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Revision 1438 - Directory Listing
Modified Wed Aug 17 12:35:52 2011 UTC (4 years, 8 months ago) by jmduarteg
An ant script for owl!
Revision 1436 - Directory Listing
Modified Wed Aug 17 10:06:53 2011 UTC (4 years, 8 months ago) by jmduarteg
Removed not needed jar (only cmview needs this one)
Revision 1434 - Directory Listing
Modified Tue Aug 16 16:02:34 2011 UTC (4 years, 8 months ago) by jmduarteg
Fixed bugs in DaliRunner
- it wouldn't run from cmview when the two chains had same pdb code and pdb chain code
- it wouldn't work with newer versions of DaliLite as apparently the output file names and formats changed 
Revision 1433 - Directory Listing
Modified Tue Aug 16 15:36:21 2011 UTC (4 years, 8 months ago) by jmduarteg
Creating owl branch from tag owl-1.9.3 for bug fixes of cmview (release 1.1). To go together with branch cmview-1.9 
Revision 924 - Directory Listing
Modified Mon Oct 26 14:20:16 2009 UTC (6 years, 6 months ago) by winkelma
merged trunk into branch
Revision 922 - Directory Listing
Modified Mon Oct 26 14:08:42 2009 UTC (6 years, 6 months ago) by winkelma
Tinker
Revision 921 - Directory Listing
Modified Mon Oct 26 14:08:19 2009 UTC (6 years, 6 months ago) by winkelma
Tinker
Revision 920 - Directory Listing
Modified Thu Oct 22 17:07:34 2009 UTC (6 years, 6 months ago) by winkelma
Tinker Runner Details
Revision 918 - Directory Listing
Modified Tue Oct 20 15:55:18 2009 UTC (6 years, 6 months ago) by winkelma
more Tinker 
Revision 913 - Directory Listing
Modified Mon Oct 19 16:27:29 2009 UTC (6 years, 6 months ago) by winkelma
Tinker integration
Revision 912 - Directory Listing
Modified Fri Oct 16 14:51:49 2009 UTC (6 years, 6 months ago) by winkelma
TINKER
Revision 911 - Directory Listing
Modified Thu Oct 15 20:28:24 2009 UTC (6 years, 6 months ago) by winkelma
Branch for tinker integration
Revision 734 - Directory Listing
Modified Wed Aug 27 14:10:07 2008 UTC (7 years, 8 months ago) by stehr
Added a serialVersionUID and got rid of an obsolete import to avoid compiler warnings
Revision 729 - Directory Listing
Modified Wed Aug 27 13:23:56 2008 UTC (7 years, 8 months ago) by duarte
Updated make-aglappe to jung beta jars.
Updated version in Manifest to 0.9.6
Revision 728 - Directory Listing
Modified Wed Aug 27 13:20:13 2008 UTC (7 years, 8 months ago) by duarte
Got rid of our fix to bug in removeEdge. Now using jung-beta that fixed the bug.
Revision 693 - Directory Listing
Modified Mon Jun 23 09:55:22 2008 UTC (7 years, 10 months ago) by stehr
branching for CMView release 1.0 based on aglappe-0.9.5
Revision 488 - Directory Listing
Modified Wed Jan 2 10:23:13 2008 UTC (8 years, 4 months ago) by duarte
T
Revision 487 - Directory Listing
Modified Thu Dec 20 11:19:54 2007 UTC (8 years, 4 months ago) by stehr
added new classes RIGEnsemble and FileTypeGuesser (used by Casp Consensus Contact prediction)
Revision 485 - Directory Listing
Modified Wed Dec 19 15:42:46 2007 UTC (8 years, 4 months ago) by duarte
Now exiting upon distgeom error
Revision 484 - Directory Listing
Modified Wed Dec 19 14:27:48 2007 UTC (8 years, 4 months ago) by stehr
changed call to graphAverager.doAveraging() into getConsensusGraph() after refactoring
Revision 483 - Directory Listing
Modified Wed Dec 19 14:25:30 2007 UTC (8 years, 4 months ago) by stehr
added methods to calculate and filter by consensus scores
Revision 482 - Directory Listing
Modified Wed Dec 19 14:23:32 2007 UTC (8 years, 4 months ago) by stehr
added missing class for RR file i/o
Revision 481 - Directory Listing
Modified Wed Dec 19 14:22:36 2007 UTC (8 years, 4 months ago) by stehr
added reading from and writing to casp contact prediction (RR) files
Revision 480 - Directory Listing
Modified Wed Dec 19 12:54:56 2007 UTC (8 years, 4 months ago) by duarte
New method calculateRadGyration
Revision 479 - Directory Listing
Modified Tue Dec 18 11:19:24 2007 UTC (8 years, 4 months ago) by duarte
Submission of commands is now async
Revision 478 - Directory Listing
Modified Mon Dec 17 17:03:24 2007 UTC (8 years, 4 months ago) by lpetzo
if the pdb file contains SEQRES records we do not allow the sequence length to be shorter than the full-length of the graph. otherwise a PdbfileFormatError is thrown in function read_data_from_file()
Revision 477 - Directory Listing
Modified Mon Dec 17 14:31:38 2007 UTC (8 years, 4 months ago) by duarte
Adapted IO methods in NodesAndEdges to JUNG framework:
added 2 classes: 
- GraphIODb: does reading and writing a Graph<V,E> from/to database
- GraphIOGDLFile: does writing of a Graph<V,E> to GDL file for aiSee exporting

