 ../
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BlastUtils.java
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642
(16 years ago)
by duarte:
Fixed bug: writeClusterGraph shouldn't try to do anything if there's only one template.
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GTGParser.java
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637
(16 years ago)
by duarte:
Now skipping lines with <PRE> tags.
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BlastRunner.java
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634
(16 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.
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GTGHitList.java
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625
(16 years ago)
by duarte:
Fixed bug: wasn't catching wrong format in GTG output
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GTGHit.java
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623
(16 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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BlastHitList.java
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622
(16 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.
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BlastHit.java
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619
(16 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.
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Sequence.java
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612
(16 years ago)
by duarte:
Now checking wheter read sequence contains spaces and throwing FastaFileFormatError
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PsipredError.java
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590
(16 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
(16 years ago)
by duarte:
Added code to run psipred.
Fixed a few minor bugs.
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BlastError.java
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577
(16 years ago)
by duarte:
New package sequence. Initial commit of classes to run blast and parse its output.
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BlastTabularParser.java
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577
(16 years ago)
by duarte:
New package sequence. Initial commit of classes to run blast and parse its output.
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