Minor fix to java docs

Load precalc sphoxel data if possible.

removing @Override annotations which were causing compilation errors for me

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.

SecondaryStructure now implements Iterable after refactoring of getIterator

JPredConnection now returns a SecondaryStructure object; some updated javadocs

Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.

New interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.

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.

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)

New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.

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Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon.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

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.