Revision 593 - Directory Listing
Modified Tue Apr 22 09:05:33 2008 UTC (14 years, 2 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 (14 years, 2 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 (14 years, 2 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 (14 years, 2 months ago) by stehr

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

Revision 583 - Directory Listing
Modified Tue Apr 8 13:02:28 2008 UTC (14 years, 2 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 (14 years, 2 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 (14 years, 2 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 (14 years, 2 months ago) by duarte

Added a main method for testing

Revision 577 - Directory Listing
Added Fri Apr 4 16:46:23 2008 UTC (14 years, 2 months ago) by duarte

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