing
Modified Mon May 14 15:34:21 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
Made Pdb.acccode public
Revision 139 - Directory Listing
Modified Mon May 14 15:29:08 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Changed default accode and chaincode to "Unknown" when reading from pdb file
Revision 138 - Directory Listing
Modified Mon May 14 14:58:29 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
FIXED BUG: wasn't setting the chain field when reading from msdsd
Revision 137 - Directory Listing
Modified Mon May 14 14:53:09 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
Made chain field in PDB class public
Revision 136 - Directory Listing
Modified Mon May 14 14:50:44 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
Revision 135 - Directory Listing
Modified Mon May 14 09:49:04 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases

New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd)
Reading chain also in Pdb in read_pdb_data_from_file
Not reading chain anymore in read_atomData of PdbaseInfo
Added oneletter2threeletter and getoneletter2threeletter to AA class
Changes in Graph:
- added db static vars and getUserName method
- new member variables graphid and sm_id
- new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db
- new method getgraphid
New Exception class GraphIdNotFoundError
Revision 134 - Directory Listing
Modified Mon May 14 07:52:10 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Implemented basic reading contacts from file
Revision 133 - Directory Listing
Modified Fri May 11 09:37:38 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!
Revision 132 - Directory Listing
Modified Thu May 10 16:04:06 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Added more tests for all cases
Revision 131 - Directory Listing
Modified Thu May 10 15:53:14 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless
Revision 130 - Directory Listing
Modified Thu May 10 15:52:24 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
NEW FEATURE: reading pdb data from msdsd
New classes MsdsdInfo and its exception classes
FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines
Revision 129 - Directory Listing
Modified Thu May 10 13:12:32 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object
New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed
Passing more data from Pdb to Graph in get_graph
New constructor in ContactMap
Revision 128 - Directory Listing
Modified Wed May 9 16:29:39 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
ContactMap and EdgeState classes moved here from CMPredict repository
Revision 127 - Directory Listing
Modified Wed May 9 14:54:02 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

Revision 126 - Directory Listing
Modified Wed May 9 12:04:35 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
MYSQLUSER now taken from unix name with new getUserName method
Revision 125 - Directory Listing
Modified Wed May 9 11:58:59 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Initial commit of testPdb, to test the proteinstructure package
Revision 124 - Directory Listing
Modified Wed May 9 11:57:24 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Added error handling for PdbaseInfo: 2 new exception classes
Revision 123 - Directory Listing
Modified Wed May 9 10:45:53 2007 UTC (10 years, 6 months ago) by duarte
Original Path: trunk
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
Revision 121 - Directory Listing
Modified Thu May 3 07:40:23 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
Updated TableSorter to compile in Java 1.5 and some trivial changes in comments
Revision 120 - Directory Listing
Modified Mon Apr 30 14:02:56 2007 UTC (10 years, 6 months ago) by stehr
Original Path: trunk
added overloaded method setDistance for use in CM2Pymol for chains without chain code
Revision 119 - Directory Listing
Modified Fri Mar 30 13:28:50 2007 UTC (10 years, 7 months ago) by dinse
Original Path: trunk

Revision 118 - Directory Listing
Modified Wed Mar 28 13:41:03 2007 UTC (10 years, 7 months ago) by dinse
Original Path: trunk

Revision 117 - Directory Listing
Modified Wed Mar 14 09:24:24 2007 UTC (10 years, 8 months ago) by dinse
Original Path: trunk
Fixed space missing in one of the queries
Revision 116 - Directory Listing
Modified Fri Mar 2 17:38:30 2007 UTC (10 years, 8 months ago) by filippis
Original Path: trunk
testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
Revision 115 - Directory Listing
Modified Fri Mar 2 13:53:04 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
Adapted to msdsd_00_07_a
Now uses MySQLConnection and PrintWriters and not mysql client through shell (got rid of that method)
Thus all methos taking new arguments user and pdbFile
New methods:
 export2file taking accession_code, chain_pdb_code 
 export2file taking chain_id, model_id

