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Revision 731 - Directory Listing
Modified Wed Aug 27 13:39:11 2008 UTC (11 years ago) by duarte
Tagging ver 1.1.0 for CMView 1.1.0. Now using jung beta1 jars.
Revision 711 - Directory Listing
Modified Thu Jul 31 09:47:58 2008 UTC (11 years, 1 month ago) by stehr
Original Path: trunk/sequence
added static method to print a ruler with sequence numbers
Revision 699 - Directory Listing
Modified Wed Jul 16 08:38:19 2008 UTC (11 years, 2 months ago) by duarte
Original Path: trunk/sequence
Fixed bug: now Sequence class considers '.' to be part of the fasta headers (in agreement with what we do in Alignment class). The 2 FASTAHEADER_REGEXes should be always kept in sync.
Revision 651 - Directory Listing
Modified Wed May 21 18:11:02 2008 UTC (11 years, 3 months ago) by duarte
Original Path: trunk/sequence
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.
Revision 642 - Directory Listing
Modified Fri May 16 17:08:04 2008 UTC (11 years, 4 months ago) by duarte
Original Path: trunk/sequence
Fixed bug: writeClusterGraph shouldn't try to do anything if there's only one template.
Revision 638 - Directory Listing
Modified Thu May 15 14:54:42 2008 UTC (11 years, 4 months ago) by stehr
Original Path: trunk/sequence
added automatic conversion of matrix file to ps visualization (using script plot_simmatrix.sh)
Revision 637 - Directory Listing
Modified Thu May 15 14:26:22 2008 UTC (11 years, 4 months ago) by duarte
Original Path: trunk/sequence
Now skipping lines with <PRE> tags.
Revision 635 - Directory Listing
Modified Thu May 15 08:44:59 2008 UTC (11 years, 4 months ago) by duarte
Original Path: trunk/sequence
Changed default gravity value and default IDENTITY_SCORE for similarity graph
Revision 634 - Directory Listing
Modified Wed May 14 14:46:38 2008 UTC (11 years, 4 months ago) by duarte
Original Path: trunk/sequence
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 (11 years, 4 months ago) by stehr
Original Path: trunk/sequence
put test code for writeClusterGraph in main method of BlastUtils
Revision 628 - Directory Listing
Modified Tue May 13 10:34:44 2008 UTC (11 years, 4 months ago) by duarte
Original Path: trunk/sequence
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
Original Path: trunk/sequence
Yet another format check
Revision 626 - Directory Listing
Modified Fri May 9 15:29:04 2008 UTC (11 years, 4 months ago) by duarte
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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, 4 months ago) by stehr
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
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
Original Path: trunk/sequence
New package sequence. Initial commit of classes to run blast and parse its output.