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Merge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4
[jalview.git] / src /
2016-04-26 Jim ProcterMerge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4 groovy/JAL-2074_upgradeto2.4.4 tree | commitdiff
2016-04-26 tcofoegbumerge tree | commitdiff
2016-04-26 tcofoegbuJAL-2071 improvement to get column data files as InputS... tree | commitdiff
2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-04-26 tcofoegbuJAL-2071 changed extension for data column config files tree | commitdiff
2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-04-26 tcofoegbuJAL-2071 resolved fts data column config file path... tree | commitdiff
2016-04-26 tcofoegbuJAL-2071 House keeping tree | commitdiff
2016-04-26 tcofoegbuJAL-2071 improvement to reduce webservice requests... tree | commitdiff
2016-04-25 Jim ProcterJAL-2074 disable security manager at start up re: lopic... tree | commitdiff
2016-04-25 tcofoegbudevelop merge tree | commitdiff
2016-04-25 tcofoegbudevelop merge tree | commitdiff
2016-04-25 tcofoegbuJAL-2071 added unit tests for FTSRestClient features/JAL-1563_uniprot-free-text-search tree | commitdiff
2016-04-25 gmungocJAL-1812 JAL-2068 only allow one Groovy console open... tree | commitdiff
2016-04-24 Jim ProcterJAL-1551 JAL-2077 formatting tree | commitdiff
2016-04-24 Jim ProcterJAL-2077 - reinstate popups on osx tree | commitdiff
2016-04-24 Jim ProcterMerge branch 'JAL-2075_features_hiddeng' into develop tree | commitdiff
2016-04-24 Jim ProcterJAL-2075 make GroovyConsole a singleton so tests requir... tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 fix: use AlignmentView.getVisibleContigs and... tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 findPosition for SeqCigar (with test) tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 formatting tree | commitdiff
2016-04-22 tcofoegbuJAL-1563 JAL-2071 Update and completed implementation... tree | commitdiff
2016-04-22 tcofoegbuJAL-2071 further refactoring, optimisation, and house... tree | commitdiff
2016-04-22 gmungocJAL-1812 JAL-2068 add Run Groovy Script to AlignFrame... tree | commitdiff
2016-04-22 gmungocJAL-2068 code and test for case of minValue == maxValue tree | commitdiff
2016-04-22 gmungocJAL-2068 framework and example scripts for pluggable... tree | commitdiff
2016-04-22 gmungocJAL-2068 Javadoc added tree | commitdiff
2016-04-22 gmungocJAL-2068 redundant implements clauses removed tree | commitdiff
2016-04-22 gmungocJAL-2068 convenience helper method for graduated score... tree | commitdiff
2016-04-20 Jim Procterfix for JAL-2072 tree | commitdiff
2016-04-19 tcofoegbuJAL-2071 architectural improvement for Plugable Free... tree | commitdiff
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... tree | commitdiff
2016-04-14 gmungocJAL-2041 clinical_significance shown on sequence featur... tree | commitdiff
2016-04-14 gmungocJAL-1421 typed map / lists, explicit imports, method... tree | commitdiff
2016-04-14 gmungocJAL-2049 small refactor of constructors to avoid code... tree | commitdiff
2016-04-14 gmungocJAL-1421 type parameter added to some collections tree | commitdiff
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer... tree | commitdiff
2016-04-14 gmungocJAL-1705 refactored/utility methods to detect e.g.... tree | commitdiff
2016-04-14 gmungocJAL-1270 JAL-653 use 'parse immediately' FeaturesFile... tree | commitdiff
2016-04-13 Jim ProcterJAL-2046 fix: patched SeqsetUtils so sequence features... tree | commitdiff
2016-04-13 Jim ProcterMerge branch 'bug/JAL-2046_ds_sharing_features_broken... tree | commitdiff
2016-04-13 tcofoegbuJAL-1270 more fix for failing Functional test tree | commitdiff
2016-04-13 tcofoegbumerge tree | commitdiff
2016-04-13 tcofoegbuJAL-2047 delay to allow table model initilisation to... tree | commitdiff
2016-04-12 gmungocJAL-2050 only hide introns if exons are present! Remove... tree | commitdiff
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ... tree | commitdiff
