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Revision 555 - Directory Listing
Modified Thu Feb 28 14:29:15 2008 UTC (9 years, 8 months ago) by duarte
Copied from: trunk revision 554
Tagging 0.9.3 for CMView release 0.9.3
Revision 553 - Directory Listing
Modified Thu Feb 28 14:27:21 2008 UTC (9 years, 8 months ago) by duarte
Original Path: trunk
Changed version in Manifest to 0.9.3
Revision 552 - Directory Listing
Modified Fri Feb 22 15:26:34 2008 UTC (9 years, 8 months ago) by duarte
Original Path: trunk
Now throwing exception in checkLengths().
Now fast checking of FASTA/PIR format (we check if first non-empty line starts with ">")
Revision 551 - Directory Listing
Modified Thu Feb 21 18:51:53 2008 UTC (9 years, 8 months ago) by duarte
Original Path: trunk
Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
Revision 550 - Directory Listing
Modified Thu Feb 21 14:26:13 2008 UTC (9 years, 8 months ago) by stehr
Original Path: trunk
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
Revision 549 - Directory Listing
Modified Thu Feb 21 09:17:24 2008 UTC (9 years, 8 months ago) by stehr
Original Path: trunk
deleted testGraphAverager from aglappe/default, now in project CaspConsensusContactPrediction
Revision 548 - Directory Listing
Modified Thu Feb 21 08:42:22 2008 UTC (9 years, 8 months ago) by duarte
Original Path: trunk
Fixed bug: write_graph_to_file now writes blank instead of "null" when pdbCode, pdbChainCode or chainCode are null.
Revision 547 - Directory Listing
Modified Wed Feb 20 16:20:26 2008 UTC (9 years, 8 months ago) by stehr
Original Path: trunk
Added constant NO_SEQ_SEP_VAL
Revision 546 - Directory Listing
Modified Wed Feb 20 15:53:51 2008 UTC (9 years, 8 months ago) by duarte
Original Path: trunk
New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble

Revision 544 - Directory Listing
Modified Tue Feb 19 16:28:47 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Updated version to 1.0-rc1
Revision 543 - Directory Listing
Modified Mon Feb 18 18:04:27 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Now forcing i<j in CASP RR files (as specified by the CASP RR format)
Revision 542 - Directory Listing
Modified Mon Feb 18 18:03:49 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Using Ca/Cg for testing as Ca/Cb is now allowed
Revision 541 - Directory Listing
Modified Thu Feb 14 18:30:47 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.
Revision 540 - Directory Listing
Modified Thu Feb 14 16:19:04 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Fixed mega-nasty bug: after introducing the PRMType enum, there was still one instance of the "type" variable being compared to a String in getCorrectedPdbAtomName method
Revision 539 - Directory Listing
Modified Thu Feb 14 13:38:29 2008 UTC (9 years, 9 months ago) by stehr
Original Path: trunk
some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)
Revision 538 - Directory Listing
Modified Thu Feb 14 11:56:26 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
New option in reconstruct: -f force constant. New constructor in TinkerRunner that takes the force constant, previous constructor will work as before with the default constant.
Revision 537 - Directory Listing
Modified Wed Feb 13 18:29:05 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Fixed another bug in GraphAverager. Was still not working correctly: was putting edges twice in the final graph. 
Also now handling correctly graph averaging for directed or undirected graphs.
Revision 536 - Directory Listing
Modified Wed Feb 13 17:44:40 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Fixed GraphAverager: wasn't working since we introduced JUNG. 
Also added some better output in checkSequences() when sequence don't match between alignment/graphs. Now we take the 2 sequences calculate a pairwise alignment (using jaligner) and output it. This is useful for picking up unobserves and similars.
Revision 535 - Directory Listing
Modified Wed Feb 13 14:11:10 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Added option to output to standard output
Revision 534 - Directory Listing
Modified Wed Feb 13 11:33:26 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Now compiling also scripts in default package
Revision 533 - Directory Listing
Modified Tue Feb 12 11:50:05 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
New constructor to read from simple graph files, i.e. list of contacts without any headers
Revision 532 - Directory Listing
Modified Fri Feb 8 12:07:10 2008 UTC (9 years, 9 months ago) by spriya
Original Path: trunk
Fixed bug: addEdgeIJ was not checking for presence of contacts
Revision 531 - Directory Listing
Modified Tue Feb 5 15:48:25 2008 UTC (9 years, 9 months ago) by spriya
Original Path: trunk
Added convenience methods: containsVertexI, addEdgeIJ
Revision 530 - Directory Listing
Modified Tue Feb 5 15:08:00 2008 UTC (9 years, 9 months ago) by spriya
Original Path: trunk
New methods getFisrt/Last residue serial
Revision 529 - Directory Listing
Modified Tue Feb 5 14:53:57 2008 UTC (9 years, 9 months ago) by spriya
Original Path: trunk
Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1
Revision 528 - Directory Listing
Modified Tue Feb 5 14:31:46 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Fixed bug in compare(), was not checking correctly for sequence matching
Revision 526 - Directory Listing
Modified Wed Jan 30 11:04:12 2008 UTC (9 years, 9 months ago) by stehr
Original Path: trunk
updated version in Manifest to 0.9.2
Revision 525 - Directory Listing
Modified Wed Jan 30 10:54:05 2008 UTC (9 years, 9 months ago) by stehr
Original Path: trunk
new package ppi with classes for protein interaction networks
Revision 524 - Directory Listing
Modified Tue Jan 29 12:03:32 2008 UTC (9 years, 9 months ago) by duarte
Original Path: trunk
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
Revision 523 - Directory Listing
Modified Thu Jan 24 16:18:16 2008 UTC (9 years, 9 months ago) by stehr
Original Path: trunk
Added new package vecmath with classes Tuple3d, Point3d, Vector3d, Point3i to replace javax.vecmath while maintaining the same interface. The idea is that our package can be used by simply changing the import statement to remove the dependency on java3d.
Revision 522 - Directory Listing
Modified Fri Jan 18 16:51:31 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
Minor change of some error message
Revision 521 - Directory Listing
Modified Wed Jan 16 17:58:38 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Fixed bug! actually it was not an abbot bug but our own, now calling AAinfo.class correctly (instead of System.getRunTime()....). With this abbot runs fine without any dirty fixes
Revision 520 - Directory Listing
Modified Wed Jan 16 15:35:36 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Fixed to be able to run CMView under Abbot (because of abbot getResourceAsStream bug). The ABBOT_FIX flag is turned off.
Revision 519 - Directory Listing
Modified Tue Jan 15 17:53:44 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
updated classpath in makefile, changed permissions to execute by all
Revision 518 - Directory Listing
Modified Tue Jan 15 16:18:33 2008 UTC (9 years, 10 months ago) by filippis
Original Path: trunk
checkConsurf: if the file is not found and the chain code given is "A", we check now also for results for NULL chain code 
Revision 517 - Directory Listing
Modified Tue Jan 15 13:19:36 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this. 
NOTE: graph averaging hasn't been tested after the change
Revision 516 - Directory Listing
Modified Mon Jan 14 14:25:14 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Removed PairwiseAlignmentGraphConverter, not needed anymore by CMView + was very buggy
Improved some comments/java docs
Revision 515 - Directory Listing
Modified Mon Jan 14 10:02:28 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
Revision 514 - Directory Listing
Modified Fri Jan 11 14:59:43 2008 UTC (9 years, 10 months ago) by filippis
Original Path: trunk
Latest scop and csa versions updated.
Revision 513 - Directory Listing
Modified Fri Jan 11 13:33:56 2008 UTC (9 years, 10 months ago) by filippis
Original Path: trunk
Fixing the fixed bug!
-if graph read is chain graph, then fullLength is set to the maximum observed residue serial
-else if graph is scop graph, then fullLength is set to the number of observed residues
NOTE:In the case of a wholechain scop graph, there might be inconsistensy between a graph I created with Pdb/RIGraph classes and stored in db and the corresponding graph i read from db. Specifically, the fullLength of graph I equals the length of the chain while the fullLength of graph i equals the number of observed residues.
Revision 512 - Directory Listing
Modified Fri Jan 11 10:57:40 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Added getCommanSeparatedResSerials to RIGCommonNbhood
Revision 511 - Directory Listing
Modified Fri Jan 11 09:42:35 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Added -f command line parameter
Revision 509 - Directory Listing
Modified Thu Jan 10 16:22:03 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
added some comments
Revision 508 - Directory Listing
Modified Thu Jan 10 15:39:00 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
Fixed bug in DSSP secondary structure assignment, first element was starting at index 0
Revision 507 - Directory Listing
Modified Thu Jan 10 14:55:35 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
changed version to 0.9.1
Revision 506 - Directory Listing
Modified Thu Jan 10 14:46:11 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
New method to convert secondary structure
Revision 505 - Directory Listing
Modified Thu Jan 10 13:37:09 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Now converting also secondary structure in pairwise alignment graph conversion
Revision 504 - Directory Listing
Modified Thu Jan 10 10:30:46 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
Fixed three compiler warnings for unused imports (DbRIGraph, Pdb) and an untyped iterator (CatalSiteSet)
Revision 503 - Directory Listing
Modified Tue Jan 8 19:51:39 2008 UTC (9 years, 10 months ago) by filippis
Original Path: trunk
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned

