 ../
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AAinfo.java
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524
(12 years ago)
by duarte:
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()
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AIGEdge.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGNode.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGraph.java
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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.
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Alignment.java
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767
(11 years ago)
by stehr:
added getGaplessColumns(start, end)
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AlignmentConstructionError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AlignmentEvaluator.java
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775
(11 years ago)
by stehr:
better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
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Box.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CaspRRFileData.java
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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.
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CaspRRFileRIGraph.java
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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.
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CatalSiteSet.java
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514
(12 years ago)
by filippis:
Latest scop and csa versions updated.
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CatalyticSite.java
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503
(12 years ago)
by filippis:
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.
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CiffileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CiffilePdb.java
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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.
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ConformationsNotSameSizeError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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ContactType.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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DbRIGraph.java
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788
(11 years ago)
by filippis:
white TO talyn
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EC.java
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502
(12 years ago)
by stehr:
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
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ECRegion.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FastaFileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileRIGraph.java
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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.
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FileTypeGuesser.java
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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
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GraphFileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIODb.java
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788
(11 years ago)
by filippis:
white TO talyn
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GraphIOGDLFile.java
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635
(11 years ago)
by duarte:
Changed default gravity value and default IDENTITY_SCORE for similarity graph
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GraphIdNotFoundError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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HashGrid.java
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737
(11 years ago)
by stehr:
Committing empty class HashGrid for later implementation
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IntPairComparator.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairSet.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Interval.java
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515
(12 years ago)
by stehr:
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
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IntervalSet.java
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592
(11 years ago)
by stehr:
fixed one null pointer bug and some spelling mistakes
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MaxClusterRunner.java
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714
(11 years ago)
by stehr:
added comment
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MsdsdInconsistentResidueNumbersError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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MsdsdPdb.java
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788
(11 years ago)
by filippis:
white TO talyn
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NbhProbDistribution.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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NbhoodBackgrnd.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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OligomericState.java
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689
(11 years ago)
by filippis:
-OligomericState class added
-Pdb
a.checkOligomeric and getOligomericState methods added
b.calcVolume, calcSurface and calcCompactnessCoefficient methods added
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PairwiseAlignmentConverter.java
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517
(12 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
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PairwiseSequenceAlignment.java
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709
(11 years ago)
by stehr:
added methods to return the residue mappings for this alignment
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PaulStructAligner.java
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788
(11 years ago)
by filippis:
white TO talyn
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Pdb.java
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787
(11 years ago)
by duarte:
First implementation of the embedding part of the EMBED algorithm by Havel: from an exact complete distance matrix gives 3d coordinates for the embedding.
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PdbChainCodeNotFoundError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbCodeNotFoundError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbLoadError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbaseInconsistencyError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbasePdb.java
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783
(11 years ago)
by duarte:
Got rid of the hardcoded mysql server, user, password. Now read from .my.cnf file
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PdbfileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbfilePdb.java
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661
(11 years ago)
by stehr:
Now enforcing that atom serials have to be in ascending order
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PirFileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PolyposeRunner.java
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775
(11 years ago)
by stehr:
better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
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PredEval.java
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682
(11 years ago)
by stehr:
now handling special cases that used to give NaN values
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ProtStructGraph.java
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725
(11 years ago)
by duarte:
Given a serialVersionUID to class to get rid of warning
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RIGCommonNbhood.java
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512
(12 years ago)
by duarte:
Added getCommanSeparatedResSerials to RIGCommonNbhood
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RIGEdge.java
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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
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RIGEnsemble.java
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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
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RIGNbhood.java
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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
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RIGNode.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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RIGraph.java
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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.
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RIGraphMinSpanningTree.java
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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.
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Scop.java
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685
(11 years ago)
by filippis:
getNumScopRes method added in Scop class
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ScopRegion.java
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589
(11 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
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SecStrucElement.java
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743
(11 years ago)
by duarte:
New tests package (should be a folder and under it packages, but for now we can't do that until we move all source code to a src folder).
Moved all existing tests to appropiate tests packages.
New test PdbParsersTest: does cif against pdbase at the moment.
Adde equals method to SecStrucElement
Added some getters to Pdb
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SecondaryStructure.java
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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.
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StructAligner.java
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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.
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StructAlignmentError.java
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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.
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Template.java
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753
(11 years ago)
by duarte:
Fixed bug: PDB/graph/scop data loading issues were not correctly implemented.
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TemplateList.java
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756
(11 years ago)
by duarte:
New static method in BlastHit to get subjectId from templateId
New member source in TemplateList
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aapairsBounds.dat
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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contactTypes.dat
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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