2016-04-11 gmungocJAL-1705 code/comment tidy only tree | commitdiff
2016-04-11 gmungocJAL-2051 fetch Ensembl Gene accessions one at a time tree | commitdiff
2016-04-11 tcofoegbumerge tree | commitdiff
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl... tree | commitdiff
2016-04-11 gmungocJAL-1705 (new preference option to) hide introns when... tree | commitdiff
2016-04-08 Jim ProcterMerge branch 'feature/JAL-2050_intronhidden' into develop tree | commitdiff
2016-04-08 Jim ProcterJAL-2050 JAL-1722 new getSelectedRange() method to... tree | commitdiff
2016-04-08 Jim ProcterJAL-2053 fix erratic hidden column marker display tree | commitdiff
2016-04-08 Jim ProcterJAL-2053 JAL-1551 javadoc and simpler code tree | commitdiff
2016-04-07 Jim ProcterJAL-1722 fix: don’t draw visible regions outside viewpo... tree | commitdiff
2016-04-06 tcofoegbumerge tree | commitdiff
2016-04-06 tcofoegbuJAL-2047 JAL-1919 fixed empty tooltip text when a cell... tree | commitdiff
2016-04-06 tcofoegbuJAL-1960 updated test to capture new behaviour improvement tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 remove javadoc tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 drop isSelected(int) in favour of original... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 catch -ve column values tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 TODO for new ColumnSelection API tree | commitdiff
2016-04-04 Jim ProcterJAL-1551 formatting tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 - note about possible side effect on JalviewLi... tree | commitdiff
2016-04-04 Jim ProcterJAL-2010 refactoring todo tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 use fast column selection test tree | commitdiff
2016-04-04 Jim ProcterJAL-969 refactor columnselection operation (during... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 faster check for a column being selected tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 javadoc tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 faster getMax/getMin selected column, with... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 JAL-1722 - store selection as ArrayList and... tree | commitdiff
2016-04-01 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsu... tree | commitdiff
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... tree | commitdiff
2016-04-01 tcofoegbuJAL-2048 Update to structureviz2 package from cytoscape tree | commitdiff
2016-04-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... tree | commitdiff
2016-04-01 gmungocJAL-1705 tweak to MapList.toString for debugging tree | commitdiff
2016-04-01 gmungocJAL-1705 generalised getLength() to handle [start1... tree | commitdiff
2016-04-01 gmungocJAL-1705 include stop codon in mapped CDS range so... tree | commitdiff
2016-04-01 gmungocJAL-2037 set DBRefEntry.version to "0" not "" in EMBL... tree | commitdiff
2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms) tree | commitdiff
2016-04-01 tcofoegbuJAL-2045 JAL-2047 improvement for sorting PDB quality... tree | commitdiff
2016-03-31 tcofoegbuJAL-2035 improvement to add binding to multiple model tree | commitdiff
2016-03-30 tcofoegbuJAL-1668 further clean-up of popup menu and NPE check... tree | commitdiff
2016-03-30 tcofoegbuJAL-2038 bug fix for NPE while setting progress message... tree | commitdiff
2016-03-28 tcofoegbumerge tree | commitdiff
2016-03-28 tcofoegbuJAL-1668 removed redundant UI elements in PopupMenu... tree | commitdiff
2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks tree | commitdiff
2016-03-28 gmungocJAL-2016 push getFeatureColourScheme(source) into Seque... tree | commitdiff
2016-03-28 gmungocJAL-2036 update AlignFrame menus when dbreffetcher... tree | commitdiff
2016-03-25 tcofoegbuJAL-2035 improvement to bind Jalview to Chimera model... tree | commitdiff
2016-03-24 tcofoegbuJAL-1919 Settings to disable duplicate generation of... tree | commitdiff
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