Revision 475 - Directory Listing
Modified Thu Dec 13 15:37:40 2007 UTC (8 years, 4 months ago) by duarte
Now maxcluster ranking works in all cases. 
Fixed some bugs and tested for both rmsd and gdt
Revision 474 - Directory Listing
Modified Thu Dec 13 13:45:01 2007 UTC (8 years, 4 months ago) by duarte
Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph
Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise
Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0
Revision 472 - Directory Listing
Modified Thu Dec 13 10:18:10 2007 UTC (8 years, 4 months ago) by lpetzo
new function: createSelectionString(TreeSet<Integer>)
Revision 471 - Directory Listing
Modified Wed Dec 12 17:17:01 2007 UTC (8 years, 4 months ago) by duarte
Added option for min range and max range filtering (-m, -M)
Fixed output of an exception
Revision 470 - Directory Listing
Modified Wed Dec 12 12:03:49 2007 UTC (8 years, 4 months ago) by stehr
Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
Revision 469 - Directory Listing
Modified Tue Dec 11 14:23:07 2007 UTC (8 years, 4 months ago) by duarte
Fixed potentially dangerous bug: was constructing edges wrongly!: with i residue number as the weight!
Revision 468 - Directory Listing
Modified Tue Dec 11 10:11:39 2007 UTC (8 years, 4 months ago) by duarte
Fixed bug: now assigning frequency 0 to case where countTotal=0 (no observations)
Revision 465 - Directory Listing
Modified Fri Dec 7 16:53:10 2007 UTC (8 years, 5 months ago) by duarte
New feature: now Pdb objects can be restricted to SCOP domains
New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
Revision 464 - Directory Listing
Modified Fri Dec 7 12:01:27 2007 UTC (8 years, 5 months ago) by lpetzo
added getter function for the cif-filename
Revision 463 - Directory Listing
Modified Thu Dec 6 19:26:59 2007 UTC (8 years, 5 months ago) by duarte
Minor change: comments
Revision 462 - Directory Listing
Modified Thu Dec 6 19:18:19 2007 UTC (8 years, 5 months ago) by duarte
Minor change: javadoc
Revision 461 - Directory Listing
Modified Thu Dec 6 19:15:50 2007 UTC (8 years, 5 months ago) by duarte
Fixed bug: in removeVertex we were calling getResidueSerial instead of getAtomSerial
Revision 460 - Directory Listing
Modified Thu Dec 6 18:14:59 2007 UTC (8 years, 5 months ago) by duarte
Now overriding removeEdge(E) to fix a bug in SparseGraph JUNG2 alpha2
Not implementing anymore SimpleGraph (was useless and it will be removed in coming JUNG2 releases)