!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added

!!!!AIGraph:
-getResidueSerial method added

RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field

DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.

testDbRIGraph added:
It reads one graph from a source db based either 
-on pdbcode, chaincode and graph properties or 
-on scop id and graph properties or 
-on a graph id 
and it writes the graph to a destination db.

Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence

CatalSiteSet:
- removeCatalSiteRes(int resser) method added

CatalyticSite:
-remRes(int resser) method added

Scop:
-remove(ScopRegion e) method added

genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.


Revision 502 - Directory Listing
Modified Tue Jan 8 11:00:15 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
Revision 501 - Directory Listing
Modified Tue Jan 8 10:04:46 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
Revision 500 - Directory Listing
Modified Mon Jan 7 13:41:26 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
New functionality: now we can get sequences and reset tags based on the order the sequences appear on the file.
Revision 499 - Directory Listing
Modified Fri Jan 4 15:00:11 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Got rid of check for equality of tags
Revision 498 - Directory Listing
Modified Thu Jan 3 17:16:03 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Now also copying the CASP RR identifier fields in RIGraph.copy() and in PairwiseAlignmentGraphConverter.converGraph().
Revision 497 - Directory Listing
Modified Thu Jan 3 14:20:03 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
Revision 496 - Directory Listing
Modified Wed Jan 2 14:11:56 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Rescued the make-aglappe.sh script from the old trunk
Revision 495 - Directory Listing
Modified Wed Jan 2 14:07:57 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
added main function and loading from Multi-model PDB files
Revision 493 - Directory Listing
Modified Wed Jan 2 13:57:31 2008 UTC (9 years, 10 months ago) by stehr
Original Path: trunk
Changed version number to 0.9
Revision 492 - Directory Listing
Modified Wed Jan 2 13:18:57 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Copied the aglappe-jung branch into trunk.

Revision 491 - Directory Listing
Modified Wed Jan 2 12:02:46 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Deleting everything in trunk to later replace with JUNG branch

