Revision
619 -
Directory Listing
Modified
Thu May 8 10:13:10 2008 UTC
(14 years, 1 month 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.
Revision
618 -
Directory Listing
Modified
Wed May 7 12:06:56 2008 UTC
(14 years, 1 month ago)
by
duarte
Initial commit of GTG parsing classes.
Added method in PdbasePdb to map observed residue sequence serials to internal (cif) residue serials
Revision
612 -
Directory Listing
Modified
Wed Apr 30 18:20:09 2008 UTC
(14 years, 1 month ago)
by
duarte
Now checking wheter read sequence contains spaces and throwing FastaFileFormatError
Revision
602 -
Directory Listing
Modified
Tue Apr 29 08:36:22 2008 UTC
(14 years, 1 month ago)
by
duarte
Moved method to writeSeqs to Sequence class.
Tidied up the help text in averageGraph
Revision
597 -
Directory Listing
Modified
Fri Apr 25 16:53:47 2008 UTC
(14 years, 2 months ago)
by
duarte
Fixed the fasta header regex to take only first token of header as sequence name (same behaviour as in Alignment class)
Revision
593 -
Directory Listing
Modified
Tue Apr 22 09:05:33 2008 UTC
(14 years, 2 months ago)
by
stehr
merged in some changes (now writing similarity matrix in blast utils)
Revision
590 -
Directory Listing
Modified
Fri Apr 11 14:43:53 2008 UTC
(14 years, 2 months ago)
by
duarte
Added code to run psipred.
Fixed a few minor bugs.
Revision
589 -
Directory Listing
Modified
Wed Apr 9 16:16:08 2008 UTC
(14 years, 2 months ago)
by
duarte
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
Revision
584 -
Directory Listing
Modified
Tue Apr 8 15:18:22 2008 UTC
(14 years, 2 months ago)
by
stehr
added BlastUtils.writeClusterGraph(String[] templateIds, outFile)
Revision
583 -
Directory Listing
Modified
Tue Apr 8 13:02:28 2008 UTC
(14 years, 2 months ago)
by
duarte
New methods to get the template ids and write them to file
Revision
581 -
Directory Listing
Modified
Tue Apr 8 11:00:45 2008 UTC
(14 years, 2 months ago)
by
stehr
Made printing hits with graphical overview the default using print() method. Print() takes no parameters, but BlastHitList.setQueryLength() has to be called once to set the length of the query. Introduced new printSome() function to output only the first n hits.
Revision
579 -
Directory Listing
Modified
Mon Apr 7 17:57:54 2008 UTC
(14 years, 2 months ago)
by
stehr
added class Sequence, added ascii-art output of blast hits to BlastHitList
Revision
578 -
Directory Listing
Modified
Mon Apr 7 15:57:24 2008 UTC
(14 years, 2 months ago)
by
duarte
Added a main method for testing
Revision
577 -
Directory Listing
Added
Fri Apr 4 16:46:23 2008 UTC
(14 years, 2 months ago)
by
duarte
New package sequence. Initial commit of classes to run blast and parse its output.