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r835
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BlastError.java 577 (11 years ago) by duarte: New package sequence. Initial commit of classes to run blast and parse its output.
BlastHit.java 801 (10 years ago) by duarte: Fixed bug: was not doing correctly the sanity checks in getAlignmentFullSeqs
BlastHitList.java 806 (10 years ago) by duarte: New method contains().
BlastRunner.java 788 (10 years ago) by filippis: white TO talyn
BlastTabularParser.java 577 (11 years ago) by duarte: New package sequence. Initial commit of classes to run blast and parse its output.
BlastUtils.java 791 (10 years ago) by filippis: white TO talyn
BlastXMLParser.java 744 (11 years ago) by duarte: Using the new XML parser in TemplateSelection. New method getQueryCoverage in BlastHit
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 788 (10 years ago) by filippis: white TO talyn
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 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
TcoffeeError.java 748 (11 years ago) by duarte: Initial commit, tcoffee runner for sequence to profile alignment
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
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