Revision 114 - Directory Listing
Modified Tue Feb 27 08:49:10 2007 UTC (10 years, 8 months ago) by duarte
Original Path: trunk
Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
Revision 113 - Directory Listing
Modified Thu Oct 19 13:22:32 2006 UTC (11 years, 1 month ago) by duarte
Original Path: trunk
Modified method getIdFromMaster to create keyTable if it didn't exist
Revision 112 - Directory Listing
Modified Mon Oct 16 15:57:50 2006 UTC (11 years, 1 month ago) by duarte
Original Path: trunk
New static method getIdFromMaster. Inserts an id in a table in key_master database and gets the last_insert_id. To be used in graph generation
Revision 110 - Directory Listing
Modified Tue Sep 19 13:04:55 2006 UTC (11 years, 2 months ago) by duarte
Original Path: trunk
New class MySQLConnectionCheck, to check whether MySQL servers are alive, uses threads
Changes in DataDistribution:
- new field: String[] nodes, initialised in constructor
- changed constructor to check for nodes that are alive, using new method nodesAlive
- renamed getNodes to getMySQLNodes. New method getNodes just returns the new field String[] nodes
DataDistributer: renamed calls to DataDistribution's getNodes to getMySQLNodes
Revision 109 - Directory Listing
Modified Tue Sep 19 09:27:12 2006 UTC (11 years, 2 months ago) by duarte
Original Path: trunk
Made loadMySQLDriver method public (needed to call it from other class) and static (makes more sense)
Revision 108 - Directory Listing
Modified Tue Sep 19 09:18:04 2006 UTC (11 years, 2 months ago) by duarte
Original Path: trunk
Added functionality to run commands in different threads
Revision 107 - Directory Listing
Modified Wed Sep 13 08:53:03 2006 UTC (11 years, 2 months ago) by duarte
Original Path: trunk
Initial commit, Hello World MySQLConnection program for newcomers
Revision 106 - Directory Listing
Modified Thu Sep 7 13:45:36 2006 UTC (11 years, 2 months ago) by duarte
Original Path: trunk
HOSTSFILE changed to new /project/StruPPi/Cluster/admin/hosts_mysql_server.txt
Revision 104 - Directory Listing
Modified Tue Aug 8 11:10:01 2006 UTC (11 years, 3 months ago) by duarte
Original Path: trunk
Modified finalizeDirs() to be tri-state: prompt, force or noremove. By default force. (using new field rmvtmp)
Getting rid of temp dir created in constructor when calling setDumpDir, otherwise an empty tmp dir was left lying around

