ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/sequence
r637
File Last Change
 ../
BlastError.java 577 (11 years ago) by duarte: New package sequence. Initial commit of classes to run blast and parse its output.
BlastHit.java 619 (11 years 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.
BlastHitList.java 622 (11 years ago) by duarte: Added code to be able to filter out template ids (pdb codes) by maximum release date. Some improvements in Hit classes.
BlastRunner.java 634 (11 years ago) by duarte: 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.
BlastTabularParser.java 577 (11 years ago) by duarte: New package sequence. Initial commit of classes to run blast and parse its output.
BlastUtils.java 635 (11 years ago) by duarte: Changed default gravity value and default IDENTITY_SCORE for similarity graph
GTGHit.java 623 (11 years ago) by duarte: 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)
GTGHitList.java 625 (11 years ago) by duarte: Fixed bug: wasn't catching wrong format in GTG output
GTGParser.java 637 (11 years ago) by duarte: Now skipping lines with <PRE> tags.
PsipredError.java 590 (11 years ago) by duarte: Added code to run psipred. Fixed a few minor bugs.
PsipredRunner.java 590 (11 years ago) by duarte: Added code to run psipred. Fixed a few minor bugs.
Sequence.java 612 (11 years ago) by duarte: Now checking wheter read sequence contains spaces and throwing FastaFileFormatError
(Current path doesn't exist after revision 950)
         12 files shown