Revision 489 - Directory Listing
Modified Wed Jan 2 11:09:19 2008 UTC (9 years, 10 months ago) by duarte
Original Path: trunk
Updated version to 0.8.7 in Manifest
Revision 467 - Directory Listing
Modified Mon Dec 10 14:37:19 2007 UTC (9 years, 11 months ago) by lpetzo
Original Path: trunk
don't touch br!!!
Revision 466 - Directory Listing
Modified Mon Dec 10 13:49:51 2007 UTC (9 years, 11 months ago) by lpetzo
Original Path: trunk
MAJOR CHANGES:
- merge the changes from the jung-branch: *Pdb loading scheme together with new methods getChains(), getModels()
- different exceptions
Revision 458 - Directory Listing
Modified Thu Dec 6 11:40:51 2007 UTC (9 years, 11 months ago) by stehr
Original Path: trunk
moved GraphAverager and testGraphAverager to repository CaspConsensusContactPrediction
Revision 446 - Directory Listing
Modified Tue Dec 4 14:51:54 2007 UTC (9 years, 11 months ago) by lpetzo
Original Path: trunk
Johannes provided us we the debugged version of noncrossing(), kept the old version for sentimental reason as noncrossing_()
Revision 445 - Directory Listing
Modified Tue Dec 4 10:18:44 2007 UTC (9 years, 11 months ago) by filippis
Original Path: trunk
Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance
Revision 439 - Directory Listing
Modified Wed Nov 28 16:39:22 2007 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Updated version in Manifest for tagging
Revision 436 - Directory Listing
Modified Wed Nov 28 13:29:55 2007 UTC (9 years, 11 months ago) by filippis
Original Path: trunk
-expBB is treated correctly now as int field in db in DBGraph and Graph classes
-null secondary structure case fixed in write_graph_to_db in Graph class
Revision 432 - Directory Listing
Modified Tue Nov 27 11:43:03 2007 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Initial commit: script to make aglappe project into one compiled jar
Revision 429 - Directory Listing
Modified Mon Nov 26 17:27:29 2007 UTC (9 years, 11 months ago) by filippis
Original Path: trunk
DbGraph-fix bug
Revision 425 - Directory Listing
Modified Fri Nov 23 17:55:51 2007 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Fixed bug in Graph constructor from sadp's ContactMap
Revision 417 - Directory Listing
Modified Thu Nov 22 11:23:49 2007 UTC (9 years, 11 months ago) by lpetzo
Original Path: trunk
abstract class implementing the Runnable interface
Revision 416 - Directory Listing
Modified Thu Nov 22 11:18:28 2007 UTC (9 years, 11 months ago) by lpetzo
Original Path: trunk
- changed the identation mode
- added some comments
Revision 414 - Directory Listing
Modified Thu Nov 22 10:09:50 2007 UTC (9 years, 11 months ago) by duarte
Original Path: trunk
Minor changes. Got rid of some warnings
Revision 413 - Directory Listing
Modified Wed Nov 21 21:23:19 2007 UTC (9 years, 11 months ago) by filippis
Original Path: trunk
createGraphDb.sh
-pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code
-index for pdb_residue_info table added
Revision 412 - Directory Listing
Modified Wed Nov 21 16:12:26 2007 UTC (9 years, 11 months ago) by filippis
Original Path: trunk
Changes in Pdb
-checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores

-writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file.
-another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false
-dump2pdbfile has also been changed in similar way
-runDssp and runNaccess now call the above methods with true pdbCompatible

Changes in genDbGraph
-1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ...
-DSSP is run with 3state
Revision 411 - Directory Listing
Modified Tue Nov 20 19:41:16 2007 UTC (10 years ago) by filippis
Original Path: trunk
minor changes
Revision 410 - Directory Listing
Modified Tue Nov 20 19:40:36 2007 UTC (10 years ago) by filippis
Original Path: trunk
minor change
Revision 409 - Directory Listing
Modified Tue Nov 20 19:09:21 2007 UTC (10 years ago) by filippis
Original Path: trunk
createGraphDb.sh added
Revision 408 - Directory Listing
Modified Tue Nov 20 18:44:03 2007 UTC (10 years ago) by filippis
Original Path: trunk
minor change
Revision 407 - Directory Listing
Modified Tue Nov 20 18:41:56 2007 UTC (10 years ago) by filippis
Original Path: trunk
contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Revision 406 - Directory Listing
Modified Tue Nov 20 16:50:32 2007 UTC (10 years ago) by duarte
Original Path: trunk
Reverting to last revision, changes made in 405 were wrong
Revision 405 - Directory Listing
Modified Tue Nov 20 16:37:54 2007 UTC (10 years ago) by duarte
Original Path: trunk
Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet
Revision 404 - Directory Listing
Modified Fri Nov 16 17:22:33 2007 UTC (10 years ago) by duarte
Original Path: trunk
Not asserting anymore pdbChainCode to be uppercase. pdb chain codes are case sensitive!
Revision 403 - Directory Listing
Modified Fri Nov 16 16:52:03 2007 UTC (10 years ago) by filippis
Original Path: trunk
OXT is taken into account now also for BB contact type
Revision 402 - Directory Listing
Modified Thu Nov 15 16:15:32 2007 UTC (10 years ago) by duarte
Original Path: trunk
Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
Revision 401 - Directory Listing
Modified Thu Nov 15 15:58:30 2007 UTC (10 years ago) by duarte
Original Path: trunk
Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
Revision 400 - Directory Listing
Modified Tue Nov 13 15:55:30 2007 UTC (10 years ago) by filippis
Original Path: trunk
-pdb_seq_num is used instead of auth_seq_num in get_ressers_mappings. Now resser2pdbresser contains all residues even the unobserved ones. This has been changed in PdbasePdb and CiffilePdb classes.

-pdb_strand_id not needed in the query in read_seq in PdbasePdb class. Asym_id and pdb_strand_id have 1-1 mapping in case sensitive mode.

-comments have been added about the entity_id-asym_id-pdb_strand_id 1-1-1 mapping and some filters in queries that are no longer necessary.
Revision 399 - Directory Listing
Modified Mon Nov 12 15:56:00 2007 UTC (10 years ago) by stehr
Original Path: trunk
added class PairwiseSequenceAlignment
Revision 398 - Directory Listing
Modified Fri Nov 9 15:12:33 2007 UTC (10 years ago) by filippis
Original Path: trunk
Minor changes
Revision 397 - Directory Listing
Modified Thu Nov 8 16:04:21 2007 UTC (10 years ago) by filippis
Original Path: trunk
Pdb code forced to lowercase in CiffilePdb
Revision 396 - Directory Listing
Modified Thu Nov 8 15:01:04 2007 UTC (10 years ago) by filippis
Original Path: trunk
Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)
Revision 395 - Directory Listing
Modified Thu Nov 8 12:53:09 2007 UTC (10 years ago) by duarte
Original Path: trunk
Initial commit. Provisional script to use the genDbGraph program when iterating through loads of structures, because of the "memory leak" problem is not possible to use directly genDbGraph to iterate over many structures (~1000)
Revision 394 - Directory Listing
Modified Thu Nov 8 12:40:01 2007 UTC (10 years ago) by duarte
Original Path: trunk
New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)
Revision 393 - Directory Listing
Modified Thu Nov 8 11:49:38 2007 UTC (10 years ago) by duarte
Original Path: trunk
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
Revision 392 - Directory Listing
Modified Thu Nov 8 11:25:06 2007 UTC (10 years ago) by stehr
Original Path: trunk
new methods getLastModelFiles and getGdtsToNative (using MaxClusterRunner)
Revision 391 - Directory Listing
Modified Thu Nov 8 11:22:40 2007 UTC (10 years ago) by stehr
Original Path: trunk
started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)
Revision 390 - Directory Listing
Modified Thu Nov 8 11:21:28 2007 UTC (10 years ago) by duarte
Original Path: trunk
Not creating anymore the score table
Revision 389 - Directory Listing
Modified Thu Nov 8 11:20:59 2007 UTC (10 years ago) by stehr
Original Path: trunk
implemented tinker reconstruction of consensus graphs created with GraphAverager
Revision 388 - Directory Listing
Modified Thu Nov 8 11:14:01 2007 UTC (10 years ago) by duarte
Original Path: trunk
New method setSequence
Revision 387 - Directory Listing
Modified Wed Nov 7 21:37:20 2007 UTC (10 years ago) by filippis
Original Path: trunk
deleted the print part in the checkCSA method in pdb class
Revision 386 - Directory Listing
Modified Wed Nov 7 17:35:26 2007 UTC (10 years ago) by lpetzo
Original Path: trunk
MODIFICATIONS
-------------

