 ../
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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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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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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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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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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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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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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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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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651
(16 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.
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BlastUtils.java
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651
(16 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.
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