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jalview.git
2016-04-25 gmungocJAL-1812 JAL-2068 only allow one Groovy console open... commit | commitdiff | tree | snapshot
2016-04-24 Jim ProcterJAL-1551 JAL-2077 formatting commit | commitdiff | tree | snapshot
2016-04-24 Jim ProcterJAL-2077 - reinstate popups on osx commit | commitdiff | tree | snapshot
2016-04-24 Jim ProcterMerge branch 'JAL-2075_features_hiddeng' into develop commit | commitdiff | tree | snapshot
2016-04-24 Jim ProcterJAL-2075 test showing hidden columns bug in feature... commit | commitdiff | tree | snapshot
2016-04-24 Jim ProcterJAL-2075 refactor FeatureScoreModel to native testNG... commit | commitdiff | tree | snapshot
2016-04-24 Jim ProcterJAL-2075 make GroovyConsole a singleton so tests requir... commit | commitdiff | tree | snapshot
2016-04-23 Jim ProcterJAL-2075 fix: use AlignmentView.getVisibleContigs and... commit | commitdiff | tree | snapshot
2016-04-23 Jim ProcterJAL-2075 findPosition for SeqCigar (with test) commit | commitdiff | tree | snapshot
2016-04-23 Jim ProcterJAL-2075 formatting commit | commitdiff | tree | snapshot
2016-04-22 gmungocJAL-1812 JAL-2068 add Run Groovy Script to AlignFrame... commit | commitdiff | tree | snapshot
2016-04-22 gmungocJAL-2068 code and test for case of minValue == maxValue commit | commitdiff | tree | snapshot
2016-04-22 gmungocJAL-2068 framework and example scripts for pluggable... commit | commitdiff | tree | snapshot
2016-04-22 gmungocJAL-2068 Javadoc added commit | commitdiff | tree | snapshot
2016-04-22 gmungocJAL-2068 redundant implements clauses removed commit | commitdiff | tree | snapshot
2016-04-22 gmungocJAL-2068 convenience helper method for graduated score... commit | commitdiff | tree | snapshot
2016-04-21 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-04-20 Jim ProcterMerge branch 'groovy/JAL-2074_upgradeto2.4.4' into... commit | commitdiff | tree | snapshot
2016-04-20 Jim ProcterJAL-2074 updated URLs and removed 'how to get groovy... commit | commitdiff | tree | snapshot
2016-04-20 Jim ProcterJAL-2074 updated groovy-all to 2.4.6-indy commit | commitdiff | tree | snapshot
2016-04-20 Jim Procterfix for JAL-2072 commit | commitdiff | tree | snapshot
2016-04-18 gmungocJAL-2067 fixed broken link commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-2041 clinical_significance shown on sequence featur... commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-1421 typed map / lists, explicit imports, method... commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-2049 small refactor of constructors to avoid code... commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-1421 type parameter added to some collections commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer... commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-1705 refactored/utility methods to detect e.g.... commit | commitdiff | tree | snapshot
2016-04-14 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-653 test updated for 'use ID for description' commit | commitdiff | tree | snapshot
2016-04-14 gmungocJAL-1270 JAL-653 use 'parse immediately' FeaturesFile... commit | commitdiff | tree | snapshot
2016-04-14 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-14 tcofoegbuJAL-1994 Removed redistributed plugin.jar from applet... commit | commitdiff | tree | snapshot
2016-04-13 Jim ProcterJAL-2046 fix: patched SeqsetUtils so sequence features... commit | commitdiff | tree | snapshot
2016-04-13 Jim ProcterJAL-2046 test to demonstrate feature duplication bug commit | commitdiff | tree | snapshot
2016-04-13 Jim ProcterMerge branch 'bug/JAL-2046_ds_sharing_features_broken... commit | commitdiff | tree | snapshot
2016-04-13 tcofoegbuJAL-1270 more fix for failing Functional test commit | commitdiff | tree | snapshot
2016-04-13 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-13 tcofoegbuJAL-1270 Fixed failing tests due to race conditions... commit | commitdiff | tree | snapshot
2016-04-13 tcofoegbuJAL-2047 delay to allow table model initilisation to... commit | commitdiff | tree | snapshot
2016-04-12 gmungocJAL-2050 only hide introns if exons are present! Remove... commit | commitdiff | tree | snapshot
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ... commit | commitdiff | tree | snapshot
2016-04-11 gmungocJAL-1705 code/comment tidy only commit | commitdiff | tree | snapshot
2016-04-11 gmungocJAL-2051 fetch Ensembl Gene accessions one at a time commit | commitdiff | tree | snapshot
2016-04-11 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl... commit | commitdiff | tree | snapshot
