ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/sequence
r712
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 651 (11 years ago) by duarte: 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.
BlastTabularParser.java 577 (11 years ago) by duarte: New package sequence. Initial commit of classes to run blast and parse its output.
BlastUtils.java 651 (11 years ago) by duarte: 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.
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 711 (11 years ago) by stehr: added static method to print a ruler with sequence numbers
(Current path doesn't exist after revision 950)
         12 files shown