Revision 102 - Directory Listing
Modified Fri Aug 4 14:34:00 2006 UTC (11 years, 3 months ago) by duarte
Original Path: trunk
Method finalizeDirs now prompts by default whether to delete temp dirs, unless new boolean field "force" is true.
Revision 98 - Directory Listing
Modified Mon Jul 24 14:37:40 2006 UTC (11 years, 4 months ago) by stehr
Original Path: trunk
Added class TableSorter to tools package
Revision 97 - Directory Listing
Modified Fri Jun 2 09:49:54 2006 UTC (11 years, 5 months ago) by duarte
Original Path: trunk
Added getters/setters to host,db,user and password in MySQLConnection
Added another constructor to QueryThread to take just the MySQLConnection as argument
Revision 96 - Directory Listing
Modified Wed May 31 11:02:12 2006 UTC (11 years, 5 months ago) by duarte
Original Path: trunk
Slight improve in insertIdsToKeyMaster method. Instead of querying in each insert for the nodeid, we get the node names to node id mapping in a HashMap through another query.
Revision 95 - Directory Listing
Modified Wed May 31 09:44:05 2006 UTC (11 years, 5 months ago) by duarte
Original Path: trunk
Adapted also ClusterConnection and checking methods in DataDistribution to text/numeric keys.
Some methods in ClusterConnection have not changed at all even though they deal with keys. I haven't changed them because they are applicable only to numeric keys:
insertIdxInMaster, getLastInsertId and getIdxSet
Revision 94 - Directory Listing
Modified Mon May 29 15:22:13 2006 UTC (11 years, 5 months ago) by duarte
Original Path: trunk
Simplified the code for dealing with text/numerical keys.
Now there's no more double methods Integer/String, rather the methos use a generic Object[] that stores either String[] or Integer[] depending on the case.
Thus modified a few methods in DataDistributer, DataDistribution and MySQLConnection.
Revision 93 - Directory Listing
Modified Wed May 24 15:44:25 2006 UTC (11 years, 6 months ago) by duarte
Original Path: trunk
Now split of data also working with text-based keys as well as numerical
MySQLConnection:
- method getAllIds4KeyAndTable now splitted into two methods one for numerical ids and another for text ids
- new methods getColumnType and isKeyNumerical
DataDistribution:
- method getIdSetsFromNodes splitted into two one for numerical ids one for text ids
DataDistributer:
- new methods: splitIdsIntoSets now splitted into two methods one numerical, one text
- change methods: splitTableToCluster, splitTable, insertIdsToKeyMaster, removePK, addPK, createNewKeyMasterTbl, removeZeros, loadSplitData, dumpSplitData to make them work for both text and numeric keys. Introduced generic type T in some of them
- some bugs corrected:
-- an important one in createNewKeyMasterTbl, was introducing record in dbs_keys with srcDb instead of destDb as it should have been
-- some bugs in loadSplitData and dumpSplitData to account for cases in which there are less ids than number of nodes and thus some nodes don't get any data. Wasn't counting with this before.
Revision 92 - Directory Listing
Modified Fri May 5 14:39:20 2006 UTC (11 years, 6 months ago) by duarte
Original Path: trunk
Made KEYMASTERDB in DataDistribution public. Now using in all other classes/programs that need KEYMASTERDB.
Revision 89 - Directory Listing
Modified Fri May 5 10:46:35 2006 UTC (11 years, 6 months ago) by duarte
Original Path: trunk
Added method to setDumpDir method
Revision 87 - Directory Listing
Modified Wed May 3 08:50:26 2006 UTC (11 years, 6 months ago) by duarte
Original Path: trunk
Improved considerably the splitTableToCluster method:
- got rid of the unnecessary step of creating partial tables before dumping.
- now directly dumping with new method dumpSplitData, a modified dumpData that dumps using a WHERE condition
- added variable NUM_CONCURRENT_SAMEHOST_WRITE_QUERIES used in dumpSplitData method. It sets the concurrency when dumping locally only from the master
Revision 86 - Directory Listing
Modified Fri Apr 28 10:31:35 2006 UTC (11 years, 6 months ago) by duarte
Original Path: trunk
Added PARALLELISM in load/dump of tables using new class QueryThread (extends Thread)
Modified methods loadData, dumpData and loadSplitData to dump/load parallely in cases that is useful by using the QueryThread class.
New method initializeDirs(String[]) to do some of the dir initialization that was in dumpData
Got rid of one of the getConnectionToNode method, not needed anymore
New important 2 final static variables: NUM_CONCURRENT_READ_QUERIES and NUM_CONCURRENT_WRITE_QUERIES. They define how much concurrency we want in reads/writes to nfs for loads/dumps
Revision 85 - Directory Listing
Modified Mon Apr 24 12:41:27 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
MAJOR change.
Split DataDistribution into 2 classes: DataDistributer and DataDistribution.
I haven't actually changed or added functionality
DataDistributer deals with the distribution of the data, while DataDistribution deals with things to do when data is already distributed, right now is only a few data checks
Note that DataDistributer now has two db fields: srcDb and destDb. This is different to before, when destDb was rather a parameter passed as arguments to the methods
Methods in DataDistributer have been tidied up a little (specially load and dump ones)
Revision 84 - Directory Listing
Modified Thu Apr 20 10:42:38 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Fixed bug in getTables4Db. Was closing the connection. Shouldn't do this!
Add method getAllIds4KeyAndTables, moved from DataDistribution. It makes more sense to have it here.