2016-04-11 gmungocJAL-391 help for reverse / complement options commit | commitdiff | tree | snapshot
2016-04-11 gmungocJAL-1705 (new preference option to) hide introns when... commit | commitdiff | tree | snapshot
2016-04-11 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-11 tcofoegbuRestored auto-deleted file from commit: ad54c1ae5bc1b93... commit | commitdiff | tree | snapshot
2016-04-08 Jim ProcterMerge branch 'feature/JAL-2050_intronhidden' into develop commit | commitdiff | tree | snapshot
2016-04-08 Jim ProcterJAL-2050 JAL-1722 new getSelectedRange() method to... commit | commitdiff | tree | snapshot
2016-04-08 Jim ProcterJAL-2053 fix erratic hidden column marker display commit | commitdiff | tree | snapshot
2016-04-08 Jim ProcterJAL-2053 JAL-1551 javadoc and simpler code commit | commitdiff | tree | snapshot
2016-04-07 Jim ProcterJAL-1722 fix: don’t draw visible regions outside viewpo... commit | commitdiff | tree | snapshot
2016-04-06 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-04-06 tcofoegbuJAL-2047 JAL-1919 fixed empty tooltip text when a cell... commit | commitdiff | tree | snapshot
2016-04-06 tcofoegbuJAL-1960 updated test to capture new behaviour improvement commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 RFC about cyclic dataset sequence references... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 revise test for ambiguous case commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 ambiguous test for addSequenceFeature when... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 RFC on addSequenceFeature behaviour after... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 test behaviour of copy constructor in differen... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 remove javadoc commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence... commit | commitdiff | tree | snapshot
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat... commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2046 basic test to make sure any derived sequence... commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterMerge branch 'optimisation/JAL-2001' into develop commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 drop isSelected(int) in favour of original... commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 catch -ve column values commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 TODO for new ColumnSelection API commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 - note about possible side effect on JalviewLi... commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2010 refactoring todo commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 use fast column selection test commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-969 refactor columnselection operation (during... commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 faster check for a column being selected commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 javadoc commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 faster getMax/getMin selected column, with... commit | commitdiff | tree | snapshot
2016-04-04 Jim ProcterJAL-2001 JAL-1722 - store selection as ArrayList and... commit | commitdiff | tree | snapshot
2016-04-01 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsu... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... commit | commitdiff | tree | snapshot
2016-04-01 tcofoegbuJAL-2048 Update to structureviz2 package from cytoscape commit | commitdiff | tree | snapshot
2016-04-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-2046 fix for broken test for deriveSequence commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-653 updated test to match parsing of multi-valued... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-1705 tweak to MapList.toString for debugging commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-1705 generalised getLength() to handle [start1... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-1705 test updated for canonicalised UNIPROT sequenc... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-1705 include stop codon in mapped CDS range so... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-2037 set DBRefEntry.version to "0" not "" in EMBL... commit | commitdiff | tree | snapshot
2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms) commit | commitdiff | tree | snapshot
2016-04-01 tcofoegbuJAL-2045 JAL-2047 improvement for sorting PDB quality... commit | commitdiff | tree | snapshot
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