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Revision 1094 - Directory Listing
Modified Wed Jun 2 13:19:21 2010 UTC (9 years, 6 months ago) by jmduarteg
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Revision 1093 - Directory Listing
Modified Wed Jun 2 08:34:04 2010 UTC (9 years, 6 months ago) by hstehr
checking in some of Michael's example files
Revision 1092 - Directory Listing
Modified Wed Jun 2 08:07:50 2010 UTC (9 years, 6 months ago) by lappe
Contact Map for server prediction directory evaluation added
Revision 1091 - Directory Listing
Modified Tue Jun 1 15:56:12 2010 UTC (9 years, 6 months ago) by cvehlow
Class OptimalSingleEnv for scoring of different substrings.
Revision 1090 - Directory Listing
Modified Tue Jun 1 12:16:52 2010 UTC (9 years, 6 months ago) by matt4077
little contact map example done
Revision 1089 - Directory Listing
Modified Tue Jun 1 11:14:05 2010 UTC (9 years, 6 months ago) by matt4077
added a package for example scripts using the library
Revision 1088 - Directory Listing
Modified Tue Jun 1 09:14:19 2010 UTC (9 years, 6 months ago) by cvehlow
max number of traces
Revision 1087 - Directory Listing
Modified Mon May 31 15:41:25 2010 UTC (9 years, 6 months ago) by jmduarteg
Improved the getRimAndCore method
Revision 1086 - Directory Listing
Modified Mon May 31 15:41:16 2010 UTC (9 years, 6 months ago) by cvehlow
Extract maximum number of traces!
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (9 years, 6 months ago) by jmduarteg
Some new methods
Revision 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (9 years, 6 months ago) by matt4077
renamed  conflicting ContactMap class.
Revision 1083 - Directory Listing
Modified Mon May 31 13:31:23 2010 UTC (9 years, 6 months ago) by hstehr
fixed bug in printf statement because pdbResSer has changed from int to String
Revision 1082 - Directory Listing
Modified Fri May 28 15:00:31 2010 UTC (9 years, 6 months ago) by jmduarteg
Fixed bug in getRimAndCore, now we do end the loop correctly at the hard cutoff value.
Revision 1081 - Directory Listing
Modified Fri May 28 14:51:46 2010 UTC (9 years, 6 months ago) by jmduarteg
Fixed bug with '-' embl cds identifiers.
Revision 1080 - Directory Listing
Modified Fri May 28 12:55:41 2010 UTC (9 years, 6 months ago) by jmduarteg
Undoing some stuff commited by error in last commit
Revision 1079 - Directory Listing
Modified Fri May 28 12:52:31 2010 UTC (9 years, 6 months ago) by jmduarteg
Improved the rim and core calculation. The pdb res serial is now a String in PisaResidue (because of insertion codes)
Revision 1078 - Directory Listing
Modified Thu May 27 10:33:41 2010 UTC (9 years, 6 months ago) by jmduarteg
Now parsing the seq_num residue number.
Revision 1077 - Directory Listing
Modified Thu May 27 09:51:50 2010 UTC (9 years, 6 months ago) by jmduarteg
Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes
Revision 1075 - Directory Listing
Modified Fri May 21 17:33:34 2010 UTC (9 years, 6 months ago) by jmduarteg
PISA connection and xml interfaces description parser
Revision 1074 - Directory Listing
Modified Fri May 21 10:02:24 2010 UTC (9 years, 6 months ago) by jmduarteg
Implemented profile counting and entropy calculation for alignment.
Revision 1073 - Directory Listing
Modified Thu May 20 15:21:10 2010 UTC (9 years, 6 months ago) by jmduarteg
Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()
Revision 1072 - Directory Listing
Modified Thu May 20 13:59:25 2010 UTC (9 years, 6 months ago) by jmduarteg
Implemented methods to run a tcoffee alignment. Now also retrieving uniprot sequences via the uniprot api.
Revision 1071 - Directory Listing
Modified Thu May 20 12:46:11 2010 UTC (9 years, 6 months ago) by cvehlow
Histogram for different sstypes --> number of nodes per trace.