Revision 83 - Directory Listing
Modified Wed Apr 19 14:02:35 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Got rid of getTables4Db in DataDistribution
Add method getTables4Db to MySQLConnection. Makes a lot more sense.
Changed accordingly the only call to the method in DataDistribution's method chkCounts
Revision 81 - Directory Listing
Modified Wed Apr 12 15:27:05 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Changed the Connection fields to be MySQLConnection.
Thanks to this, simplify considerably a lot of the methods by using the MySQLConnection methods.
Got rid of method loadSQLDriver and URL final field
Revision 80 - Directory Listing
Modified Wed Apr 12 14:59:37 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Introduced better javadoc comments in constructors.
Revision 79 - Directory Listing
Modified Wed Apr 12 11:03:01 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Modified insertIdsToKeyMaster method. Now removing pk in table before inserting, then removing zeros and adding finally the pk back. At that point mysql should complain if there are duplicates
New methods to deal with key_master database actions. They belong in another class, but for the moment here.
- createNewKeyMasterTbl
- removePK
- addPK
- removeZeros
Revision 78 - Directory Listing
Modified Wed Apr 12 08:52:25 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Got rid of method createNewKeyMasterTbl
Didn't belong here but in DataDistribution (at least for now)

Revision 77 - Directory Listing
Modified Wed Apr 12 08:26:36 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Bug in new method createNewKeyMasterTbl
The query for inserting the new record in dbs_keys was totally wrong
Wrote something more correct and simpler!
Revision 76 - Directory Listing
Modified Tue Apr 11 16:00:26 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Minor change, in getHostId4Ifx one of the error messages was being written to out, now to err
Revision 75 - Directory Listing
Modified Tue Apr 11 14:33:39 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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.
Revision 74 - Directory Listing
Modified Tue Apr 11 14:27:17 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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.
Revision 73 - Directory Listing
Modified Tue Apr 11 10:42:54 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 72 - Directory Listing
Modified Tue Apr 11 10:29:39 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 71 - Directory Listing
Modified Mon Apr 10 16:01:01 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 70 - Directory Listing
Modified Fri Apr 7 14:49:02 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
KEYMASTERDB had value for testing, change that back.
Revision 69 - Directory Listing
Modified Fri Apr 7 14:44:08 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added method insertIdsToKeyMaster
Added call to the new insertIdsToKeyMaster in splitTableToCluster method
Revision 68 - Directory Listing
Modified Fri Apr 7 13:26:05 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 67 - Directory Listing
Modified Fri Apr 7 12:59:18 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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.
Revision 66 - Directory Listing
Modified Fri Apr 7 09:31:08 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Made MASTER final static variable also public. It is in use by other classes.
Revision 65 - Directory Listing
Modified Fri Apr 7 09:26:03 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 64 - Directory Listing
Modified Thu Apr 6 14:47:09 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added method getCreateIndex4Table
Revision 63 - Directory Listing
Modified Thu Apr 6 12:18:18 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Fixed bug in getAllIndexes4Table, the SELECT needed a DISTINCT
Revision 62 - Directory Listing
Modified Thu Apr 6 12:15:37 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Got rid of method dbExists. Was useless and not working.
Revision 61 - Directory Listing
Modified Thu Apr 6 10:07:22 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added method setSqlMode, to set sql_mode server variable
Revision 60 - Directory Listing
Modified Thu Apr 6 09:24:28 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 59 - Directory Listing
Modified Thu Apr 6 08:24:15 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 58 - Directory Listing
Modified Wed Apr 5 08:45:23 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Now executeSQL method throws exception instead of catching it. Thought it was better than the calling class deals with these exceptions.
Revision 57 - Directory Listing
Modified Wed Apr 5 07:38:32 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added getConnectionObject
Added printDbSizeInfo and 2 getRange methods from utils4DB
Made private the loadMySQLDriver and readConnectionFile methods

