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Revision 1346 - Directory Listing
Modified Fri Mar 18 08:25:07 2011 UTC (9 years, 7 months ago) by jmduarteg
Now detecting type of sequence: protein/nucleotide
Revision 1340 - Directory Listing
Modified Sun Mar 13 17:44:18 2011 UTC (9 years, 7 months ago) by hstehr
Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta
Revision 1335 - Directory Listing
Modified Wed Mar 9 08:38:35 2011 UTC (9 years, 7 months ago) by jmduarteg
Now throwing InterruptedException. Refactor BlastErro to BlastException
Revision 1334 - Directory Listing
Modified Wed Mar 9 08:13:04 2011 UTC (9 years, 7 months ago) by jmduarteg
Refactoring xxxError to xxxException
Revision 1329 - Directory Listing
Modified Sat Mar 5 15:38:12 2011 UTC (9 years, 7 months ago) by jmduarteg
Important change: now the PDB file reader will try to read and fix the numbering of PDB files. Whenever the alignment is wrong it will realign and renumber using the jaligner package. The result of reading original PDB files now will be the same as that of reading CIF files, including proper mapping of classical PDB numbers to SEQRES residue serials (as in CIF). 
There is one change of behaviour in comparison to before: when no SEQRES present the sequence is taken to be that of ATOM lines instead of padding it with Xs.
Still in this version the re-alignment is not perfect as there are some times when ambiguities occur and they are not solved (e.g. in 2nwr where alignment in an unobserved loop can be at two possible places for a GLY). That is anyway a rather minor problem (coordinates are still fine, just the chain is not ordered correctly at 1 or 2 points) and rare (~1% of files)
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (9 years, 7 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1317 - Directory Listing
Modified Wed Feb 9 17:41:17 2011 UTC (9 years, 8 months ago) by jmduarteg
Catching if the server returns non-requested records and throwin IOException for it.
Revision 1310 - Directory Listing
Modified Mon Jan 31 16:49:11 2011 UTC (9 years, 8 months ago) by jmduarteg
Fixed bug: was not checking whether the uniprot japi was actually returning all requested records for ids given when using getMultipleEntries. Now checking, logging it and removing the not-found ids from the homolog list.
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (9 years, 9 months ago) by jmduarteg
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (9 years, 9 months ago) by jmduarteg
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
Revision 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (9 years, 9 months ago) by jmduarteg
Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
Revision 1300 - Directory Listing
Modified Wed Jan 12 10:22:15 2011 UTC (9 years, 9 months ago) by jmduarteg
Better docs
Revision 1298 - Directory Listing
Modified Tue Jan 11 14:35:17 2011 UTC (9 years, 9 months ago) by jmduarteg
Now storing the query coverage cutoff.
Revision 1285 - Directory Listing
Modified Thu Dec 2 11:03:18 2010 UTC (9 years, 10 months ago) by jmduarteg
Now throwing MatchNotFound exception instead of catching it.
Revision 1284 - Directory Listing
Modified Mon Nov 29 10:06:28 2010 UTC (9 years, 10 months ago) by cvehlow
Overrides removed
Revision 1273 - Directory Listing
Modified Thu Oct 28 13:56:03 2010 UTC (9 years, 11 months ago) by jmduarteg
Fixed buf: EMBL DB fetch returns sequences now in upper case, we were not converting properly to lower case in one place, now should be fixed.
Revision 1267 - Directory Listing
Modified Thu Oct 21 16:26:54 2010 UTC (10 years ago) by jmduarteg
Now possible to not retrieve any CDS data
Revision 1260 - Directory Listing
Modified Fri Oct 8 15:00:58 2010 UTC (10 years ago) by jmduarteg
Using the new UniprotVerMismatchException instead of IOException
Revision 1259 - Directory Listing
Modified Fri Oct 8 13:45:56 2010 UTC (10 years ago) by jmduarteg
New exception for mismatching uniprot versions
Revision 1253 - Directory Listing
Modified Wed Oct 6 17:01:19 2010 UTC (10 years ago) by jmduarteg
Some minor updates
Revision 1172 - Directory Listing
Modified Wed Aug 4 15:26:03 2010 UTC (10 years, 2 months ago) by jmduarteg
Now using apache commons logging
Revision 1168 - Directory Listing
Modified Mon Aug 2 16:47:37 2010 UTC (10 years, 2 months ago) by jmduarteg
Now catching the case when the best translation contains stop codons. This is usually due to a wrong genetic code, but for the moment it's still very difficult to know the genetic code from encoding organelle+organism taxonomy, so this is the temporary solution.