Revision 1070 - Directory Listing
Modified Wed May 19 16:20:42 2010 UTC (9 years, 6 months ago) by jmduarteg
Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
Revision 1069 - Directory Listing
Modified Tue May 18 14:53:34 2010 UTC (9 years, 6 months ago) by jmduarteg
New methods to retrieve uniprot data and embl cds for a single homolog
Revision 1068 - Directory Listing
Modified Tue May 18 09:31:39 2010 UTC (9 years, 6 months ago) by cvehlow
HandOverThetaPhiRanges
Revision 1067 - Directory Listing
Modified Wed May 12 16:36:24 2010 UTC (9 years, 7 months ago) by hstehr
fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()
Revision 1066 - Directory Listing
Modified Wed May 12 12:00:11 2010 UTC (9 years, 7 months ago) by hstehr
new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
Revision 1064 - Directory Listing
Modified Tue May 11 14:57:20 2010 UTC (9 years, 7 months ago) by hstehr
fixed a bug in GraphAverager.getGraphWithTopContacts() which caused a null pointer exception in jung.SparseGraph.addEdge(), this may even be a bug in jung
Revision 1063 - Directory Listing
Modified Mon May 10 10:23:03 2010 UTC (9 years, 7 months ago) by stehr
Creating constructor which was apparently lost during some previous refactoring but which was needed by class cccp.testGraphAverager
Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (9 years, 7 months ago) by stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision 1061 - Directory Listing
Modified Fri May 7 14:13:07 2010 UTC (9 years, 7 months ago) by hstehr
Adding the possibility to set the timeout for a JPredConnection. Next step is to add this as a user variable to CMView
Revision 1060 - Directory Listing
Modified Fri May 7 11:53:13 2010 UTC (9 years, 7 months ago) by hstehr
New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
Revision 1059 - Directory Listing
Modified Wed May 5 14:28:19 2010 UTC (9 years, 7 months ago) by jmduarteg
Fixed java doc
Revision 1058 - Directory Listing
Modified Mon May 3 16:57:21 2010 UTC (9 years, 7 months ago) by cvehlow
Load from zip-file!
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (9 years, 7 months ago) by matt4077
add psi/phi constraints from secondary structure to tinker reconstructions
Revision 1056 - Directory Listing
Modified Fri Apr 30 11:31:45 2010 UTC (9 years, 7 months ago) by stehr
New example implementation of ResidueContactScoringFunction
Revision 1055 - Directory Listing
Modified Wed Apr 28 15:08:53 2010 UTC (9 years, 7 months ago) by jmduarteg
Removed code left over from debugging.
Revision 1054 - Directory Listing
Modified Wed Apr 28 13:37:00 2010 UTC (9 years, 7 months ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (9 years, 7 months ago) by hstehr
Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph
Revision 1051 - Directory Listing
Modified Tue Apr 27 15:34:38 2010 UTC (9 years, 7 months ago) by jmduarteg
Minor fix to java docs
Revision 1050 - Directory Listing
Modified Tue Apr 27 12:39:52 2010 UTC (9 years, 7 months ago) by cvehlow
Load precalc sphoxel data if possible.
Revision 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (9 years, 7 months ago) by hstehr
removing @Override annotations which were causing compilation errors for me
Revision 1048 - Directory Listing
Modified Tue Apr 27 08:24:18 2010 UTC (9 years, 7 months ago) by jmduarteg
New classes UniprotHomolog and UniprotHomologList to contain a set of homologs of a given sequence, including the blast hit data, embl cds coding sequences etc.
Revision 1047 - Directory Listing
Modified Mon Apr 26 16:13:36 2010 UTC (9 years, 7 months ago) by jmduarteg
SecondaryStructure now implements Iterable after refactoring of getIterator
Revision 1046 - Directory Listing
Modified Mon Apr 26 15:26:59 2010 UTC (9 years, 7 months ago) by hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision 1045 - Directory Listing
Modified Mon Apr 26 12:55:28 2010 UTC (9 years, 7 months ago) by jmduarteg
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
Revision 1044 - Directory Listing
Modified Mon Apr 26 10:37:14 2010 UTC (9 years, 7 months ago) by hstehr
New interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.
Revision 1043 - Directory Listing
Modified Thu Apr 22 12:21:37 2010 UTC (9 years, 7 months ago) by jmduarteg
Fixed blast parsing bug: was parsing the Hit_def tag instead of the Hit_id tag for the subject id. When formatdb is run with option "-o T" then indices are properly generated and Hit_id contains the correct tag.
Revision 1042 - Directory Listing
Modified Wed Apr 21 16:11:08 2010 UTC (9 years, 7 months ago) by jmduarteg
New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
Revision 1041 - Directory Listing
Modified Wed Apr 21 13:24:18 2010 UTC (9 years, 7 months ago) by hstehr
New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.
