Revision 619 - Directory Listing
Modified Thu May 8 10:13:10 2008 UTC (13 years, 2 months ago) by duarte

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

Revision 618 - Directory Listing
Modified Wed May 7 12:06:56 2008 UTC (13 years, 3 months ago) by duarte

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

Revision 612 - Directory Listing
Modified Wed Apr 30 18:20:09 2008 UTC (13 years, 3 months ago) by duarte

Now checking wheter read sequence contains spaces and throwing FastaFileFormatError

Revision 602 - Directory Listing
Modified Tue Apr 29 08:36:22 2008 UTC (13 years, 3 months ago) by duarte

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

Revision 597 - Directory Listing
Modified Fri Apr 25 16:53:47 2008 UTC (13 years, 3 months ago) by duarte

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

Revision 593 - Directory Listing
Modified Tue Apr 22 09:05:33 2008 UTC (13 years, 3 months ago) by stehr

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

Revision 590 - Directory Listing
Modified Fri Apr 11 14:43:53 2008 UTC (13 years, 3 months ago) by duarte

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

Revision 589 - Directory Listing
Modified Wed Apr 9 16:16:08 2008 UTC (13 years, 3 months ago) by duarte

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

Revision 584 - Directory Listing
Modified Tue Apr 8 15:18:22 2008 UTC (13 years, 3 months ago) by stehr

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

Revision 583 - Directory Listing
Modified Tue Apr 8 13:02:28 2008 UTC (13 years, 3 months ago) by duarte

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

Revision 581 - Directory Listing
Modified Tue Apr 8 11:00:45 2008 UTC (13 years, 3 months ago) by stehr

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.

Revision 579 - Directory Listing
Modified Mon Apr 7 17:57:54 2008 UTC (13 years, 3 months ago) by stehr

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

Revision 578 - Directory Listing
Modified Mon Apr 7 15:57:24 2008 UTC (13 years, 3 months ago) by duarte

Added a main method for testing

Revision 577 - Directory Listing
Added Fri Apr 4 16:46:23 2008 UTC (13 years, 4 months ago) by duarte

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