2018-06-20 |
hansonr | JAL-3032 for (var var |
tree | commitdiff |
2018-05-15 |
gmungoc | JAL-1264 exclude score-only from 'Add Reference Annotat... |
tree | commitdiff |
2018-05-07 |
gmungoc | JAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject |
tree | commitdiff |
2018-05-07 |
gmungoc | JAL-1767 save PCA D and E vectors instead of 'details... |
tree | commitdiff |
2018-05-04 |
gmungoc | JAL-1767 refactorings to enable faithful restore of... |
tree | commitdiff |
2018-04-27 |
gmungoc | JAL-1767 refactoring and tidying of RotatableCanvas... |
tree | commitdiff |
2018-04-26 |
gmungoc | JAL-2962 remove Change Parameters menu from PCA panel |
tree | commitdiff |
2018-04-26 |
gmungoc | JAL-2962 code tidying/documentation (non-functional... |
tree | commitdiff |
2018-04-25 |
gmungoc | JAL-1767 minor field tidying prior to functional changes |
tree | commitdiff |
2018-04-16 |
gmungoc | JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... |
tree | commitdiff |
2018-03-30 |
gmungoc | JAL-2939 simplified way of getting hmm consensus residue |
tree | commitdiff |
2018-03-26 |
gmungoc | JAL-2939 always store Information profile |
tree | commitdiff |
2018-03-20 |
gmungoc | JAL-2629 InformationThread.findOrCreateAnnotation and... |
tree | commitdiff |
2018-03-19 |
gmungoc | JAL-2620 parse genetic code tables from standard file... |
tree | commitdiff |
2018-03-16 |
gmungoc | JAL-2620 alternative genetic code translation tables |
tree | commitdiff |
2018-03-16 |
gmungoc | Merge branch 'develop' into trialMerge |
tree | commitdiff |
2018-03-14 |
gmungoc | JAL-2933 pass viewport in Finder constructor, find... bug/JAL-2839findWithHidden |
tree | commitdiff |
2018-03-14 |
gmungoc | JAL-2933 gui and applet Finder hold a FinderI per viewport |
tree | commitdiff |
2018-03-14 |
gmungoc | JAL-2839 refactored out getNextVisibleSequenceRegion |
tree | commitdiff |
2018-03-13 |
gmungoc | JAL-2839 refactored analysis.Finder and tests |
tree | commitdiff |
2018-03-09 |
gmungoc | JAL-2839 Finder refactoring prior to fixing the defect |
tree | commitdiff |
2018-03-07 |
Jim Procter | Merge branch 'releases/Release_2_10_4_Branch' into... |
tree | commitdiff |
2018-03-07 |
gmungoc | JAL-2629 storage and lifecycle of alignment/group HMM... |
tree | commitdiff |
2018-02-28 |
gmungoc | JAL-2629 some tidying of Hmmer commands (wip) |
tree | commitdiff |
2018-02-27 |
Jim Procter | Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104 |
tree | commitdiff |
2018-02-23 |
gmungoc | JAL-2599 parser and datamodel use primitive double... |
tree | commitdiff |
2018-02-22 |
gmungoc | JAL-2629 tidy unit tests, constants etc |
tree | commitdiff |
2018-02-20 |
gmungoc | Merge branch 'develop' into features/mchmmer |
tree | commitdiff |
2018-02-09 |
gmungoc | JAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666 |
tree | commitdiff |
2018-02-09 |
gmungoc | JAL-2789 code format changes only (before functional... |
tree | commitdiff |
2018-02-05 |
gmungoc | JAL-2897 more informative description on synonymous... |
tree | commitdiff |
2018-02-05 |
gmungoc | Merge branch 'spikes/mungo' into trialMerge |
tree | commitdiff |
2018-02-05 |
gmungoc | JAL-2897 more informative description on synonymous... |
tree | commitdiff |
