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Revision 1117 - Directory Listing
Modified Thu Jun 17 09:52:30 2010 UTC (10 years, 1 month ago) by jmduarteg
Now checking codon length before translating
Revision 1116 - Directory Listing
Modified Thu Jun 17 09:48:22 2010 UTC (10 years, 1 month ago) by jmduarteg
Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.
Revision 1114 - Directory Listing
Modified Wed Jun 16 10:26:22 2010 UTC (10 years, 2 months ago) by jmduarteg
New feature: code for dna to protein translation
Revision 1112 - Directory Listing
Modified Tue Jun 15 08:44:52 2010 UTC (10 years, 2 months ago) by jmduarteg
Now getting also gene encoding organelle from uniprot api
Revision 1106 - Directory Listing
Modified Thu Jun 10 09:24:30 2010 UTC (10 years, 2 months ago) by jmduarteg
Implemented caching of blast in UniprotHomologList
Revision 1104 - Directory Listing
Modified Wed Jun 9 17:04:36 2010 UTC (10 years, 2 months ago) by jmduarteg
Now reading uniprot version from reldate.txt and checking against the uniprot api version
Revision 1103 - Directory Listing
Modified Wed Jun 9 16:11:18 2010 UTC (10 years, 2 months ago) by jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision 1098 - Directory Listing
Modified Tue Jun 8 09:10:32 2010 UTC (10 years, 2 months ago) by jmduarteg
Fixed bug: was nullpointing at retrieveUniprotKBData because of a single uniprot id can have multiple blast hits and was using the uni ids as unique identifiers => the lookup map was failing. Now the lookup map is from uniIds to lists of homologs(hits)
Revision 1097 - Directory Listing
Modified Mon Jun 7 10:17:58 2010 UTC (10 years, 2 months ago) by jmduarteg
Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.
Revision 1095 - Directory Listing
Modified Wed Jun 2 15:06:46 2010 UTC (10 years, 2 months ago) by jmduarteg
Fixed bug: was nullpointing when the letter encountered in counting the column was unknown.
Revision 1094 - Directory Listing
Modified Wed Jun 2 13:19:21 2010 UTC (10 years, 2 months ago) by jmduarteg
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (10 years, 2 months ago) by jmduarteg
Some new methods
Revision 1081 - Directory Listing
Modified Fri May 28 14:51:46 2010 UTC (10 years, 2 months ago) by jmduarteg
Fixed bug with '-' embl cds identifiers.
Revision 1074 - Directory Listing
Modified Fri May 21 10:02:24 2010 UTC (10 years, 2 months ago) by jmduarteg
Implemented profile counting and entropy calculation for alignment.
Revision 1073 - Directory Listing
Modified Thu May 20 15:21:10 2010 UTC (10 years, 2 months ago) by jmduarteg
Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()
Revision 1072 - Directory Listing
Modified Thu May 20 13:59:25 2010 UTC (10 years, 2 months ago) by jmduarteg
Implemented methods to run a tcoffee alignment. Now also retrieving uniprot sequences via the uniprot api.
Revision 1069 - Directory Listing
Modified Tue May 18 14:53:34 2010 UTC (10 years, 2 months ago) by jmduarteg
New methods to retrieve uniprot data and embl cds for a single homolog
Revision 1055 - Directory Listing
Modified Wed Apr 28 15:08:53 2010 UTC (10 years, 3 months ago) by jmduarteg
Removed code left over from debugging.
Revision 1054 - Directory Listing
Modified Wed Apr 28 13:37:00 2010 UTC (10 years, 3 months ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1051 - Directory Listing
Modified Tue Apr 27 15:34:38 2010 UTC (10 years, 3 months ago) by jmduarteg
Minor fix to java docs
Revision 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (10 years, 3 months ago) by hstehr
removing @Override annotations which were causing compilation errors for me
Revision 1048 - Directory Listing
Modified Tue Apr 27 08:24:18 2010 UTC (10 years, 3 months ago) by jmduarteg
New classes UniprotHomolog and UniprotHomologList to contain a set of homologs of a given sequence, including the blast hit data, embl cds coding sequences etc.
