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contactTypes.dat 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
aapairsBounds.dat 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
TemplateList.java 756 (11 years ago) by duarte: New static method in BlastHit to get subjectId from templateId New member source in TemplateList
Template.java 753 (11 years ago) by duarte: Fixed bug: PDB/graph/scop data loading issues were not correctly implemented.
StructAlignmentError.java 747 (11 years ago) by duarte: Initial commit of StructAligner interface and implementation PaulStructAligner. New reader in Alignment: now we can read CLUSTAL alignment files, not extensively tested. Also Alignment now only throws generic FileFormatErrors instead of specific file format errors.
StructAligner.java 747 (11 years ago) by duarte: Initial commit of StructAligner interface and implementation PaulStructAligner. New reader in Alignment: now we can read CLUSTAL alignment files, not extensively tested. Also Alignment now only throws generic FileFormatErrors instead of specific file format errors.
SecondaryStructure.java 639 (11 years ago) by duarte: Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class. New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references. New method in Alignment to print a "graphical" matching of secondary structures.
SecStrucElement.java 818 (10 years ago) by stehr: added method getTypeDescription to output a string representation of the secondary structure type (currently not distinguishing between different numbers of states)
ScopRegion.java 589 (11 years ago) by duarte: New classes Template, TemplateList to be used in homology modelling pipeline. Modified BlastUtils to use TemplateList class
Scop.java 685 (11 years ago) by filippis: getNumScopRes method added in Scop class
RIGraphMinSpanningTree.java 705 (11 years ago) by duarte: New class RIGraphMinSpanningTree for getting the Minimum Spanning Tree of a RIGraph. This is simply a wrapper around JUNG's PrimMinimumSpanningTree. New method setSerials2NodesMap in RIGraph.
RIGraph.java 842 (10 years ago) by duarte: New method to filter on minWeight
RIGNode.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
RIGNbhood.java 529 (11 years ago) by spriya: 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
RIGEnsemble.java 688 (11 years ago) by duarte: Fixed bugs in averageGraph: - output of benchmark statistics and pairwise comparison was overlapping - benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes) Improved: - better handling of modes through mode variable that takes 1 of 3 states - better input check - in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph - changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph - now allowing alignments that contain other sequences than the target and the templates - new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
RIGEdge.java 546 (11 years ago) by duarte: 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
RIGCommonNbhood.java 840 (10 years ago) by duarte: New method getMotifNoGaps
ProtStructGraph.java 725 (11 years ago) by duarte: Given a serialVersionUID to class to get rid of warning
PredEval.java 682 (11 years ago) by stehr: now handling special cases that used to give NaN values
PolyposeRunner.java 775 (11 years ago) by stehr: better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
PirFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbfilePdb.java 836 (10 years ago) by duarte: Fixed bug (an old one!): the atomser2coord and atomser2resser maps contained also hydrogen atoms whilst the resset_atom2atomserial map contained only non-H atoms. Now all contain only non-H. The "bug" only surfaced after the rewrite of the Pdb.writeAtoms method: writing the atom lines would give a NullPointer when encountering a Hydrogen (if the read pdb entry contained Hyrdrogens).
PdbfileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbasePdb.java 836 (10 years ago) by duarte: Fixed bug (an old one!): the atomser2coord and atomser2resser maps contained also hydrogen atoms whilst the resset_atom2atomserial map contained only non-H atoms. Now all contain only non-H. The "bug" only surfaced after the rewrite of the Pdb.writeAtoms method: writing the atom lines would give a NullPointer when encountering a Hydrogen (if the read pdb entry contained Hyrdrogens).