2018-01-30 |
gmungoc | JAL-1793 update spike build to latest incl stop and... |
tree | commitdiff |
2018-01-30 |
gmungoc | JAL-2898 show 'stop_gained' variants on peptide sequences |
tree | commitdiff |
2018-01-30 |
gmungoc | JAL-2897 generate peptide variants for synonymous codon... |
tree | commitdiff |
2018-01-30 |
gmungoc | JAL-2897 formatting change only prior to functional... |
tree | commitdiff |
2017-11-08 |
kiramt | Merge branch 'develop' into feature/JAL-2759 |
tree | commitdiff |
2017-10-27 |
gmungoc | JAL-1793 spike branch updated to latest |
tree | commitdiff |
2017-10-27 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF |
tree | commitdiff |
2017-10-26 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF |
tree | commitdiff |
2017-10-26 |
Jim Procter | Merge branch 'features/JAL-2685pairwiseSeqLimits' into... |
tree | commitdiff |
2017-10-05 |
gmungoc | JAL-2738 update spikes/mungo |
tree | commitdiff |
2017-10-05 |
gmungoc | JAL-2755 transfer chromosomal reference from transcript... |
tree | commitdiff |
2017-10-04 |
gmungoc | JAL-2738 match consequence "Allele" to VCF allele;... |
tree | commitdiff |
2017-10-03 |
kiramt | JAL-2674 testing |
tree | commitdiff |
2017-10-03 |
gmungoc | JAL-2738 copy to spikes/mungo |
tree | commitdiff |
2017-09-29 |
kiramt | JAL-2674 finish with iterators for now |
tree | commitdiff |
2017-09-28 |
kiramt | JAL-2647 more iterators |
tree | commitdiff |
2017-09-26 |
gmungoc | JAL-2738 JAL-2154 add DBRef from transcript to synthesi... |
tree | commitdiff |
2017-09-25 |
gmungoc | JAL-2738 one constant in codebase for "alleles" attribu... |
tree | commitdiff |
2017-09-21 |
gmungoc | JAL-2738 compute VCF on peptide, extract AF (allele... |
tree | commitdiff |
2017-09-04 |
gmungoc | JAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon |
tree | commitdiff |
2017-09-01 |
gmungoc | JAL-2617 omit stop codon from synthesized CDS sequence |
tree | commitdiff |
2017-08-30 |
gmungoc | JAL-2685 tweaks to output spacing, updated TestAlignSeq... |
tree | commitdiff |
2017-08-30 |
gmungoc | JAL-2685 use actual selection for report of pairwise... |
tree | commitdiff |
2017-08-28 |
tzvanaalten | JAL-2629 add option to set HMM Logo letter height to... |
tree | commitdiff |
2017-08-25 |
TZVanaalten | JAL-2629 hmm annotation consensus characters are now... |
tree | commitdiff |
2017-08-21 |
gmungoc | Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList |
tree | commitdiff |
2017-08-18 |
TZVanaalten | Merge branch 'develop' into features/hmmer |
tree | commitdiff |
2017-08-18 |
TZVanaalten | JAL-2668 add tests for HMMER commands, annotation and io |
tree | commitdiff |
2017-08-17 |
TZVanaalten | JAL-2629 add documentation to previous work |
tree | commitdiff |
2017-08-16 |
Jim Procter | JAL-2418 add GPL to main sources |
tree | commitdiff |
2017-08-16 |
Jim Procter | JAL-2418 source formatting |
tree | commitdiff |
2017-08-16 |
TZVanaalten | JAL-2599 HMM annotation now shows consensus characters... |
tree | commitdiff |
2017-08-16 |
TZVanaalten | JAL-2599 fix background frequency storage and correct... |
tree | commitdiff |
2017-08-10 |
TZVanaalten | JAL-2629 hmmalign now correctly creates a new frame |
tree | commitdiff |
2017-08-02 |
