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Revision 452 - Directory Listing
Modified Tue Dec 4 15:40:17 2007 UTC (12 years 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 (12 years ago) by duarte
Fixed for new exceptions thrown by Pdb.load()
Revision 450 - Directory Listing
Modified Tue Dec 4 15:21:35 2007 UTC (12 years ago) by lpetzo
... some more comments
Revision 449 - Directory Listing
Modified Tue Dec 4 15:20:15 2007 UTC (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years ago) by lpetzo
an abstract getter
Revision 435 - Directory Listing
Modified Wed Nov 28 12:11:11 2007 UTC (12 years 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 (12 years 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 (12 years ago) by duarte
Added more comments

Revision 431 - Directory Listing
Modified Tue Nov 27 08:48:28 2007 UTC (12 years 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 (12 years ago) by duarte
Fixed tester after changes in getAllCommonNnhSizes
Revision 428 - Directory Listing
Modified Mon Nov 26 16:01:11 2007 UTC (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years 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 (12 years ago) by duarte
Re-branching for JUNG2 development
Revision 418 - Directory Listing
Modified Thu Nov 22 13:59:33 2007 UTC (12 years 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 (12 years 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 (13 years, 10 months ago) by filippis
Initial import of tools