Revision
634 -
Directory Listing
Modified
Wed May 14 14:46:38 2008 UTC
(14 years, 1 month 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.
Revision
633 -
Directory Listing
Modified
Wed May 14 12:08:52 2008 UTC
(14 years, 1 month ago)
by
stehr
put test code for writeClusterGraph in main method of BlastUtils
Revision
628 -
Directory Listing
Modified
Tue May 13 10:34:44 2008 UTC
(14 years, 1 month ago)
by
duarte
Now writeClusterGraph uses rmsd for similarity measure instead of GDT (maxcluster was failing almost always with GDT)
Revision
627 -
Directory Listing
Modified
Fri May 9 16:02:01 2008 UTC
(14 years, 1 month ago)
by
duarte
Yet another format check
Revision
626 -
Directory Listing
Modified
Fri May 9 15:29:04 2008 UTC
(14 years, 1 month ago)
by
duarte
Added one more file format check.
Revision
625 -
Directory Listing
Modified
Fri May 9 14:57:37 2008 UTC
(14 years, 1 month ago)
by
duarte
Fixed bug: wasn't catching wrong format in GTG output
Revision
623 -
Directory Listing
Modified
Fri May 9 14:10:27 2008 UTC
(14 years, 1 month 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)
Revision
622 -
Directory Listing
Modified
Fri May 9 12:56:27 2008 UTC
(14 years, 1 month ago)
by
duarte
Added code to be able to filter out template ids (pdb codes) by maximum release date.
Some improvements in Hit classes.
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, 2 months 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.