New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.

Improved the selection of representative CDS

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.

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

Implemented caching of blast in UniprotHomologList

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

Implemented caching for EMBWSDBfetchConnection

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.

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.

Some new methods

Fixed bug with '-' embl cds identifiers.

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.

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

Removed code left over from debugging.

Minor changes, couple of new methods.

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.

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

Fixed some docs and indentation

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

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.

some cosmetic changes

New methods for writing sequence in Fasta format

New method contains().

Fixed bug: was not doing correctly the sanity checks in getAlignmentFullSeqs

white TO talyn

white TO talyn

New method in BlastHit to transform the BlastHit local alignment into one that contains the full sequences of subject and query.

Rewrote the secondary structure handling in Alignment. Also changed first parameter in writeFasta to be a PrintStream not an OutputStream

New static method in BlastHit to get subjectId from templateId
New member source in TemplateList

New method getAlignmentWithTemplateIDtag

BlastHitList: new method getHit(subjectId), a new lookup HastMap member added for that.
TemplateList: new method get(i)
Sequence: new convenience method writeToFastaFile

Now cleaning up correctly paul temp files
Now closing tcoffee's log properly

Now we can run blast with multi threads option

Initial commit, tcoffee runner for sequence to profile alignment

Now BlastHit printing works correctly for query identifier strings of any length

Using the new XML parser in TemplateSelection.
New method getQueryCoverage in BlastHit

New tests package (should be a folder and under it packages, but for now we can't do that until we move all source code to a src folder).
Moved all existing tests to appropiate tests packages.
New test PdbParsersTest: does cif against pdbase at the moment.
Adde equals method to SecStrucElement
Added some getters to Pdb

New BlastXMLParser together with BlastParsersTest Junit test for both xml and tabular parsers.
Added some new fields in BlastHist and BlastHitList.
Blast running methods in BlastRunner now take a new parameter: noFiltering.

Created getters for missing fields in BlastHit. 
New method removeAll in TemplateList.

added static method to print a ruler with sequence numbers

Fixed bug: now Sequence class considers '.' to be part of the fasta headers (in agreement with what we do in Alignment class). The 2 FASTAHEADER_REGEXes should be always kept in sync.

New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.

Fixed bug: writeClusterGraph shouldn't try to do anything if there's only one template.

added automatic conversion of matrix file to ps visualization (using script plot_simmatrix.sh)

Now skipping lines with <PRE> tags.

Changed default gravity value and default IDENTITY_SCORE for similarity graph

Fixed bug in BlastUtils.writeClusterGraph: was not working at all. Wrong curly brackets, was still using a GDT cutoff instead of rmsd and was never getting Pdb correctly out of the Template.
Two new members in Template: GTGHit and BlastHit, so we can reference back to the hit if needed (like if we want to get the evalue/score). Got rid on MySQLConnection as a member, not very nice design, now a parameter for the specific methods that need to query for PDB data.

put test code for writeClusterGraph in main method of BlastUtils

Now writeClusterGraph uses rmsd for similarity measure instead of GDT (maxcluster was failing almost always with GDT)

Yet another format check

Added one more file format check.

Fixed bug: wasn't catching wrong format in GTG output

Fixed bug: now catching when the mapping of observed residue sequence serials to internal residue serials is out of range, which happens in some extremely rare cases (because GTG uses pre-remediation data)

Added code to be able to filter out template ids (pdb codes) by maximum release date.
Some improvements in Hit classes.

Added methods to be able to print "graphical" output for GTGHits, all equivalent to the methods in BlastHit
Added compare() and writeIdsToFile() in TemplateList.

Initial commit of GTG parsing classes.
Added method in PdbasePdb to map observed residue sequence serials to internal (cif) residue serials

Now checking wheter read sequence contains spaces and throwing FastaFileFormatError

Moved method to writeSeqs to Sequence class.
Tidied up the help text in averageGraph

Fixed the fasta header regex to take only first token of header as sequence name (same behaviour as in Alignment class)

merged in some changes (now writing similarity matrix in blast utils)

Added code to run psipred.
Fixed a few minor bugs.

New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class

added BlastUtils.writeClusterGraph(String[] templateIds, outFile)

New methods to get the template ids and write them to file

Made printing hits with graphical overview the default using print() method. Print() takes no parameters, but BlastHitList.setQueryLength() has to be called once to set the length of the query. Introduced new printSome() function to output only the first n hits.

added class Sequence, added ascii-art output of blast hits to BlastHitList

Added a main method for testing

New package sequence. Initial commit of classes to run blast and parse its output.