 ../
|
BlastError.java
|
577
(14 years ago)
by duarte:
New package sequence. Initial commit of classes to run blast and parse its output.
|
|
BlastHit.java
|
742
(13 years ago)
by duarte:
New BlastXMLParser together with BlastParsersTest Junit test for both xml and tabular parsers.
Added some new fields in BlastHist and BlastHitList.
Blast running methods in BlastRunner now take a new parameter: noFiltering.
|
|
BlastHitList.java
|
742
(13 years ago)
by duarte:
New BlastXMLParser together with BlastParsersTest Junit test for both xml and tabular parsers.
Added some new fields in BlastHist and BlastHitList.
Blast running methods in BlastRunner now take a new parameter: noFiltering.
|
|
BlastRunner.java
|
742
(13 years ago)
by duarte:
New BlastXMLParser together with BlastParsersTest Junit test for both xml and tabular parsers.
Added some new fields in BlastHist and BlastHitList.
Blast running methods in BlastRunner now take a new parameter: noFiltering.
|
|
BlastTabularParser.java
|
577
(14 years ago)
by duarte:
New package sequence. Initial commit of classes to run blast and parse its output.
|
|
BlastUtils.java
|
651
(14 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
|
742
(13 years ago)
by duarte:
New BlastXMLParser together with BlastParsersTest Junit test for both xml and tabular parsers.
Added some new fields in BlastHist and BlastHitList.
Blast running methods in BlastRunner now take a new parameter: noFiltering.
|
|
GTGHit.java
|
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)
|
|
GTGHitList.java
|
625
(14 years ago)
by duarte:
Fixed bug: wasn't catching wrong format in GTG output
|
|
GTGParser.java
|
637
(14 years ago)
by duarte:
Now skipping lines with <PRE> tags.
|
|
PsipredError.java
|
590
(14 years ago)
by duarte:
Added code to run psipred.
Fixed a few minor bugs.
|
|
PsipredRunner.java
|
590
(14 years ago)
by duarte:
Added code to run psipred.
Fixed a few minor bugs.
|
|
Sequence.java
|
711
(14 years ago)
by stehr:
added static method to print a ruler with sequence numbers
|