PdbaseInconsistencyError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbLoadError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbCodeNotFoundError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbChainCodeNotFoundError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Pdb.java 828 (10 years ago) by stehr: New static methods for conveniently loading PDB objects without needing to deal with exceptions (loadStructureOrExit, loadStructureOrNull)
PaulStructAligner.java 788 (11 years ago) by filippis: white TO talyn
PairwiseSequenceAlignment.java 709 (11 years ago) by stehr: added methods to return the residue mappings for this alignment
PairwiseAlignmentConverter.java 517 (11 years ago) by duarte: 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
OligomericState.java 689 (11 years ago) by filippis: -OligomericState class added -Pdb a.checkOligomeric and getOligomericState methods added b.calcVolume, calcSurface and calcCompactnessCoefficient methods added
NbhoodBackgrnd.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
NbhProbDistribution.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
MsdsdPdb.java 788 (11 years ago) by filippis: white TO talyn
MsdsdInconsistentResidueNumbersError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
ModelPdb.java 822 (10 years ago) by duarte: Now Reconstructer can also take RIGraphs with "unobserved" residues (i.e. with missing nodes). Model pdb files that Reconstructer creates now contain strictly only CA atoms.
MaxClusterRunner.java 714 (11 years ago) by stehr: added comment
IntervalSet.java 592 (11 years ago) by stehr: fixed one null pointer bug and some spelling mistakes
Interval.java 515 (11 years ago) by stehr: Interval: allow spaces in residue selection strings RIGNbhood: added method getNeighbors
IntPairSet.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
IntPairComparator.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
HashGrid.java 737 (11 years ago) by stehr: Committing empty class HashGrid for later implementation
GraphIdNotFoundError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
GraphIOGDLFile.java 635 (11 years ago) by duarte: Changed default gravity value and default IDENTITY_SCORE for similarity graph
GraphIODb.java 788 (11 years ago) by filippis: white TO talyn
GraphFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
GeometryTools.java 827 (10 years ago) by stehr: New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
FileTypeGuesser.java 550 (11 years ago) by stehr: changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
FileRIGraph.java 712 (11 years ago) by duarte: Switching to JUNG2-beta1: - got rid of our custom fix to removeEdge - now both addVertex and removeVertex are correctly implemented: they update properly the nodes2serials map.
FileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
FastaFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
ECRegion.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
EC.java 502 (11 years ago) by stehr: EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning Interval: added typing to Comparator to avoid eclipse warning
DbRIGraph.java 788 (11 years ago) by filippis: white TO talyn
ContactType.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
ConformationsNotSameSizeError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
CiffilePdb.java 836 (10 years ago) by duarte: Fixed bug (an old one!): the atomser2coord and atomser2resser maps contained also hydrogen atoms whilst the resset_atom2atomserial map contained only non-H atoms. Now all contain only non-H. The "bug" only surfaced after the rewrite of the Pdb.writeAtoms method: writing the atom lines would give a NullPointer when encountering a Hydrogen (if the read pdb entry contained Hyrdrogens).
CiffileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
CatalyticSite.java 829 (10 years ago) by stehr: updated to latest CSA version, added toString() methods
CatalSiteSet.java 829 (10 years ago) by stehr: updated to latest CSA version, added toString() methods
CaspRRFileRIGraph.java 712 (11 years ago) by duarte: Switching to JUNG2-beta1: - got rid of our custom fix to removeEdge - now both addVertex and removeVertex are correctly implemented: they update properly the nodes2serials map.
CaspRRFileData.java 644 (11 years ago) by duarte: New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8. Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.
Box.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
BackboneCoords.java 827 (10 years ago) by stehr: New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
AminoAcid.java 816 (10 years ago) by stehr: New enum class AminoAcid
AlignmentEvaluator.java 775 (11 years ago) by stehr: better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
AlignmentConstructionError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Alignment.java 767 (11 years ago) by stehr: added getGaplessColumns(start, end)
AIGraph.java 712 (11 years ago) by duarte: Switching to JUNG2-beta1: - got rid of our custom fix to removeEdge - now both addVertex and removeVertex are correctly implemented: they update properly the nodes2serials map.
AIGNode.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
AIGEdge.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
AAinfo.java 837 (10 years ago) by duarte: Changed the value of the unobserved residue constant from "?" to "X". This is to fix CMView that had a lot of problems with it.
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