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.