Revision 1040 - Directory Listing
Modified Wed Apr 21 10:44:19 2010 UTC (9 years, 7 months ago) by jmduarteg
New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
Revision 1039 - Directory Listing
Modified Tue Apr 20 10:19:32 2010 UTC (9 years, 7 months ago) by cvehlow
New class gmbp for handling (saving) angle (theta-phi) ranges for certain contacts (iNum-jNum combinations);
Revision 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (9 years, 7 months ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (9 years, 7 months ago) by matt4077
adding phi/psi constraints to edges
Revision 1036 - Directory Listing
Modified Mon Apr 19 14:27:11 2010 UTC (9 years, 7 months ago) by jmduarteg
Changed return type of addFeature to boolean to match the java Collection interface
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (9 years, 7 months ago) by jmduarteg
Extracted the EC data parsing code to its own connection class.
Revision 1034 - Directory Listing
Modified Mon Apr 19 12:42:21 2010 UTC (9 years, 7 months ago) by jmduarteg
Extracted Scop parsing code to its own connection class.
Revision 1033 - Directory Listing
Modified Mon Apr 19 12:26:22 2010 UTC (9 years, 7 months ago) by jmduarteg
Extracted the CSA parsing code to its own connection class.
Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (9 years, 7 months ago) by jmduarteg
Extracted the calc-vol and calc-surf runner code to its own Runner class.
Revision 1031 - Directory Listing
Modified Mon Apr 19 10:00:34 2010 UTC (9 years, 7 months ago) by jmduarteg
Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon. Oligomeric state should be implemented as some kind of feature.
Revision 1030 - Directory Listing
Modified Mon Apr 19 09:39:07 2010 UTC (9 years, 7 months ago) by jmduarteg
Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.
Revision 1029 - Directory Listing
Modified Mon Apr 19 09:01:51 2010 UTC (9 years, 7 months ago) by jmduarteg
Fixed hard-coded resources paths broken since major restructuring of project.
Revision 1028 - Directory Listing
Modified Fri Apr 16 13:21:40 2010 UTC (9 years, 7 months ago) by cvehlow
Faster SQL queries
Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (9 years, 7 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1026 - Directory Listing
Modified Thu Apr 15 15:28:29 2010 UTC (9 years, 7 months ago) by cvehlow
changes
Revision 1025 - Directory Listing
Modified Thu Apr 15 09:28:23 2010 UTC (9 years, 7 months ago) by jmduarteg
Remove hard-coded MySQL parameters. Please use always .my.cnf files for MySQL parameters!
Revision 1024 - Directory Listing
Modified Wed Apr 14 15:59:13 2010 UTC (9 years, 7 months ago) by cvehlow

Revision 1023 - Directory Listing
Modified Tue Apr 13 17:14:22 2010 UTC (9 years, 7 months ago) by cvehlow
FloatPairSet first commit
Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (9 years, 8 months ago) by stehr
new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)
Revision 1021 - Directory Listing
Modified Fri Apr 9 15:30:15 2010 UTC (9 years, 8 months ago) by hstehr
adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()
Revision 1020 - Directory Listing
Modified Fri Apr 9 15:22:20 2010 UTC (9 years, 8 months ago) by cvehlow
Classes for sphoxel and nbhstraces handling. csv handling
Revision 1019 - Directory Listing
Modified Fri Apr 9 13:16:07 2010 UTC (9 years, 8 months ago) by cvehlow
First version of class for sphoxel computation.
Revision 1018 - Directory Listing
Modified Fri Apr 9 10:40:29 2010 UTC (9 years, 8 months ago) by hstehr
removing a warning in owl.embed.contactmaps.Demes
Revision 1017 - Directory Listing
Modified Fri Apr 9 09:42:32 2010 UTC (9 years, 8 months ago) by jmduarteg
New methods for random sampling a RIGraph and randomly adding noise. The code was already somewhere in the embed package but here seems more convenient.
