Made contacts public

New method getAllEdgeNbhSizes

NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object

Added basic compare method to the Graph class and test class compareCMs

Tagging version 0.5 for release of CM2PyMol version 0.5

Changed to version 0.5

FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning

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

New class GenericContact. To store a generic contact, i.e. a pair of residue types

Fixed bug: calculateEntropy was wrong when a pi was 0

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

New class NbhProbDistribution
In NodeNbh implemented a few static classes to convert between different motifs and to match motifs using differing criteria

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

Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact

Made public getUserName

New static method getUserName and new constructor with only server and db

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

original version to be saved ... 

running version summing delta Rank
still to implement sum(deltza) for entropy etc. 

Got rid of some unnecessary warnings

version of iterateNBHood for the uppercase background info 
pdb_reps_graph_4_2 for briefer output & calculation 

Running version, takes graph_id and resnr as input 

First version of exchange routine contact vs. CN - non functional 

New functionality: added methods to get node/edge neighbours

added Manifest

Updated test class for Pdb/Graph objects

made Graph.directed public

tab-Formatted output added

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

FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database

FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!

Now passing also chaincode from Pdb object to Graph object in get_graph

Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file

Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality

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

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

working version for each single nbring residue 

- functional

min-info - functional

list of infogain per neighbouring residue 
- still buggy w.r.t. x elimination 

Max.Info Gain still with problems if only negative (loss) of info 

Made cutoff and ct public

Made some fields public: sequence, accode, chaincode, model

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

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

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

Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)

Made Pdb.acccode public

Changed default accode and chaincode to "Unknown" when reading from pdb file

FIXED BUG: wasn't setting the chain field when reading from msdsd

Made chain field in PDB class public

FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes

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

Implemented basic reading contacts from file

New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!

Added more tests for all cases

2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless

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

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

ContactMap and EdgeState classes moved here from CMPredict repository

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

MYSQLUSER now taken from unix name with new getUserName method

Initial commit of testPdb, to test the proteinstructure package

Added error handling for PdbaseInfo: 2 new exception classes

Initial commit of the proteinstructure package. Contains classes to use pdb protein structures

tagged version 0.3.4

Updated TableSorter to compile in Java 1.5 and some trivial changes in comments

added overloaded method setDistance for use in CM2Pymol for chains without chain code

Fixed space missing in one of the queries

testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java

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

Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server

Modified method getIdFromMaster to create keyTable if it didn't exist

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

Tagging version 0.3.3. at rev110 after adding some renaming getNodes method to getMySQLNodes in DataDistribution and adding some functionality

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

Made loadMySQLDriver method public (needed to call it from other class) and static (makes more sense)

Added functionality to run commands in different threads

Initial commit, Hello World MySQLConnection program for newcomers

HOSTSFILE changed to new /project/StruPPi/Cluster/admin/hosts_mysql_server.txt

Tagging at rev104, slight modifications in DataDistributer. To be used with a slightly improved dumpnload.java

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

Tag 0.3.1 at rev 102. Introduced slight modifications in DataDistributer class to use with dumpnload.java

Method finalizeDirs now prompts by default whether to delete temp dirs, unless new boolean field "force" is true.

tools version 0.3 from rev98. To use with jed (includes new TableSorter)

Sorry that was wrong!!

tools version 0.3 from rev98. To use with jed (includes new TableSorter)

Added class TableSorter to tools package

Added getters/setters to host,db,user and password in MySQLConnection
Added another constructor to QueryThread to take just the MySQLConnection as argument

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.

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

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.

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.

Made KEYMASTERDB in DataDistribution public. Now using in all other classes/programs that need KEYMASTERDB.

Creating of tools version 0.2:
Freeze of tools package at rev89.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)

This tag was wrongly created, should have contained a tools directory as a subdir. Deleting it

Added method to setDumpDir method

Creating of tools version 0.2:
Freeze of tools package at rev87.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)

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

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

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)

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.

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

Creation of tools version 0.1:
Freezing tools rev81 to tag tools-0.1
I am planning to change completely some of the classes: DataDistribution and ClusterConnection. Will continue developing on trunk while we have this freeze so others can use programs as they are now.

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

Introduced better javadoc comments in constructors.

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

Got rid of method createNewKeyMasterTbl
Didn't belong here but in DataDistribution (at least for now)

Bug in new method createNewKeyMasterTbl
The query for inserting the new record in dbs_keys was totally wrong
Wrote something more correct and simpler!

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 examples added and the current ones modified according to Graph2Pml changes

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.

Now using constructor without key and createStatement with key, since createStatement without key is not allowed anymore (is now private)

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.

updated commentary

deleted, file was a copy of makenbhtable.java, original file was lost

initial import

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

Deleted old tools.trunk files

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

Adding getDbSizeInfo method into utils4DB program

Adding files utils*

Package tools changed to tools.trunk because code could not compile!

The name of the report table can be passed as argument now (default value is report as previous)

Comments in system.out.println & Dealing with no password cases

Initial import of tools