Revision 56 - Directory Listing
Modified Tue Apr 4 17:27:58 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
execUpdateQuery method added and code in comments was removed
Revision 55 - Directory Listing
Modified Tue Apr 4 15:27:49 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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)
Revision 54 - Directory Listing
Modified Wed Mar 29 14:26:03 2006 UTC (11 years, 7 months ago) by stehr
Original Path: trunk
initial import
Revision 53 - Directory Listing
Modified Wed Mar 29 13:01:40 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
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
Revision 52 - Directory Listing
Modified Wed Mar 29 12:49:13 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Changed error message printed in getHostId4Idx
Revision 51 - Directory Listing
Modified Wed Mar 29 12:29:56 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added setKeyDb method, to be used in testing, i.e. with this method we can change from another class the default MASTERDB database.
Revision 50 - Directory Listing
Modified Tue Mar 28 15:05:31 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
More examples added and the current ones modified according to Graph2Pml changes
Revision 49 - Directory Listing
Modified Tue Mar 28 15:04:24 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
More flexibility in coloring, popDefaults/setDefaults methods plus comments
Revision 48 - Directory Listing
Modified Tue Mar 28 15:03:32 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
Refresh method added plus refresh added before saving image
Revision 47 - Directory Listing
Modified Mon Mar 27 21:01:06 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
Added cgo functionality/examples in Graph2Pml and testGraph2Pml
Revision 46 - Directory Listing
Modified Mon Mar 27 20:59:42 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
PyMol class: adding refresh in saveImage methods
Revision 45 - Directory Listing
Modified Mon Mar 27 16:32:22 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
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
Revision 44 - Directory Listing
Modified Wed Mar 22 17:14:01 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
In PyMol class, objectNameQuotes class variable is replaced by the method parameter called variable. Graph2Pml is modified accrodingly.
Revision 43 - Directory Listing
Modified Wed Mar 22 09:30:40 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added executeSql method
Revision 42 - Directory Listing
Modified Tue Mar 21 19:13:20 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding Graph2Pml and testGraph2Pml classes (non functional code!)
Revision 41 - Directory Listing
Modified Tue Mar 21 18:41:48 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
getRange methods now return double array instead of Float array. Previous code is into comments.
Revision 40 - Directory Listing
Modified Tue Mar 21 18:21:00 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding Msdsd2Pdb and PyMol classes
Revision 39 - Directory Listing
Modified Tue Mar 21 17:21:54 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding comments
Revision 38 - Directory Listing
Modified Mon Mar 20 11:37:12 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added getAllIdxAndClients method:
gets all ids and client_names for a certain key
Revision 37 - Directory Listing
Modified Fri Mar 17 11:22:19 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Some changes in error messages to be more clear.
Revision 36 - Directory Listing
Modified Fri Mar 17 11:03:15 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Now using constructor without key and createStatement with key, since createStatement without key is not allowed anymore (is now private)
Revision 35 - Directory Listing
Modified Fri Mar 17 11:00:33 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Clean up a bit and added some more comments
Revision 34 - Directory Listing
Modified Fri Mar 17 10:48:03 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
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.
Revision 33 - Directory Listing
Modified Wed Mar 15 11:58:24 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Changed all error printing in catches to STDERR instead of STDOUT
Revision 32 - Directory Listing
Modified Tue Mar 14 09:45:57 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
New exec method taking only a String argument wasn't working. Fixed the bug.
Revision 31 - Directory Listing
Modified Tue Mar 14 07:40:32 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added exec method to take only a string as argument.
Revision 30 - Directory Listing
Modified Fri Mar 10 15:19:32 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
introduced generics, so class will compile in Java 5, not sure though whether the functionality is the same as before, will need more testing
Revision 29 - Directory Listing
Modified Fri Mar 10 10:57:12 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
changed server port to standard
Revision 28 - Directory Listing
Modified Fri Mar 10 10:56:22 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
prevent overlong commands from being sent to the server
Revision 27 - Directory Listing
Modified Thu Mar 9 17:12:43 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
initial import
Revision 26 - Directory Listing
Modified Thu Mar 9 15:55:56 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
fixed bug for very long command strings (> 255 characters)
Revision 25 - Directory Listing
Modified Thu Mar 9 10:11:16 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk

