Some refactoring

Now implementing HasFeatures

New class UniprotEntry. Things make a lot more sense now...

Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.

RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.

Now checking codon length before translating

Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.

New feature: code for dna to protein translation

Now getting also gene encoding organelle from uniprot api

Now getPdbResSerFromResSer and getResSerFromPdbResSer will return null/-1 whenever there's no mapping. Allows then for checking from the caller.

Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.

Now parsing the symmetry operators.

Fixed bug: was nullpointing with empty cache files

Implemented caching of blast in UniprotHomologList

Our own copy file method! :-)

Now reading uniprot version from reldate.txt and checking against the uniprot api version

Implemented caching for EMBWSDBfetchConnection

Now serializable (to be able to write them to file)

Fixed bug: was nullpointing at retrieveUniprotKBData because of a single uniprot id can have multiple blast hits and was using the uni ids as unique identifiers => the lookup map was failing. Now the lookup map is from uniIds to lists of homologs(hits)

Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.

Minor doc fix

Fixed bug: was nullpointing when the letter encountered in counting the column was unknown.

Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.

Improved the getRimAndCore method

Some new methods

renamed  conflicting ContactMap class.

fixed bug in printf statement because pdbResSer has changed from int to String

Fixed bug in getRimAndCore, now we do end the loop correctly at the hard cutoff value.

Fixed bug with '-' embl cds identifiers.

Improved the rim and core calculation. The pdb res serial is now a String in PisaResidue (because of insertion codes)

Now parsing the seq_num residue number.

Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes

PISA connection and xml interfaces description parser

Implemented profile counting and entropy calculation for alignment.

Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()

Implemented methods to run a tcoffee alignment. Now also retrieving uniprot sequences via the uniprot api.

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.

New methods to retrieve uniprot data and embl cds for a single homolog

fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()

new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()

fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public

Adding the possibility to set the timeout for a JPredConnection. Next step is to add this as a user variable to CMView

New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.

add psi/phi constraints from secondary structure to tinker reconstructions

New example implementation of ResidueContactScoringFunction

Removed code left over from debugging.

Minor changes, couple of new methods.

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

Minor fix to java docs

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.

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.

Fixed some docs and indentation

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()

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.

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: 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