class SADP:
- added exception handling stuff for exceptions thrown by class Alignment
Revision 385 - Directory Listing
Modified Wed Nov 7 17:32:43 2007 UTC (10 years ago) by lpetzo
Original Path: trunk
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError

MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
 * writeFasta
 
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class

class GraphFileFormatError:
- s. class CiffileFormatError

class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment

class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter

class PdbFileFormatError:
- s. class CifffileFormatError
Revision 384 - Directory Listing
Modified Tue Nov 6 18:53:11 2007 UTC (10 years ago) by filippis
Original Path: trunk
hasCSA and getCSA methods added in Pdb.java
Revision 383 - Directory Listing
Modified Tue Nov 6 18:35:17 2007 UTC (10 years ago) by filippis
Original Path: trunk
inSameSheet, isOther and getSheetSerial methods added in SecStrucElement
Revision 382 - Directory Listing
Modified Tue Nov 6 15:42:05 2007 UTC (10 years ago) by filippis
Original Path: trunk
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table

Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
Revision 381 - Directory Listing
Modified Fri Nov 2 17:27:56 2007 UTC (10 years ago) by lpetzo
Original Path: trunk
a generic pair class
Revision 380 - Directory Listing
Modified Fri Nov 2 17:26:43 2007 UTC (10 years ago) by lpetzo
Original Path: trunk
added a new version of getDiffDistMap(...) that take a sequence alignment as an input to allow for residue mappings between two pdb-models of different size
Revision 379 - Directory Listing
Modified Fri Nov 2 14:22:54 2007 UTC (10 years ago) by stehr
Original Path: trunk
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph

Revision 378 - Directory Listing
Modified Thu Nov 1 15:46:58 2007 UTC (10 years ago) by stehr
Original Path: trunk
finally implemented the setCutoff method ;)
Revision 377 - Directory Listing
Modified Thu Nov 1 15:02:56 2007 UTC (10 years ago) by stehr
Original Path: trunk
fixed nasty bug in constructor Graph(sequence) (residue indexing was wrong)
Revision 376 - Directory Listing
Modified Thu Nov 1 14:14:24 2007 UTC (10 years ago) by stehr
Original Path: trunk
added method setCutoff() and some javadocs
Revision 375 - Directory Listing
Modified Thu Nov 1 11:43:13 2007 UTC (10 years ago) by duarte
Original Path: trunk
Cleaned up. More command line parameters
Revision 374 - Directory Listing
Modified Wed Oct 31 16:40:29 2007 UTC (10 years ago) by duarte
Original Path: trunk
Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters
Revision 373 - Directory Listing
Modified Wed Oct 31 15:25:46 2007 UTC (10 years ago) by duarte
Original Path: trunk
Fixed (yet again) the report output, now also outputting size (number of residues) of protein
Revision 372 - Directory Listing
Modified Wed Oct 31 10:20:22 2007 UTC (10 years ago) by lpetzo
Original Path: trunk

Revision 371 - Directory Listing
Modified Thu Oct 25 15:33:49 2007 UTC (10 years ago) by lpetzo
Original Path: trunk
Class ContactMap:
- Exception ContactMapConstructionError is thrown if the construction of a contact map from a Graph object fails.
- changed method to determine the number of nodes of a graph object.
- changed method to iterate through the set of edges of the graph (though the previous version seemed to be much more efficient ...)

Class SADP:
- added some new members controlling to input order of the contact maps (preservedInputOrder)
- the progress status of the run() method is send to a Retriever object
- added getters and setter for all data member.
- implemented methods to compute the sequence alignment and the node matching
- a couple of changes in method main
Revision 370 - Directory Listing
Modified Thu Oct 25 15:19:22 2007 UTC (10 years ago) by lpetzo
Original Path: trunk
to be thrown if the construction of a contact map from a proteinstructure.Graph instance fails
Revision 369 - Directory Listing
Modified Thu Oct 25 13:51:00 2007 UTC (10 years ago) by lpetzo
Original Path: trunk
This package provides a set of very basic abstract classes serving as interfaces to very basic tasks such as:

1. condition checkings (class Checker),
2. data retrieval (class Retriever) and 
3. pure workers that perform any kind of actions that do not depend on any kind of input data (class Doer).