Revision 459 - Directory Listing
Modified Thu Dec 6 15:05:43 2007 UTC (8 years, 5 months ago) by stehr
moved GraphAverager to subpackage, added removeVertex function to RIGraph and AIGraph, added getEdgeFromSerials and containsEdgeIJ functions to ProtStructGraph
Revision 457 - Directory Listing
Modified Thu Dec 6 11:04:49 2007 UTC (8 years, 5 months ago) by duarte
Initial commit: script to dump sequences of pdb entries
Revision 456 - Directory Listing
Modified Tue Dec 4 19:03:54 2007 UTC (8 years, 5 months ago) by duarte
Now also reads secondary structure
Revision 455 - Directory Listing
Modified Tue Dec 4 19:01:47 2007 UTC (8 years, 5 months ago) by duarte
Minor change : fixed comments
Revision 454 - Directory Listing
Modified Tue Dec 4 18:58:14 2007 UTC (8 years, 5 months ago) by duarte
Fixed bug: getCommaSeparatedResSerials was failing when there was 0 neighbors
Revision 453 - Directory Listing
Modified Tue Dec 4 18:46:00 2007 UTC (8 years, 5 months ago) by duarte
Fixed bug: -r option was not being set by default
Revision 452 - Directory Listing
Modified Tue Dec 4 15:40:17 2007 UTC (8 years, 5 months ago) by duarte
New class NbhoodBackgrnd representing a set of neighbourhoods loaded from a set of graphs of a non redundant pdb structures set.
Rewrote RIGNbhood so that the TreeMap now contains also the central residue. Added methods equals() and match().
Adapted RIGraph.getNbhood to the new constructor in RIGNbhood
Revision 451 - Directory Listing
Modified Tue Dec 4 15:37:08 2007 UTC (8 years, 5 months ago) by duarte
Fixed for new exceptions thrown by Pdb.load()
Revision 450 - Directory Listing
Modified Tue Dec 4 15:21:35 2007 UTC (8 years, 5 months ago) by lpetzo
... some more comments
Revision 449 - Directory Listing
Modified Tue Dec 4 15:20:15 2007 UTC (8 years, 5 months ago) by lpetzo
Johannes provided us we the debugged version of noncrossing(), kept the old version for sentimental reason as noncrossing_()
Revision 448 - Directory Listing
Modified Tue Dec 4 15:19:15 2007 UTC (8 years, 5 months ago) by lpetzo
class *Pdb:
- implemented new exception handling scheme for function Getter.get() -> getChains() and getModels() throw all possible exceptions encapsulated in GetterError exceptions
Revision 447 - Directory Listing
Modified Tue Dec 4 15:11:22 2007 UTC (8 years, 5 months ago) by lpetzo
class Getter:
- function get() is now throwing GetterError exception

class GetterError:
- wrapper exception for all type of exceptions thrown in the get() function of class Getter
Revision 444 - Directory Listing
Modified Tue Dec 4 10:18:21 2007 UTC (8 years, 5 months ago) by filippis
Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance
Revision 443 - Directory Listing
Modified Fri Nov 30 13:38:35 2007 UTC (8 years, 5 months ago) by duarte
Now not using ORDER BY in nodes and edges queries, was useless and slowing down queries
Now reading correctly empty graphs, just keeping it empty without throwing exception
Revision 442 - Directory Listing
Modified Fri Nov 30 10:36:09 2007 UTC (8 years, 5 months ago) by duarte
Memory leak problem is gone with rewrite in jung! Now genDbGraph/genGraph work without needing an external shell script to do the loop. Thus removing runGenDbGraph.sh
Revision 441 - Directory Listing
Modified Thu Nov 29 15:19:37 2007 UTC (8 years, 5 months ago) by duarte
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
Revision 438 - Directory Listing
Modified Wed Nov 28 15:44:57 2007 UTC (8 years, 5 months ago) by filippis
AAInfo
-isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+"
-isOverlapping method has been added

AIGEdge
-copy method added

AIGNode
-equals and copy methods has been added

AIGraph
-getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed
-distances are now set for RIGNodes in getRIGraph
-for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph
-we set now the secondaryStructure object of RIGraph in getRIGraph
-addGraph has been added

Box
-we throw away wrong check in getDistancesWithinBox - read the comment

DbRIGraph
-constructors now take argument directed and directionality doesn't depend anymore on isCrossed
-distances are read also from db and set for RIGEdges