TZVanaalten | JAL-2599 fix for HMM logo not normalising correctly |
tree | commitdiff |
2017-08-02 |
TZVanaalten | JAL-2599 fix for information annotation buttons |
tree | commitdiff |
2017-07-27 |
TZVanaalten | JAL-2629 moved HMM storage location to placeholder... |
tree | commitdiff |
2017-07-20 |
TZVanaalten | JAL-2599 add ability to process RNA HMMer files |
tree | commitdiff |
2017-07-18 |
TZVanaalten | JAL-2599 complete documentation for HMM and HMMFile... |
tree | commitdiff |
2017-07-14 |
TZVanaalten | add partial button fix to annotation and statistics... features/hmmer_statistics |
tree | commitdiff |
2017-07-12 |
TZVanaalten | test HMM annotaTION |
tree | commitdiff |
2017-07-11 |
TZVanaalten | complete Information Content annotation |
tree | commitdiff |
2017-06-14 |
gmungoc | JAL-2598 Sequence.getSequence return a copy of the... |
tree | commitdiff |
2017-06-09 |
gmungoc | JAL-2446 merged to spike branch |
tree | commitdiff |
2017-06-01 |
gmungoc | JAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn |
tree | commitdiff |
2017-05-31 |
gmungoc | JAL-2574 preparation for Sequence.findFeatures(col1... |
tree | commitdiff |
2017-05-25 |
gmungoc | JAL-2557 removal of Sequence.sequenceFeatures |
tree | commitdiff |
2017-05-25 |
gmungoc | JAL-2050 make SequenceFeature.score final, adjust const... |
tree | commitdiff |
2017-05-23 |
gmungoc | JAL-2490 find features for export as GFF, JAL-2548... |
tree | commitdiff |
2017-05-22 |
gmungoc | JAL-2544 check feature overlaps selection region |
tree | commitdiff |
2017-05-19 |
gmungoc | JAL-2544 only include features in selected columns... |
tree | commitdiff |
2017-05-19 |
gmungoc | JAL-2490 performant lookup of features for sorting |
tree | commitdiff |
2017-05-19 |
gmungoc | JAL-2505 unit test for sort by feature density, Javadoc |
tree | commitdiff |
2017-05-18 |
gmungoc | JAL-2490 initial unit tests prior to refactoring |
tree | commitdiff |
2017-05-16 |
gmungoc | JAL-2505 refactored method removed |
tree | commitdiff |
2017-05-16 |
gmungoc | Merge branch 'develop' into features/JAL-2446NCList |
tree | commitdiff |
2017-05-16 |
gmungoc | JAL-2505 set helix number as feature group in SequenceF... |
tree | commitdiff |
2017-05-16 |
gmungoc | JAL-2403 simplify instantiation / configuration of... |
tree | commitdiff |
2017-05-15 |
gmungoc | JAL-2480 redundant code removed |
tree | commitdiff |
2017-05-12 |
gmungoc | JAL-2525 get sequence features for Ontology term(s... |
tree | commitdiff |
2017-05-09 |
gmungoc | JAL-2505 use constructors to set (what will be) final... |
tree | commitdiff |
2017-05-04 |
Jim Procter | Merge branch 'features/JAL-2393customMatrices' into... |
tree | commitdiff |
2017-05-04 |
Jim Procter | Merge branch 'features/JAL-2393customMatrices' into... |
tree | commitdiff |
2017-05-03 |
Jim Procter | JAL-1933 show occupancy in tooltip for row |
tree | commitdiff |
2017-05-02 |
gmungoc | JAL-2499 JAL-2403 push 'configure for view' inside... |
tree | commitdiff |
2017-04-28 |
gmungoc | Merge branch 'develop' into features/JAL-2393customMatrices |
tree | commitdiff |
2017-04-27 |
Jim Procter | JAL-1933 shade occupancy from light grey to black for... |
tree | commitdiff |
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