Revision 1166 - Directory Listing
Modified Fri Jul 30 14:58:26 2010 UTC (10 years, 2 months ago) by jmduarteg
Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)
Revision 1164 - Directory Listing
Modified Fri Jul 30 09:56:39 2010 UTC (10 years, 2 months ago) by jmduarteg
Now returning null for the representative CDS when the gene encoding organelle is not nucleus/plasmid. Before the whole program would stop, which wasn't ideal. Eventually we will need to use the proper genetic code when needed.
Revision 1162 - Directory Listing
Modified Wed Jul 28 09:15:19 2010 UTC (10 years, 3 months ago) by jmduarteg
Allowing plasmids as gene encoding organelles without having to treat them especially as they don't have a different genetic code.
Revision 1159 - Directory Listing
Modified Fri Jul 23 14:56:35 2010 UTC (10 years, 3 months ago) by jmduarteg
Reverting change made in last revision. It intended to fix a bug for a particular test case (don't know anymore which one!) but it actually broke most other cases.
Revision 1157 - Directory Listing
Modified Wed Jul 7 15:31:14 2010 UTC (10 years, 3 months ago) by jmduarteg
Fixed bug, wasn't computing the nucleotide alignment correctly (was missing the last codon)
Revision 1155 - Directory Listing
Modified Wed Jul 7 13:15:06 2010 UTC (10 years, 3 months ago) by jmduarteg
Implemented a simple skimming strategy. Put back some debug level logging to info level, logging aint' easy!
Revision 1154 - Directory Listing
Modified Wed Jul 7 10:39:28 2010 UTC (10 years, 3 months ago) by jmduarteg
And all other amiguous codons
Revision 1153 - Directory Listing
Modified Wed Jul 7 08:46:37 2010 UTC (10 years, 3 months ago) by jmduarteg
Another ambiguous nucleotide letter
Revision 1151 - Directory Listing
Modified Tue Jul 6 16:58:04 2010 UTC (10 years, 3 months ago) by jmduarteg
Fixed bug: was null pointing with null cache file (which is a valid value)
Revision 1149 - Directory Listing
Modified Mon Jul 5 16:46:57 2010 UTC (10 years, 3 months ago) by jmduarteg
Changed level of some logging messages

Revision 1148 - Directory Listing
Modified Mon Jul 5 16:16:44 2010 UTC (10 years, 3 months ago) by jmduarteg
New removeRedundancy method
Revision 1147 - Directory Listing
Modified Mon Jul 5 08:35:15 2010 UTC (10 years, 3 months ago) by jmduarteg
Implemented logging with log4j library
Revision 1146 - Directory Listing
Modified Fri Jul 2 09:54:46 2010 UTC (10 years, 3 months ago) by jmduarteg
Now can write sequences with or without query
Revision 1145 - Directory Listing
Modified Thu Jul 1 16:05:26 2010 UTC (10 years, 3 months ago) by jmduarteg
Now can filter also on query coverage
Revision 1144 - Directory Listing
Modified Thu Jul 1 10:09:55 2010 UTC (10 years, 3 months ago) by jmduarteg
Changed the order of checks in isReferenceSeqPositionReliable
Revision 1143 - Directory Listing
Modified Thu Jul 1 10:02:53 2010 UTC (10 years, 3 months ago) by jmduarteg
New methods to check for reliability of positions with respect of the CDS matching
Revision 1142 - Directory Listing
Modified Wed Jun 30 09:55:27 2010 UTC (10 years, 3 months ago) by jmduarteg
Now nucleotide alignment contains reference sequence as well. Moved entropy and kaks calc methods to UniprotHomologList.