Each of these classes is a subclass of class Action which only purpose is to store the object affected by the subclasses action method.
Revision 368 - Directory Listing
Modified Thu Oct 25 09:38:02 2007 UTC (10 years ago) by duarte
Original Path: trunk
Now parsing tinker's error function value, changed report file format (again!!)
Revision 367 - Directory Listing
Modified Wed Oct 24 13:29:15 2007 UTC (10 years ago) by duarte
Original Path: trunk
Changed name of native output pdb file
Revision 366 - Directory Listing
Modified Tue Oct 23 10:54:29 2007 UTC (10 years ago) by duarte
Original Path: trunk
Now throwing all exceptions
Revision 365 - Directory Listing
Modified Tue Oct 23 08:36:58 2007 UTC (10 years ago) by duarte
Original Path: trunk
New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object
Revision 363 - Directory Listing
Modified Fri Oct 19 15:45:49 2007 UTC (10 years, 1 month ago) by filippis
Original Path: trunk
Method writeUndirUnweightGraphToNetworkFiles added in Graph class
Revision 362 - Directory Listing
Modified Thu Oct 18 15:08:09 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
renamed precision to accuracy (in accordance with Casp)
Revision 361 - Directory Listing
Modified Wed Oct 17 17:40:18 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now weights are kept in the Edge objects rather than separately in a member variable in Graph
Revision 360 - Directory Listing
Modified Wed Oct 17 16:10:28 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files
Revision 359 - Directory Listing
Modified Wed Oct 17 15:45:30 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now can do multiple contact types/cutoffs per pdb structure
Revision 358 - Directory Listing
Modified Wed Oct 17 13:22:01 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now closing db connection. Better help string.
Revision 357 - Directory Listing
Modified Wed Oct 17 08:01:13 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)
Revision 356 - Directory Listing
Modified Sat Oct 13 15:55:41 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Fixed bug: wasn't tokenising well when first field in line was quoted
Revision 355 - Directory Listing
Modified Fri Oct 12 18:42:37 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n
Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format
Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal
Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor
Revision 354 - Directory Listing
Modified Thu Oct 11 15:32:08 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Fixed bug: was outputing an empty column before the 'total' column
Revision 353 - Directory Listing
Modified Thu Oct 11 13:00:12 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Changed constructor with all parameters to protected, now shouldn't be used at all outside of package
Revision 352 - Directory Listing
Modified Thu Oct 11 12:49:08 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
Revision 351 - Directory Listing
Modified Thu Oct 11 12:43:54 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
added some test programs to default package
Revision 350 - Directory Listing
Modified Thu Oct 11 12:38:07 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions
Revision 349 - Directory Listing
Modified Thu Oct 11 12:29:42 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now writing also original pdb file
Fixed output of rmsd: now only few decimal figures output
Revision 348 - Directory Listing
Modified Thu Oct 11 12:09:57 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now tinker.log has also baseName in file name
Revision 347 - Directory Listing
Modified Thu Oct 11 08:54:50 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Writing report to file instead of standard output
Catching unknown errors in runDistgeom (all other non-zero exit values)
Revision 346 - Directory Listing
Modified Thu Oct 11 08:38:36 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Doing more input error checks
In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used
Revision 345 - Directory Listing
Modified Wed Oct 10 16:27:12 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Fixed documentation
Revision 344 - Directory Listing
Modified Wed Oct 10 16:24:50 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
cathing InterruptedException from TinkerRunner
Revision 343 - Directory Listing
Modified Wed Oct 10 16:19:18 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
fixed bug when running distgeom, now waiting for process to exit before checking exit status
Revision 342 - Directory Listing
Modified Wed Oct 10 15:52:36 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
added error handling for killed tinker process with error code 139 (presumably out of memory)
Revision 341 - Directory Listing
Modified Wed Oct 10 15:14:55 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now capturing exit status 137 (2 instances of tinker running in same machine)
Now outputting progress per model
Revision 340 - Directory Listing
Modified Wed Oct 10 15:13:45 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Fixed the output
Revision 339 - Directory Listing
Modified Wed Oct 10 14:18:11 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now much faster thanks to hashing on pairs (separate script create the hash tables)
Revision 338 - Directory Listing
Modified Fri Oct 5 11:56:28 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason!
Throwing less exceptions in ConstraintsMaker
Revision 337 - Directory Listing
Modified Thu Oct 4 10:12:49 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
Added two new constructors for Graph (sequence only and no parameters), changed interface of GraphAverager (pass target sequence instead of target graph), extracted constant DEFAULT_WEIGHT in Edge.
Revision 336 - Directory Listing
Modified Tue Oct 2 16:14:20 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
Revision 335 - Directory Listing
Modified Tue Oct 2 14:59:28 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"
Revision 334 - Directory Listing
Modified Tue Oct 2 07:35:26 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
New class NodesAndEdges (simple graph class), some added javadocs
Revision 333 - Directory Listing
Modified Mon Oct 1 17:17:42 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Now does correct atom mapping for any atom of any residue ONLY for amber prm files
createConstraints does not work yet with multi atom contact types
Got rid of all the commented out mapAtoms code + some refactoring
Revision 332 - Directory Listing
Modified Mon Oct 1 16:20:06 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
added constructor for trivial alignment, renamed getSequence to getAlignedSequence
Revision 331 - Directory Listing
Modified Mon Oct 1 16:12:48 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference
Revision 330 - Directory Listing
Modified Mon Oct 1 15:57:22 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
added a weight field to Edge class (set using alternative constructor, maintaining backwards compatibility)
Revision 329 - Directory Listing
Modified Mon Oct 1 15:41:28 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs
Revision 328 - Directory Listing
Modified Mon Oct 1 10:57:08 2007 UTC (10 years, 1 month ago) by duarte
Original Path: trunk
First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo
Revision 327 - Directory Listing
Modified Mon Oct 1 08:23:57 2007 UTC (10 years, 1 month ago) by stehr
Original Path: trunk
fixed missing references to constants in class AA
Revision 326 - Directory Listing
Modified Thu Sep 20 14:49:55 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly
Revision 325 - Directory Listing
Modified Thu Sep 20 10:48:55 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
added parsing of residue selection strings
Revision 324 - Directory Listing
Modified Tue Sep 18 16:28:58 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
2 new methods: getAllAtomSerials, getAtomCoord
Revision 323 - Directory Listing
Modified Tue Sep 18 14:13:14 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Moved tinker stuff to its own package
Revision 322 - Directory Listing
Modified Tue Sep 18 13:59:33 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Initial commit of TinkerRunner and exception class to go with it TinkerError
Revision 321 - Directory Listing
Modified Tue Sep 18 08:44:30 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
added test program for difference distance maps, updated Manifest to v0.8.5
Revision 320 - Directory Listing
Modified Tue Sep 18 08:38:33 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
added calculation of difference distance map
Revision 319 - Directory Listing
Modified Mon Sep 17 16:10:32 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
added constructors for loading from online pdb
Revision 318 - Directory Listing
Modified Mon Sep 17 10:37:31 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
added some javadoc comments
Revision 317 - Directory Listing
Modified Thu Sep 13 16:09:10 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Fixed some comments
Revision 316 - Directory Listing
Modified Thu Sep 13 08:47:55 2007 UTC (10 years, 2 months ago) by lpetzo
Original Path: trunk
initial version of sadp
Revision 315 - Directory Listing
Modified Thu Sep 13 08:13:40 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Now parsing each element in different methods (re-opening the file). Parsing first pdbx_poly_seq_scheme so we get the chainCode that we can use for reading the rest
Now taking care of cases where struct_sheet_range is not a loop element
In tokeniseFields now also unquoting double-quoted strings
Tested on a set of 12000 entries
Revision 314 - Directory Listing
Modified Wed Sep 12 14:50:48 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Checking number of fields per line in loop elements and throwing exception if count is not correect
Doing tokenisation of lines through new function that takes care of possible quoted string with spaces
New exception CiffileFormatError
Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception

Revision 313 - Directory Listing
Modified Mon Sep 10 08:22:40 2007 UTC (10 years, 2 months ago) by lappe
Original Path: trunk
short form to compress nbstrings = condense multiple occurence of a symbol in the nbhstring to 1. Still a bitz buggy. sometimes 2 symbols are left in ? 
Revision 312 - Directory Listing
Modified Mon Sep 10 07:43:00 2007 UTC (10 years, 2 months ago) by lappe
Original Path: trunk

Revision 311 - Directory Listing
Modified Thu Aug 30 17:31:38 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Fixed buf: sometimes struct_conf can be non-loop elements, now also taking care of that particular case
Revision 310 - Directory Listing
Modified Thu Aug 30 16:00:08 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Bug with '?' in auth_seq_num was not really fixed. Now should be fine: behaviour is the same as PdbasePdb
Revision 309 - Directory Listing
Modified Thu Aug 30 15:55:53 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Fixed bug: needed to read alt locs in advance in another scan of the file because the order of the elements in the cif file is not guaranteed. As read of atom_site needs of alt locs, we need to do first the parsing of atom_sites_alt
Revision 308 - Directory Listing
Modified Thu Aug 30 14:54:38 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Fixed bugs:
- was reading HETATM lines as well as ATOM in atom_site
- auth_seq_num with '?' not taken now when populating the pdbresser2resser map (same behaviour as in PdbasePdb)
- now using chainCodeStr and auth_asym_id to identify chains in pdbx_poly_seq_scheme, struct_conf and struct_sheet_range. atom_site is not guaranteed to appear in file before all the others so we can't rely on having read a chainCode (asym_id) when parsing the other elements
Revision 307 - Directory Listing
Modified Thu Aug 30 10:41:55 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Now taking indices for fields from parsed field names. Still only minimal testing
Revision 306 - Directory Listing
Modified Thu Aug 30 09:09:24 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
First implementation of mmCIF file parser. Tested minimally.
Revision 305 - Directory Listing
Modified Wed Aug 29 09:46:32 2007 UTC (10 years, 2 months ago) by duarte
Original Path: trunk
Got rid of useless (and potential bug) chainCode=getChainCode (self reference!)
Revision 303 - Directory Listing
Modified Mon Aug 27 14:29:18 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
added writeResultsToFile()
Revision 302 - Directory Listing
Modified Mon Aug 27 14:28:23 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
changes to calcGridDensity, now also counts number of neighbouring non-empty grid cells
Revision 301 - Directory Listing
Modified Mon Aug 27 14:26:48 2007 UTC (10 years, 2 months ago) by stehr
Original Path: trunk
changed constant for unknown pdb code from "Unknown" to XXXX
Revision 300 - Directory Listing
Modified Wed Aug 22 14:59:10 2007 UTC (10 years, 2 months ago) by lappe
Original Path: trunk
Faster version that writes to stdoutput, minor changes 
Revision 299 - Directory Listing
Modified Wed Aug 22 14:55:21 2007 UTC (10 years, 2 months ago) by lappe
Original Path: trunk
only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell
Revision 298 - Directory Listing
Modified Wed Aug 22 14:55:01 2007 UTC (10 years, 2 months ago) by lappe
Original Path: trunk
only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell 
Revision 297 - Directory Listing
Modified Tue Aug 21 14:06:53 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
Faster version that writes to stdoutput
Revision 296 - Directory Listing
Modified Tue Aug 21 09:11:57 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
Lame version that directly updates a table ...
have to change to stdoutput 
Revision 295 - Directory Listing
Modified Tue Aug 21 08:45:59 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
Cleaned up and debugged version (sc/bb were xchanged)   
Revision 294 - Directory Listing
Modified Mon Aug 20 15:19:54 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other)
Revision 293 - Directory Listing
Modified Mon Aug 20 12:10:13 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
1st version for the pdb_reps25_graph_4_2
Revision 292 - Directory Listing
Modified Mon Aug 20 12:09:13 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other) 
Revision 291 - Directory Listing
Modified Mon Aug 20 09:22:36 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
1st version scoring with pdb_reps_graph_4_2 and full nbhood string
Revision 290 - Directory Listing
Modified Mon Aug 20 09:21:59 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
1st version scoring with pdb_reps_graph_4_2 and full nbhood string
Revision 289 - Directory Listing
Modified Mon Aug 20 09:21:22 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
1st version scoring with pdb_reps_graph_4_2 and full nbhood string 
Revision 288 - Directory Listing
Modified Fri Aug 17 15:03:22 2007 UTC (10 years, 3 months ago) by spriya
Original Path: trunk
Better checks for sequence equality in compare
Revision 287 - Directory Listing
Modified Fri Aug 17 14:32:14 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Now also filling chain_pdb_code in write_graph_to_db
Revision 286 - Directory Listing
Modified Fri Aug 17 12:40:00 2007 UTC (10 years, 3 months ago) by spriya
Original Path: trunk
Fixed bug in  compare, wasn't assigning new weights
Revision 285 - Directory Listing
Modified Thu Aug 16 15:10:11 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed a few bugs in reading of list file
Better output and error messages
Revision 284 - Directory Listing
Modified Thu Aug 16 14:57:31 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
Revision 283 - Directory Listing
Modified Wed Aug 15 10:22:36 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Wasn't deep copying secondary structure when passing it to Graph
Revision 282 - Directory Listing
Modified Tue Aug 14 16:15:59 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore
Revision 281 - Directory Listing
Modified Tue Aug 14 13:49:52 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
fixed little bug in NodeNbh
Revision 280 - Directory Listing
Modified Tue Aug 14 12:38:51 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
changed internal implementation of runDssp method (not using getFullLength anymore)
Revision 279 - Directory Listing
Modified Tue Aug 14 12:26:28 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed bug in Graph constructor: was not getting correct fullLength (related to last bug fix)
Revision 278 - Directory Listing
Modified Tue Aug 14 12:14:04 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed bug with getFullLength when reading from pdb file
Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers
New member variables obsLength and fullLength
Revision 277 - Directory Listing
Modified Tue Aug 14 10:54:24 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
New script genGraph (generates graph to files)
Better error messages in both
Revision 276 - Directory Listing
Modified Tue Aug 14 10:53:27 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Added secondary structure to write_graph_to_db
New method getNumSecStructureElements in SecondaryStructure
Revision 275 - Directory Listing
Modified Tue Aug 14 10:28:01 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph
Revision 274 - Directory Listing
Modified Tue Aug 14 10:26:32 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
Added new SecondaryStructure object to Pdb and Graph
Revision 273 - Directory Listing
Modified Tue Aug 14 09:13:07 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 272 - Directory Listing
Modified Tue Aug 14 09:12:41 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 271 - Directory Listing
Modified Tue Aug 14 09:12:21 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 270 - Directory Listing
Modified Tue Aug 14 09:11:59 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 269 - Directory Listing
Modified Tue Aug 14 09:11:18 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 268 - Directory Listing
Modified Tue Aug 14 09:11:07 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 267 - Directory Listing
Modified Tue Aug 14 09:10:58 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 266 - Directory Listing
Modified Tue Aug 14 09:10:47 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk

Revision 265 - Directory Listing
Modified Tue Aug 14 09:10:29 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
final version 
incl. pessimistic tie-break
Revision 264 - Directory Listing
Modified Mon Aug 13 13:53:13 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Initial commit of genDbGraph script
Revision 263 - Directory Listing
Modified Mon Aug 13 11:48:23 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed potential bug in regex for ATOM lines
Revision 262 - Directory Listing
Modified Mon Aug 13 08:55:05 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Was still not fixed!, forgot to insert X for non standard aa
Revision 261 - Directory Listing
Modified Mon Aug 13 08:53:11 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed reading of SEQRES, was putting nulls for non-standard aas
Revision 260 - Directory Listing
Modified Fri Aug 10 18:30:47 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Implemented write_graph_to_db
New member variable model in Graph, thus changed constructor
New methods to get degree of a node in Graph
New methos in NodeNbh to write other kinds of neighbourhood strings
Revision 259 - Directory Listing
Modified Fri Aug 10 16:40:44 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Revision 258 - Directory Listing
Modified Fri Aug 10 16:06:53 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size
Revision 257 - Directory Listing
Modified Thu Aug 9 16:43:32 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)
Revision 256 - Directory Listing
Modified Thu Aug 9 14:21:39 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Added getNumAtoms
Revision 255 - Directory Listing
Modified Thu Aug 9 13:45:10 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')
Revision 254 - Directory Listing
Modified Thu Aug 9 13:28:02 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Also writing graph to file
Revision 253 - Directory Listing
Modified Thu Aug 9 13:24:12 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Initial commit. Script to benchmark the graph generation algorithm 
Revision 252 - Directory Listing
Modified Thu Aug 9 10:37:14 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Made constructor public
Revision 250 - Directory Listing
Modified Mon Aug 6 14:48:37 2007 UTC (10 years, 3 months ago) by stehr
Original Path: trunk
added application to count grid density, suppressed warning for secondary structure reassignment
Revision 249 - Directory Listing
Modified Sat Aug 4 17:53:11 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
New methods containsContact and resetContacts
Revision 248 - Directory Listing
Modified Sat Aug 4 17:50:00 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Added method hasTag
Revision 247 - Directory Listing
Modified Sat Aug 4 17:07:23 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Made regex a constant and added | and \\-
Revision 246 - Directory Listing
Modified Sat Aug 4 17:00:58 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Doing now everythin with maps (using seqTags) rather than arrays. Cleaned up, refactored, using more consistent naming
Revision 245 - Directory Listing
Modified Sat Aug 4 15:40:20 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Added reverse map (from sequences serials to alignment serials) and did a bit of refactoring
Revision 244 - Directory Listing
Modified Wed Aug 1 14:34:36 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Initial commit of Alignmnent, a class representing a multiple sequence alignment
Revision 243 - Directory Listing
Modified Wed Aug 1 14:21:09 2007 UTC (10 years, 3 months ago) by lappe
Original Path: trunk
Added correction by matrix size (yields avgdeltaRank)
plus correction jcnsize-1 for direct nbs 
and pessimistic tie-break 
Revision 242 - Directory Listing
Modified Wed Aug 1 07:47:18 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Got rid of doneRes ArrayList in getRanks, was redundant
Revision 241 - Directory Listing
Modified Tue Jul 31 16:38:13 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Now dealing correctly with ties.
Implemented getResiduesSortedByRank
Changed dist to be a TreeMap
Revision 240 - Directory Listing
Modified Tue Jul 31 13:51:59 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed bug in delEdge. Wasn't taking care of if contact was given as i>j in undirected case. Also recount of contacts and set of modified to true was wrong
Revision 239 - Directory Listing
Modified Mon Jul 30 10:57:28 2007 UTC (10 years, 3 months ago) by duarte
Original Path: trunk
Fixed bug in addEdge method. In case of undirected we need to check that the contact is inserted in the right order j>i
Revision 238 - Directory Listing
Modified Fri Jul 20 10:02:03 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Optimised slightly the compareTo method in Edge
Revision 237 - Directory Listing
Modified Thu Jul 19 14:23:35 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
Revision 236 - Directory Listing
Modified Thu Jul 19 12:57:29 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Fixed bug. Was not doing correctly reflection along smallest principal axis in is_reflection case
Revision 235 - Directory Listing
Modified Thu Jul 19 12:43:12 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Implemented rmsd calculation (based on Jama matrix package)
rmsd method still not taking care of unobserved or missing atoms. Also not returning individual distances between optimally superimposed structures (although it can calculate them in commented out code)