Revision 1016 - Directory Listing
Modified Fri Apr 9 09:18:35 2010 UTC (9 years, 8 months ago) by jmduarteg
Added a supresswarnings tag (it's simply unused code)
Revision 1015 - Directory Listing
Modified Fri Apr 9 09:16:04 2010 UTC (9 years, 8 months ago) by jmduarteg
Fixed import (was a compile error)
Revision 1014 - Directory Listing
Modified Thu Apr 8 16:34:26 2010 UTC (9 years, 8 months ago) by gmueller
cone peeling algorithm as implemented in sathyas classes, does not contain any public constructors, must use public statics
Revision 1013 - Directory Listing
Modified Thu Apr 1 10:49:30 2010 UTC (9 years, 8 months ago) by matt4077
resolving conflicts
Revision 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (9 years, 8 months ago) by hstehr
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
Revision 1011 - Directory Listing
Modified Wed Mar 31 20:21:01 2010 UTC (9 years, 8 months ago) by jmduarteg
Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 
Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (9 years, 8 months ago) by hstehr
refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 8 months ago) by hstehr
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
Revision 1008 - Directory Listing
Modified Wed Mar 31 14:03:27 2010 UTC (9 years, 8 months ago) by hstehr
refactoring: adapting test packages to match new package structure
Revision 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (9 years, 8 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
Revision 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (9 years, 8 months ago) by hstehr
refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (9 years, 8 months ago) by hstehr
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 1004 - Directory Listing
Modified Wed Mar 31 11:59:33 2010 UTC (9 years, 8 months ago) by hstehr
starting refactoring: first creating packages owl and owl.core
Revision 1002 - Directory Listing
Modified Tue Mar 30 11:22:07 2010 UTC (9 years, 8 months ago) by gmueller
latest version of gabriel (embed.contactmaps)
Revision 1001 - Directory Listing
Modified Tue Mar 30 11:09:04 2010 UTC (9 years, 8 months ago) by gmueller
latest version of gabriel
Revision 1000 - Directory Listing
Modified Mon Mar 29 10:20:38 2010 UTC (9 years, 8 months ago) by jmduarteg
Now DsspRunner is purely static (makes more sense)
Revision 999 - Directory Listing
Modified Mon Mar 29 10:06:42 2010 UTC (9 years, 8 months ago) by jmduarteg
Fixed the dsspRunner call (now it's static).
Revision 998 - Directory Listing
Modified Mon Mar 29 10:04:04 2010 UTC (9 years, 8 months ago) by jmduarteg
Minor refactoring and comment fixes
Revision 997 - Directory Listing
Modified Mon Mar 29 09:41:31 2010 UTC (9 years, 8 months ago) by lappe
Turns the RIGraph into a GMatrix 
public void convert2GMatrix( GMatrix A)
Revision 996 - Directory Listing
Modified Thu Mar 25 12:07:41 2010 UTC (9 years, 8 months ago) by matt4077
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.  
Revision 995 - Directory Listing
Modified Thu Mar 25 11:48:27 2010 UTC (9 years, 8 months ago) by jmduarteg
Removed the executable property
Revision 994 - Directory Listing
Modified Wed Mar 24 15:09:16 2010 UTC (9 years, 8 months ago) by hstehr
new method AminoAcid.valuesInOrderOfHydrophobicity()
Revision 989 - Directory Listing
Modified Fri Mar 19 09:00:00 2010 UTC (9 years, 8 months ago) by hstehr
adding a method RIGraph.getOrderedNeighbors(Node) because the default method getNeighbors(Node) returns the neighbours in non-deterministic order(!) which caused me lots of trouble
Revision 988 - Directory Listing
Modified Thu Mar 18 12:02:13 2010 UTC (9 years, 8 months ago) by jmduarteg
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.

Revision 987 - Directory Listing
Modified Thu Mar 18 11:08:58 2010 UTC (9 years, 8 months ago) by jmduarteg
New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class)
Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!)
Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.

Revision 986 - Directory Listing
Modified Wed Mar 17 11:45:59 2010 UTC (9 years, 8 months ago) by matt4077
fixing a bug where floats in CASP RR files are rendered with comma for those unfortunate people stuck on german computers. 
Revision 985 - Directory Listing
Modified Tue Mar 16 13:47:40 2010 UTC (9 years, 8 months ago) by hstehr
Adding new package owl.connections with connector classes to online databases and services. Starting with PhosphoSitePlusConnection for accessing a database of posttranslational modifications and PDomainsConnection for accessing a very useful webservice which calculates structural domains using a variety of methods including Scop, Cath, DomainParser, ProteinDomainParser and others.
Revision 984 - Directory Listing
Modified Tue Mar 16 13:24:35 2010 UTC (9 years, 8 months ago) by hstehr
Commiting an old change of some constant in PolyposeRunner. I forgot what this does but it must be good :)
Revision 983 - Directory Listing
Modified Tue Mar 16 13:22:26 2010 UTC (9 years, 8 months ago) by hstehr
adding some convenience methods to IntervalSet
Revision 982 - Directory Listing
Modified Tue Mar 16 13:01:01 2010 UTC (9 years, 8 months ago) by hstehr
Restoring deleted class Pair because it is needed by one of my programs. 