Revision 1140 - Directory Listing
Modified Tue Jun 29 08:49:34 2010 UTC (10 years, 3 months ago) by jmduarteg
Fixed bug: now nucleotide alignment is in same order as protein alignment
Revision 1139 - Directory Listing
Modified Mon Jun 28 17:44:19 2010 UTC (10 years, 3 months ago) by jmduarteg
Fixed bug: when retrieving (or reading from cache) embl cds sequences and embl dbfetch doesn't have a certain identifier, then we were adding nulls to the list of emblcds sequences of the UniprotHomologList (resulting in a null pointer down the line)
Revision 1137 - Directory Listing
Modified Mon Jun 28 13:38:32 2010 UTC (10 years, 4 months ago) by jmduarteg
Now checking the sequence identity of the representative CDS to be above a minimum value.
Revision 1136 - Directory Listing
Modified Mon Jun 28 12:49:31 2010 UTC (10 years, 4 months ago) by jmduarteg
New ambiguous nucleotide w.
Revision 1133 - Directory Listing
Modified Fri Jun 25 13:36:03 2010 UTC (10 years, 4 months ago) by jmduarteg
Fixed bug: getNucleotideAlignment was nullpointing when encountering a null return from getRepresentativeCDS() (which happens whenever there is no representative CDS for the particular UniprotEntry). Now checking for nulls before using the homolog in the alignment.
Revision 1132 - Directory Listing
Modified Fri Jun 25 13:01:53 2010 UTC (10 years, 4 months ago) by jmduarteg
New SelectonRunner class. More taxonomy information retrieved from uniprot.
Revision 1126 - Directory Listing
Modified Tue Jun 22 12:19:07 2010 UTC (10 years, 4 months ago) by jmduarteg
New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.
Revision 1123 - Directory Listing
Modified Mon Jun 21 12:50:54 2010 UTC (10 years, 4 months ago) by jmduarteg
Improved the selection of representative CDS
Revision 1122 - Directory Listing
Modified Mon Jun 21 10:48:05 2010 UTC (10 years, 4 months ago) by jmduarteg
Some refactoring
Revision 1121 - Directory Listing
Modified Fri Jun 18 16:02:55 2010 UTC (10 years, 4 months ago) by jmduarteg
Now implementing HasFeatures
Revision 1120 - Directory Listing
Modified Fri Jun 18 13:29:34 2010 UTC (10 years, 4 months ago) by jmduarteg
New class UniprotEntry. Things make a lot more sense now...
Revision 1119 - Directory Listing
Modified Fri Jun 18 11:55:46 2010 UTC (10 years, 4 months ago) by jmduarteg
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
Revision 1117 - Directory Listing
Modified Thu Jun 17 09:52:30 2010 UTC (10 years, 4 months ago) by jmduarteg
Now checking codon length before translating
Revision 1116 - Directory Listing
Modified Thu Jun 17 09:48:22 2010 UTC (10 years, 4 months 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, 4 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, 4 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, 4 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, 4 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, 4 months ago) by jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision 1098 - Directory Listing
Modified Tue Jun 8 09:10:32 2010 UTC (10 years, 4 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, 4 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, 4 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, 4 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, 4 months ago) by jmduarteg
Some new methods
Revision 1081 - Directory Listing
Modified Fri May 28 14:51:46 2010 UTC (10 years, 5 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, 5 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, 5 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, 5 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, 5 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, 6 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, 6 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, 6 months ago) by jmduarteg
Minor fix to java docs
Revision 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (10 years, 6 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, 6 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, 6 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, 6 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (10 years, 6 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, 6 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, 6 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, 8 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, 2 months 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, 2 months 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, 11 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, 11 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, 11 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, 11 months ago) by filippis
Original Path: trunk/sequence
white TO talyn
Revision 763 - Directory Listing
Modified Thu Sep 25 15:19:45 2008 UTC (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month ago) by duarte
Original Path: trunk/sequence
New method getAlignmentWithTemplateIDtag
Revision 752 - Directory Listing
Modified Wed Sep 17 13:44:30 2008 UTC (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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, 2 months 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, 3 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 (12 years, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 months ago) by duarte
Original Path: trunk/sequence
New package sequence. Initial commit of classes to run blast and parse its output.