Pdb
-get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed
-there is check for forbidden cts in get_graph
-cts with + are taken into account in get_graph

RIGEdge
-setAtomWeight and setDistance methods have been added

RIGNode
-equals method has been added

RIGraph
-getObsLength has been deleted
-we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast

genDbGraph
-argument for directionality is now added


Revision 437 - Directory Listing
Modified Wed Nov 28 15:43:52 2007 UTC (8 years, 5 months ago) by lpetzo
an abstract getter
Revision 435 - Directory Listing
Modified Wed Nov 28 12:11:11 2007 UTC (8 years, 5 months ago) by duarte
Reverted to unobserved RIGNodes not present in the RIGraph
Revision 434 - Directory Listing
Modified Wed Nov 28 09:34:44 2007 UTC (8 years, 5 months ago) by duarte
Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false.
Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes.
New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
Revision 433 - Directory Listing
Modified Tue Nov 27 17:58:26 2007 UTC (8 years, 5 months ago) by duarte
Added more comments

Revision 431 - Directory Listing
Modified Tue Nov 27 08:48:28 2007 UTC (8 years, 5 months ago) by duarte
Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :
Revision 430 - Directory Listing
Modified Mon Nov 26 18:20:04 2007 UTC (8 years, 5 months ago) by duarte
Fixed tester after changes in getAllCommonNnhSizes
Revision 428 - Directory Listing
Modified Mon Nov 26 16:01:11 2007 UTC (8 years, 5 months ago) by duarte
Fixed bug: was missing last sequence element when adding gap nodes
Revision 427 - Directory Listing
Modified Mon Nov 26 15:57:37 2007 UTC (8 years, 5 months ago) by duarte
Fixed bug in PairwiseAlignmentGraphConverter: was not adding the nodes for gaps, also some other minor bugs fixed in copying of objects
Fixed bug in getAllCommonNbhSizes, 1) now returning a HashMap on 
Pair<Integer>, not Pair<RIGNode> 2) was filling cells when size=0
Added method getIncidentNodes to IntPairSet as a temporary fix

Revision 426 - Directory Listing
Modified Fri Nov 23 18:04:15 2007 UTC (8 years, 5 months ago) by duarte
Now PairWiseAlignmentConverter and PairwiseAlignmentGraphConverter work in the new JUNG framework.
New class IntPairComparator
Now sorting output in RIGraph.write_graph_to_file
Revision 424 - Directory Listing
Modified Fri Nov 23 14:21:33 2007 UTC (8 years, 5 months ago) by duarte
Added last i/o method from old Graph (write to file in Ioannis network format)
Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods
Fixed the write_graph_to_file method name in executables in default package

Revision 423 - Directory Listing
Modified Fri Nov 23 13:37:17 2007 UTC (8 years, 5 months ago) by duarte
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
Revision 422 - Directory Listing
Modified Fri Nov 23 10:08:40 2007 UTC (8 years, 5 months ago) by duarte
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
Revision 421 - Directory Listing
Modified Thu Nov 22 19:42:11 2007 UTC (8 years, 5 months ago) by duarte
Now graph generation in Pdb also works when we pass a crossed contact type with overlapping atom sets, e.g. ALL/BB (changes were: added a couple of new conditions in Box and in Pdb's AIGraph getGraph(ct,cutoff))
Loads of better comments
Revision 420 - Directory Listing
Modified Thu Nov 22 17:27:44 2007 UTC (8 years, 5 months ago) by duarte
First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there.
NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Revision 419 - Directory Listing
Modified Thu Nov 22 14:09:18 2007 UTC (8 years, 5 months ago) by duarte
Re-branching for JUNG2 development
Revision 418 - Directory Listing
Modified Thu Nov 22 13:59:33 2007 UTC (8 years, 5 months ago) by duarte
Deleted the branch, we are going to branch from a newer revision
Revision 415 - Directory Listing
Modified Thu Nov 22 10:19:16 2007 UTC (8 years, 5 months ago) by duarte
Branching for development of new graph framework using JUNG2
Revision 1 - Directory Listing
Added Wed Jan 18 17:48:52 2006 UTC (10 years, 3 months ago) by filippis
Initial import of tools