Revision 981 - Directory Listing
Modified Tue Mar 16 12:53:13 2010 UTC (9 years, 8 months ago) by hstehr
Introducing new StructuralDomainFeature for structural domains as defined by SCOP, CATH, DomainParser etc.
Revision 977 - Directory Listing
Modified Tue Feb 23 17:41:08 2010 UTC (9 years, 9 months ago) by duarte
Better error message for no tinker paths set up
Revision 973 - Directory Listing
Modified Tue Feb 23 14:32:00 2010 UTC (9 years, 9 months ago) by duarte
Moving the CASP project into OWL as the casp package.
Revision 970 - Directory Listing
Modified Tue Feb 23 11:47:05 2010 UTC (9 years, 9 months ago) by duarte
Now PDB data will be loaded from online PDB's ftp if no PDBASE_DB specified in config file
Revision 969 - Directory Listing
Modified Tue Feb 23 11:20:32 2010 UTC (9 years, 9 months ago) by duarte
Now configuration (tinker paths) is read from config file.
Revision 968 - Directory Listing
Modified Mon Feb 22 16:03:45 2010 UTC (9 years, 9 months ago) by duarte
Updated make-aglappe script (and renamed to make-owl).
Changed aglappe strings to OWL (following new name of library)
Revision 965 - Directory Listing
Modified Thu Feb 18 15:25:10 2010 UTC (9 years, 9 months ago) by duarte
Fixed paths of tests (was missing the src directory since we moved everything under src)
Revision 964 - Directory Listing
Modified Tue Feb 16 12:01:40 2010 UTC (9 years, 9 months ago) by gmueller
new class for sparse double matrices
Revision 963 - Directory Listing
Modified Tue Feb 16 12:00:55 2010 UTC (9 years, 9 months ago) by gmueller
some new classes
Revision 962 - Directory Listing
Modified Tue Feb 16 11:51:18 2010 UTC (9 years, 9 months ago) by gmueller
minor changes, that now fit into the renewed version
Revision 961 - Directory Listing
Modified Mon Feb 15 11:55:40 2010 UTC (9 years, 9 months ago) by duarte
Now analyseHistone will output the coordinates of the side chains of ARGs (NH1 atom) and LYSs (NZ atom) instead of the CA atoms.
Some new methods in Pdb
Revision 960 - Directory Listing
Modified Fri Feb 12 15:34:09 2010 UTC (9 years, 9 months ago) by duarte
New executable class from my workspace.
Revision 959 - Directory Listing
Modified Fri Feb 12 15:25:33 2010 UTC (9 years, 9 months ago) by duarte
Moved IntervalTest class to test.tools package
Revision 958 - Directory Listing
Modified Fri Feb 12 15:22:36 2010 UTC (9 years, 9 months ago) by duarte
Moved Interval* and IntPair* classes to tools package
Revision 957 - Directory Listing
Modified Fri Feb 12 15:06:04 2010 UTC (9 years, 9 months ago) by duarte
Added some useful tools to the default package from my workspace. More clean up.
Revision 956 - Directory Listing
Modified Fri Feb 12 14:46:46 2010 UTC (9 years, 9 months ago) by duarte
Removed some obsolete classes.
Revision 955 - Directory Listing
Modified Tue Feb 9 10:44:24 2010 UTC (9 years, 10 months ago) by duarte
Now removed variable and put back code that shouldn't have been commented out
Revision 954 - Directory Listing
Modified Tue Feb 9 10:43:02 2010 UTC (9 years, 10 months ago) by duarte
Commented out some unused variables to get rid of warnings
Revision 953 - Directory Listing
Modified Mon Feb 8 15:36:45 2010 UTC (9 years, 10 months ago) by duarte
Refactoring of inconsistently named methods in RIGraph
Revision 952 - Directory Listing
Modified Fri Feb 5 16:41:47 2010 UTC (9 years, 10 months ago) by duarte
Added some new prediction measures for DecoyScoreSet: rank, delta rmsd, n% enrichment value
Extended the range of the distance bins.
Revision 951 - Directory Listing
Added Fri Jan 29 16:12:34 2010 UTC (9 years, 10 months ago) by duarte
Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.