Revision 379 - (view) (annotate) - [select for diffs]
Modified Fri Nov 2 14:22:54 2007 UTC (16 years, 10 months ago) by stehr
File length: 4999 byte(s)
Diff to previous 360

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 360 - (view) (annotate) - [select for diffs]
Modified Wed Oct 17 16:10:28 2007 UTC (16 years, 11 months ago) by stehr
File length: 4493 byte(s)
Diff to previous 345

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 345 - (view) (annotate) - [select for diffs]
Modified Wed Oct 10 16:27:12 2007 UTC (16 years, 11 months ago) by duarte
File length: 3785 byte(s)
Diff to previous 337

Fixed documentation

Revision 337 - (view) (annotate) - [select for diffs]
Modified Thu Oct 4 10:12:49 2007 UTC (16 years, 11 months ago) by stehr
File length: 3831 byte(s)
Diff to previous 334

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 334 - (view) (annotate) - [select for diffs]
Modified Tue Oct 2 07:35:26 2007 UTC (17 years ago) by stehr
File length: 3761 byte(s)
Diff to previous 331

New class NodesAndEdges (simple graph class), some added javadocs

Revision 331 - (view) (annotate) - [select for diffs]
Modified Mon Oct 1 16:12:48 2007 UTC (17 years ago) by duarte
File length: 3445 byte(s)
Diff to previous 329

Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference

Revision 329 - (view) (annotate) - [select for diffs]
Added Mon Oct 1 15:41:28 2007 UTC (17 years ago) by duarte
File length: 3075 byte(s)

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