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Revision 1021 - Directory Listing
Modified Fri Apr 9 15:30:15 2010 UTC (9 years, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 months ago) by matt4077
resolving conflicts
Revision 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (9 years, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 months ago) by gmueller
latest version of gabriel
Revision 1000 - Directory Listing
Modified Mon Mar 29 10:20:38 2010 UTC (9 years, 4 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, 4 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, 4 months ago) by jmduarteg
Minor refactoring and comment fixes
Revision 997 - Directory Listing
Modified Mon Mar 29 09:41:31 2010 UTC (9 years, 4 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, 4 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, 4 months ago) by jmduarteg
Removed the executable property
Revision 994 - Directory Listing
Modified Wed Mar 24 15:09:16 2010 UTC (9 years, 4 months ago) by hstehr
new method AminoAcid.valuesInOrderOfHydrophobicity()
Revision 989 - Directory Listing
Modified Fri Mar 19 09:00:00 2010 UTC (9 years, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 6 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, 6 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, 6 months ago) by gmueller
some new classes
Revision 962 - Directory Listing
Modified Tue Feb 16 11:51:18 2010 UTC (9 years, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 months ago) by duarte
Removed some obsolete classes.
Revision 955 - Directory Listing
Modified Tue Feb 9 10:44:24 2010 UTC (9 years, 6 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, 6 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, 6 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, 6 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, 6 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.