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Revision 628 - Directory Listing
Modified Tue May 13 10:34:44 2008 UTC (11 years, 4 months 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 (11 years, 4 months ago) by duarte
Yet another format check
Revision 626 - Directory Listing
Modified Fri May 9 15:29:04 2008 UTC (11 years, 4 months ago) by duarte
Added one more file format check.
Revision 625 - Directory Listing
Modified Fri May 9 14:57:37 2008 UTC (11 years, 4 months 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 (11 years, 4 months 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 (11 years, 4 months 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 (11 years, 4 months 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 (11 years, 4 months 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 (11 years, 4 months 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 (11 years, 4 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 (11 years, 4 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 months ago) by stehr
added BlastUtils.writeClusterGraph(String[] templateIds, outFile)
Revision 583 - Directory Listing
Modified Tue Apr 8 13:02:28 2008 UTC (11 years, 5 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 (11 years, 5 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 (11 years, 5 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 (11 years, 5 months ago) by duarte
Added a main method for testing
Revision 577 - Directory Listing
Added Fri Apr 4 16:46:23 2008 UTC (11 years, 5 months ago) by duarte
New package sequence. Initial commit of classes to run blast and parse its output.