 ../
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BlastError.java
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577
(14 years ago)
by duarte:
New package sequence. Initial commit of classes to run blast and parse its output.
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BlastHit.java
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801
(13 years ago)
by duarte:
Fixed bug: was not doing correctly the sanity checks in getAlignmentFullSeqs
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BlastHitList.java
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806
(13 years ago)
by duarte:
New method contains().
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BlastRunner.java
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788
(13 years ago)
by filippis:
white TO talyn
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BlastTabularParser.java
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577
(14 years ago)
by duarte:
New package sequence. Initial commit of classes to run blast and parse its output.
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BlastUtils.java
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791
(13 years ago)
by filippis:
white TO talyn
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BlastXMLParser.java
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744
(13 years ago)
by duarte:
Using the new XML parser in TemplateSelection.
New method getQueryCoverage in BlastHit
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GTGHit.java
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623
(14 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)
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GTGHitList.java
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625
(14 years ago)
by duarte:
Fixed bug: wasn't catching wrong format in GTG output
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GTGParser.java
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788
(13 years ago)
by filippis:
white TO talyn
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PsipredError.java
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590
(14 years ago)
by duarte:
Added code to run psipred.
Fixed a few minor bugs.
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PsipredRunner.java
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590
(14 years ago)
by duarte:
Added code to run psipred.
Fixed a few minor bugs.
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Sequence.java
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883
(12 years ago)
by stehr:
some cosmetic changes
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TcoffeeError.java
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748
(13 years ago)
by duarte:
Initial commit, tcoffee runner for sequence to profile alignment
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TcoffeeRunner.java
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760
(13 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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