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r777
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BlastTabularParser.java 577 (12 years ago) by duarte: New package sequence. Initial commit of classes to run blast and parse its output.
BlastError.java 577 (12 years ago) by duarte: New package sequence. Initial commit of classes to run blast and parse its output.
PsipredError.java 590 (12 years ago) by duarte: Added code to run psipred. Fixed a few minor bugs.
PsipredRunner.java 590 (12 years ago) by duarte: Added code to run psipred. Fixed a few minor bugs.
GTGHit.java 623 (12 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 (12 years ago) by duarte: Fixed bug: wasn't catching wrong format in GTG output
GTGParser.java 637 (12 years ago) by duarte: Now skipping lines with <PRE> tags.
BlastUtils.java 651 (12 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.
BlastXMLParser.java 744 (11 years ago) by duarte: Using the new XML parser in TemplateSelection. New method getQueryCoverage in BlastHit
TcoffeeError.java 748 (11 years ago) by duarte: Initial commit, tcoffee runner for sequence to profile alignment
BlastRunner.java 750 (11 years ago) by duarte: Now we can run blast with multi threads option
Sequence.java 752 (11 years ago) by duarte: BlastHitList: new method getHit(subjectId), a new lookup HastMap member added for that. TemplateList: new method get(i) Sequence: new convenience method writeToFastaFile
BlastHitList.java 752 (11 years ago) by duarte: BlastHitList: new method getHit(subjectId), a new lookup HastMap member added for that. TemplateList: new method get(i) Sequence: new convenience method writeToFastaFile
TcoffeeRunner.java 760 (11 years ago) by duarte: Rewrote the secondary structure handling in Alignment. Also changed first parameter in writeFasta to be a PrintStream not an OutputStream
BlastHit.java 763 (11 years ago) by duarte: New method in BlastHit to transform the BlastHit local alignment into one that contains the full sequences of subject and query.
(Current path doesn't exist after revision 950)
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