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.

New class gmbp for handling (saving) angle (theta-phi) ranges for certain contacts (iNum-jNum combinations);

revert. wasn't the best idea.

adding phi/psi constraints to edges

Changed return type of addFeature to boolean to match the java Collection interface

Extracted the EC data parsing code to its own connection class.

Extracted Scop parsing code to its own connection class.

Extracted the CSA parsing code to its own connection class.

Extracted the calc-vol and calc-surf runner code to its own Runner class.

Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon.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.

Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.

Fixed hard-coded resources paths broken since major restructuring of project.

Faster SQL queries

Fixed some docs and indentation

changes

Remove hard-coded MySQL parameters. Please use always .my.cnf files for MySQL parameters!

FloatPairSet first commit

new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)

adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()

Classes for sphoxel and nbhstraces handling. csv handling

First version of class for sphoxel computation.

removing a warning in owl.embed.contactmaps.Demes

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.

Added a supresswarnings tag (it's simply unused code)

Fixed import (was a compile error)

cone peeling algorithm as implemented in sathyas classes, does not contain any public constructors, must use public statics

resolving conflicts

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

Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 

refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests

refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features

refactoring: adapting test packages to match new package structure

refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl

refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker

refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

starting refactoring: first creating packages owl and owl.core