Revision 234 - Directory Listing
Modified Tue Jul 10 14:14:58 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge
Revision 233 - Directory Listing
Modified Tue Jul 10 13:01:50 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Added method getCopy
Revision 232 - Directory Listing
Modified Tue Jul 10 13:00:23 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Now checking in addEdge that we don't duplicate edges
New methods: get2ndshell, copyKeepingNodes
Revision 231 - Directory Listing
Modified Tue Jul 10 09:57:20 2007 UTC (10 years, 4 months ago) by lappe
Original Path: trunk
production - stable
Revision 230 - Directory Listing
Modified Mon Jul 9 15:35:01 2007 UTC (10 years, 4 months ago) by stehr
Original Path: trunk
added class NodeSet
Revision 229 - Directory Listing
Modified Mon Jul 9 15:02:24 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases
Revision 228 - Directory Listing
Modified Mon Jul 9 14:32:47 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)
Revision 227 - Directory Listing
Modified Fri Jul 6 14:23:51 2007 UTC (10 years, 4 months ago) by lappe
Original Path: trunk
single residue target Evaluation in target* tables 
added verbosity level VL to shrink output 
Revision 226 - Directory Listing
Modified Fri Jul 6 13:43:30 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct
Revision 225 - Directory Listing
Modified Fri Jul 6 12:41:48 2007 UTC (10 years, 4 months ago) by lappe
Original Path: trunk
Only cosmetic changes to polish the output 
Revision 224 - Directory Listing
Modified Thu Jul 5 13:42:37 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster
Revision 223 - Directory Listing
Modified Thu Jul 5 10:17:30 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Added cross contacts to isValidCT
Revision 222 - Directory Listing
Modified Wed Jul 4 15:39:01 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval
Revision 221 - Directory Listing
Modified Wed Jul 4 14:50:25 2007 UTC (10 years, 4 months ago) by lappe
Original Path: trunk
minor bugfix in reportResults( cnsize*deltarank) call
Revision 219 - Directory Listing
Modified Tue Jul 3 15:38:21 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)
Revision 218 - Directory Listing
Modified Fri Jun 29 09:13:52 2007 UTC (10 years, 4 months ago) by lappe
Original Path: trunk

Revision 217 - Directory Listing
Modified Fri Jun 29 09:04:00 2007 UTC (10 years, 4 months ago) by stehr
Original Path: trunk
now casting pdb codes to lower and pdb chain codes to upper in all constructors
Revision 216 - Directory Listing
Modified Fri Jun 29 08:30:55 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Fixed bug: ATOM lines printing was locale dependant, thus was printing ',' for decimal separators in some locales
Revision 215 - Directory Listing
Modified Thu Jun 28 15:43:04 2007 UTC (10 years, 4 months ago) by stehr
Original Path: trunk
some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
Revision 214 - Directory Listing
Modified Thu Jun 28 14:09:16 2007 UTC (10 years, 4 months ago) by lappe
Original Path: trunk
debugged version of the iteration/validation of nbhoodstrings 
with added temp_table hashing for speedup (factor ca. 10x) 
needs additional (empty) database <nbhashtables> for storage
 
Revision 213 - Directory Listing
Modified Thu Jun 28 09:38:49 2007 UTC (10 years, 4 months ago) by lappe
Original Path: trunk
Buggy version : 2nd to n2th row have same values 
as the first row - ? temp_nbhood stays the same?  
Revision 212 - Directory Listing
Modified Thu Jun 28 09:26:34 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Fixed bug in regex introduced in last revision
Revision 211 - Directory Listing
Modified Thu Jun 28 09:22:26 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Fixed graph file format checking, was not working properly
Revision 210 - Directory Listing
Modified Wed Jun 27 15:57:39 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Now throwing also SQLExceptions for individual queries, not just for connections
Revision 209 - Directory Listing
Modified Wed Jun 27 15:14:31 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Throwing exception also in case graph file not in right format at all (no #AGLAPPE in 1st line)
Fixed bug: was not reading correctly #PDB CHAIN CODE
Revision 208 - Directory Listing
Modified Wed Jun 27 14:42:12 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
Revision 207 - Directory Listing
Modified Wed Jun 27 11:06:34 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs

Revision 206 - Directory Listing
Modified Tue Jun 26 17:01:48 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Major refactoring:
 accode -> pdbCode
 chaincode -> pdbChainCode
 chain -> chainCode
Major change of signatures (publics to privates)
Implemented getters for needed member variables
Major clean up
Revision 203 - Directory Listing
Modified Tue Jun 26 14:25:58 2007 UTC (10 years, 4 months ago) by duarte
Original Path: trunk
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
Revision 202 - Directory Listing
Modified Thu Jun 21 17:18:11 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
MySQLConnection now throwing SQLException on connect
Many files changed following this: all calling classes now re-throwing or catching the SQLException
Revision 200 - Directory Listing
Modified Mon Jun 18 17:43:43 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
New isValidCT methods in AA
New method get_resser_from_atomser in Pdb
Revision 199 - Directory Listing
Modified Mon Jun 18 09:03:39 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Implemented getRanks()
Revision 198 - Directory Listing
Modified Mon Jun 18 08:47:26 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
AA class is now db independent:
Hard coded getaas2atoms, not getting it anymore from db.
Revision 196 - Directory Listing
Modified Wed Jun 13 15:05:31 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Added toString and getMotifFullGaps missing in EdgeNbh
Revision 195 - Directory Listing
Modified Wed Jun 13 14:24:43 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Made contactTypes a String[]
Revision 194 - Directory Listing
Modified Wed Jun 13 10:57:00 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Added contactTypes method and made private methods private
Revision 193 - Directory Listing
Modified Wed Jun 13 07:57:31 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Moved motif static methods to Background class. They didn't belong here
Revision 192 - Directory Listing
Modified Tue Jun 12 18:27:20 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Made contacts public
Revision 191 - Directory Listing
Modified Tue Jun 12 17:15:17 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
New method getAllEdgeNbhSizes
Revision 190 - Directory Listing
Modified Tue Jun 12 13:38:46 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object

Revision 189 - Directory Listing
Modified Tue Jun 12 10:38:29 2007 UTC (10 years, 5 months ago) by duarte
Original Path: trunk
Added basic compare method to the Graph class and test class compareCMs
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, 5 months ago) by lappe
Original Path: trunk

Revision 168 - Directory Listing
Modified Thu May 24 16:19:48 2007 UTC (10 years, 5 months ago) by lappe
Original Path: trunk

Revision 167 - Directory Listing
Modified Thu May 24 16:19:21 2007 UTC (10 years, 5 months ago) by lappe
Original Path: trunk

Revision 166 - Directory Listing
Modified Thu May 24 16:19:00 2007 UTC (10 years, 5 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, 5 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, 5 months ago) by stehr
Original Path: trunk
added Manifest
Revision 162 - Directory Listing
Modified Thu May 24 10:46:39 2007 UTC (10 years, 5 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, 5 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, 5 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, 5 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, 5 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, 3 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, 5 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, 6 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, 7 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, 9 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, 9 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