Revision 1045 - Directory Listing
Modified Mon Apr 26 12:55:28 2010 UTC (10 years, 3 months ago) by jmduarteg
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (10 years, 4 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (10 years, 4 months ago) by hstehr
refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (10 years, 4 months ago) by hstehr
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (10 years, 4 months ago) by hstehr
Copied from: trunk/src/sequence revision 1002
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 951 - Directory Listing
Modified Fri Jan 29 16:12:34 2010 UTC (10 years, 6 months ago) by duarte
Original Path: trunk/src/sequence
Copied from: trunk/sequence revision 949
Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
Revision 883 - Directory Listing
Modified Tue Aug 11 14:37:16 2009 UTC (11 years ago) by stehr
Original Path: trunk/sequence
some cosmetic changes
Revision 876 - Directory Listing
Modified Fri Aug 7 13:35:42 2009 UTC (11 years ago) by stehr
Original Path: trunk/sequence
New methods for writing sequence in Fasta format
Revision 806 - Directory Listing
Modified Thu Nov 20 14:29:04 2008 UTC (11 years, 8 months ago) by duarte
Original Path: trunk/sequence
New method contains().
Revision 801 - Directory Listing
Modified Mon Nov 17 13:40:10 2008 UTC (11 years, 8 months ago) by duarte
Original Path: trunk/sequence
Fixed bug: was not doing correctly the sanity checks in getAlignmentFullSeqs
Revision 791 - Directory Listing
Modified Mon Nov 3 15:44:41 2008 UTC (11 years, 9 months ago) by filippis
Original Path: trunk/sequence
white TO talyn
Revision 788 - Directory Listing
Modified Mon Nov 3 15:13:59 2008 UTC (11 years, 9 months ago) by filippis
Original Path: trunk/sequence
white TO talyn
Revision 763 - Directory Listing
Modified Thu Sep 25 15:19:45 2008 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/sequence
New method in BlastHit to transform the BlastHit local alignment into one that contains the full sequences of subject and query.
Revision 760 - Directory Listing
Modified Wed Sep 24 18:18:53 2008 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/sequence
Rewrote the secondary structure handling in Alignment. Also changed first parameter in writeFasta to be a PrintStream not an OutputStream
Revision 756 - Directory Listing
Modified Tue Sep 23 18:07:25 2008 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/sequence
New static method in BlastHit to get subjectId from templateId
New member source in TemplateList
Revision 755 - Directory Listing
Modified Tue Sep 23 15:00:46 2008 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/sequence
New method getAlignmentWithTemplateIDtag
Revision 752 - Directory Listing
Modified Wed Sep 17 13:44:30 2008 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/sequence
BlastHitList: new method getHit(subjectId), a new lookup HastMap member added for that.
TemplateList: new method get(i)
Sequence: new convenience method writeToFastaFile
Revision 751 - Directory Listing
Modified Tue Sep 16 16:35:34 2008 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/sequence
Now cleaning up correctly paul temp files
Now closing tcoffee's log properly

Revision 750 - Directory Listing
Modified Tue Sep 16 13:15:25 2008 UTC (11 years, 10 months ago) by duarte
Original Path: trunk/sequence
Now we can run blast with multi threads option
Revision 748 - Directory Listing
Modified Sun Sep 14 21:47:56 2008 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/sequence
Initial commit, tcoffee runner for sequence to profile alignment
Revision 745 - Directory Listing
Modified Thu Sep 11 12:57:10 2008 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/sequence
Now BlastHit printing works correctly for query identifier strings of any length
Revision 744 - Directory Listing
Modified Thu Sep 11 11:09:27 2008 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/sequence
Using the new XML parser in TemplateSelection.
New method getQueryCoverage in BlastHit
Revision 743 - Directory Listing
Modified Thu Sep 11 10:06:22 2008 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/sequence
New tests package (should be a folder and under it packages, but for now we can't do that until we move all source code to a src folder).
Moved all existing tests to appropiate tests packages.
New test PdbParsersTest: does cif against pdbase at the moment.
Adde equals method to SecStrucElement
Added some getters to Pdb

Revision 742 - Directory Listing
Modified Wed Sep 10 17:23:37 2008 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/sequence
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.
Revision 741 - Directory Listing
Modified Tue Sep 9 10:47:21 2008 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/sequence
Created getters for missing fields in BlastHit. 
New method removeAll in TemplateList.
Revision 711 - Directory Listing
Modified Thu Jul 31 09:47:58 2008 UTC (12 years 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 (12 years, 1 month 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 (12 years, 2 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 3 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 months ago) by duarte
Original Path: trunk/sequence
New package sequence. Initial commit of classes to run blast and parse its output.