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

latest version of gabriel (embed.contactmaps)

latest version of gabriel

Now DsspRunner is purely static (makes more sense)

Fixed the dsspRunner call (now it's static).

Minor refactoring and comment fixes

Turns the RIGraph into a GMatrix 
public void convert2GMatrix( GMatrix A)

reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.  

Removed the executable property

new method AminoAcid.valuesInOrderOfHydrophobicity()

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

Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.

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.

fixing a bug where floats in CASP RR files are rendered with comma for those unfortunate people stuck on german computers. 

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.

Commiting an old change of some constant in PolyposeRunner. I forgot what this does but it must be good :)

adding some convenience methods to IntervalSet

Restoring deleted class Pair because it is needed by one of my programs. 

Introducing new StructuralDomainFeature for structural domains as defined by SCOP, CATH, DomainParser etc.

Better error message for no tinker paths set up

Moving the CASP project into OWL as the casp package.

Now PDB data will be loaded from online PDB's ftp if no PDBASE_DB specified in config file

Now configuration (tinker paths) is read from config file.

Updated make-aglappe script (and renamed to make-owl).
Changed aglappe strings to OWL (following new name of library)

Fixed paths of tests (was missing the src directory since we moved everything under src)

new class for sparse double matrices

some new classes

minor changes, that now fit into the renewed version

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

New executable class from my workspace.

Moved IntervalTest class to test.tools package

Moved Interval* and IntPair* classes to tools package

Added some useful tools to the default package from my workspace. More clean up.

Removed some obsolete classes.

Now removed variable and put back code that shouldn't have been commented out

Commented out some unused variables to get rid of warnings

Refactoring of inconsistently named methods in RIGraph

Added some new prediction measures for DecoyScoreSet: rank, delta rmsd, n% enrichment value
Extended the range of the distance bins.

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.