Revision 24 - Directory Listing
Modified Thu Mar 9 10:08:44 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
moved executables (classes with main function) to root directory
Revision 23 - Directory Listing
Modified Wed Mar 8 15:25:45 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
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
Revision 22 - Directory Listing
Modified Tue Mar 7 13:22:37 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
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.
Revision 21 - Directory Listing
Modified Tue Mar 7 11:50:37 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
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.

Revision 20 - Directory Listing
Modified Mon Mar 6 15:19:40 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
updated commentary
Revision 19 - Directory Listing
Modified Mon Mar 6 15:15:57 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
deleted, file was a copy of makenbhtable.java, original file was lost
Revision 18 - Directory Listing
Modified Mon Mar 6 15:03:46 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
initial import

Revision 17 - Directory Listing
Modified Mon Mar 6 09:20:16 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Grouped all the setIdxColumn and setMasterTable into setKey.
Also rationalised a bit the constructors by calling one from the other.
Revision 16 - Directory Listing
Modified Mon Mar 6 08:32:55 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added package tools.
Revision 15 - Directory Listing
Modified Mon Mar 6 08:25:22 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Initial commit of the ClusterConnection class + small test class to test it out.

Revision 14 - Directory Listing
Modified Mon Mar 6 08:05:31 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
removed ununsed imports and variables
Revision 13 - Directory Listing
Modified Fri Mar 3 15:15:31 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding SystemCmd class
Revision 12 - Directory Listing
Modified Thu Mar 2 17:21:28 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
removed some debug code

Revision 11 - Directory Listing
Modified Thu Mar 2 15:42:09 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
Corrected some bad mistake

Revision 10 - Directory Listing
Modified Thu Mar 2 11:42:06 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
Initial commit of the remote-pymol-from-java stuff

Revision 9 - Directory Listing
Modified Tue Feb 14 11:00:40 2006 UTC (11 years, 9 months ago) by filippis
Original Path: trunk
Adding R class
Revision 8 - Directory Listing
Modified Mon Jan 23 09:20:44 2006 UTC (11 years, 10 months ago) by duarte
Original Path: trunk
Deleted old tools.trunk files
Revision 7 - Directory Listing
Modified Mon Jan 23 09:19:47 2006 UTC (11 years, 10 months ago) by duarte
Original Path: trunk
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
Revision 6 - Directory Listing
Modified Wed Jan 18 19:07:41 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Adding getDbSizeInfo method into utils4DB program
Revision 5 - Directory Listing
Modified Wed Jan 18 18:52:48 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Adding files utils*
Revision 4 - Directory Listing
Modified Wed Jan 18 18:49:01 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Package tools changed to tools.trunk because code could not compile!
Revision 3 - Directory Listing
Modified Wed Jan 18 18:23:39 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
The name of the report table can be passed as argument now (default value is report as previous)
Revision 2 - Directory Listing
Modified Wed Jan 18 18:10:10 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Comments in system.out.println & Dealing with no password cases
Revision 1 - Directory Listing
Added Wed Jan 18 17:48:52 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Initial import of tools