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Merge branch 'features/JAL-2295setChimeraAttributes' into features/JAL-2351jmolExchange
[jalview.git] / src /
2016-12-08 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... features/JAL-2351jmolExchange tree | commitdiff
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-12-08 gmungocJAL-2359 add Window menu entry only after all danger... tree | commitdiff
2016-12-07 gmungocJAL-2356 use cached Sifts file if not expired tree | commitdiff
2016-12-07 gmungocJAL-2354 handle error response when fetching features tree | commitdiff
2016-12-07 gmungocJAL-2344 handle null format, simplify JalviewFileChoose... tree | commitdiff
2016-12-06 gmungocJAL-2351 first refactoring and outline of read/write... tree | commitdiff
2016-12-05 gmungocJAL-1753 JAL-1596 JAL-1933 ensure AWT updates are on... tree | commitdiff
2016-12-05 gmungocMerge branch 'features/JAL-1933_occupancy' into feature... tree | commitdiff
2016-12-04 Jim ProcterJAL-1933 show occupancy count as a tooltip tree | commitdiff
2016-12-04 Jim ProcterJAL-1933 switch from gap count to occupancy tree | commitdiff
2016-12-02 gmungocMerge branch 'features/JAL-1933_occupancy' into feature... tree | commitdiff
2016-12-02 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-12-02 gmungocJAL-1933 gap value as description; minor formatting tree | commitdiff
2016-12-01 Jim ProcterJAL-1933 update the bounds for the Gap annotation row... tree | commitdiff
2016-12-01 Jim ProcterJAL-1933 basic hack to get gap counts shown as an annot... tree | commitdiff
2016-11-30 Jim ProcterMerge branch 'features/JAL-2320_closeChimeraAction... tree | commitdiff
2016-11-30 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-30 gmungocJAL-2344 use ".cif" for saved mmCIF file (and refactor... tree | commitdiff
2016-11-29 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-29 gmungocJAL-2344 corrected conversion of Type enum to FileFormat features/JAL-2344FileFormatI tree | commitdiff
2016-11-29 gmungocJAL-2344 FileFormat.isStructureFile replaces tree | commitdiff
2016-11-28 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-28 tcofoegbuMerge branch 'features/JAL-2326_JOptionPane-refactoring... tree | commitdiff
2016-11-28 gmungocJAL-2344 added FileFormatI.isStructureFile() tree | commitdiff
2016-11-28 gmungocJAL-2345 cache generated ImageIcon per file path tree | commitdiff
2016-11-25 gmungocJAL-2344 dynamically determine recognised extensions... tree | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-25 gmungocJAL-2344 override to ignore (obsolete?) JalviewFileView tree | commitdiff
2016-11-25 gmungocJAL-2344 use .equals() to compare FileFormatI objects tree | commitdiff
2016-11-24 gmungocDistinguish text-only output formats and others (.jar... tree | commitdiff
2016-11-24 tcofoegbuJAL-2326 updated references of JOptionPane to JvOptionPane tree | commitdiff
2016-11-24 Jim ProcterJAL-2325 applied BSD license for chimera/StrucViz2... tree | commitdiff
2016-11-24 gmungocFurther tweaks to get tests passing tree | commitdiff
2016-11-24 tcofoegbuJAL-2326 added layer of abstraction between Jalview... tree | commitdiff
2016-11-24 Jim ProcterJAL-2325 apply license to new source files tree | commitdiff
2016-11-24 gmungocFileFormatI further tweaks, clean compile tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'bug/JAL-2323disulfideOverview' into develop tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'documentation/JAL-2325_release2101' into... tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... tree | commitdiff
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-22 Jim ProcterJAL-2197 changed tooltip for Jnet annotation rows to... tree | commitdiff
2016-11-22 tcofoegbuMerge branch 'bug/JAL-2277_refactorPrintUnwrapped'... tree | commitdiff
2016-11-22 Jim ProcterMerge branch 'features/JAL-2177_update_jmol_to_14.6... tree | commitdiff
2016-11-22 gmungocJAL-2337 fix: only adjust once for scroll offset bug/JAL-2277_refactorPrintUnwrapped tree | commitdiff
2016-11-22 gmungocJAL-1919 JAL-2177 handle empty pdbentries list correctly features/JAL-2177_update_jmol_to_14.6.4_2016.10.26 tree | commitdiff
2016-11-22 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... tree | commitdiff
2016-11-22 tcofoegbuJAL-2322 added runnable interface to HTMLOutput class... tree | commitdiff
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi... tree | commitdiff
2016-11-22 Jim ProcterJAL-1738 JAL-345 changed keystroke to ‘B’ (with modifie... tree | commitdiff
2016-11-22 gmungocJAL-2277 refactored AlignmentPanel.printUnwrapped to... tree | commitdiff
2016-11-21 tcofoegbuJAL-2277 bug fix for mis-alligned graphics output for... tree | commitdiff
2016-11-21 Jim ProcterJAL-2335 patched FeatureRendererModel.findFeaturesAtRes... bug/JAL-2323disulfideOverview tree | commitdiff
2016-11-21 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-11-21 tcofoegbuJAL-2332 bugfix to enable structure chooser opening... tree | commitdiff
2016-11-21 gmungocJAL-2333 corrected select columns with 'contact' feature tree | commitdiff
2016-11-21 gmungocMerge branch 'develop' into bug/JAL-2323disulfideOverview tree | commitdiff
2016-11-18 gmungocJAL-98 with the two types missing from last commit... bug/JAL-98consensusMemory tree | commitdiff
2016-11-17 gmungocJAL-2323 revert to thread-safe iteration over array... tree | commitdiff
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns tree | commitdiff
2016-11-17 gmungocJAL-98 javadoc, third party acknowledgements (and very... tree | commitdiff
2016-11-17 gmungocJAL-2327 disulfide bond abstracted to SequenceFeature... tree | commitdiff
2016-11-17 gmungocJAL-2327 add isContactFeature tree | commitdiff
2016-11-16 Jim ProcterMerge branch 'features/JAL-1723_sequenceReport' into... tree | commitdiff
2016-11-16 gmungocJAL-2296 unit test for reading Chimera attributes to... tree | commitdiff
2016-11-16 gmungocJAL-2323 render disulfide bond correctly on overview... tree | commitdiff
2016-11-16 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-11-16 tcofoegbuJAL-2322 JAL-2309 replaced references to isheadless... tree | commitdiff
2016-11-16 gmungocJAL-2324 fix and tests for comparison of Float.NaN... tree | commitdiff
2016-11-16 gmungocJAL-2319 corrected reporting of SIFTS mapping tree | commitdiff
2016-11-16 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-16 gmungocJAL-2296 don't copy attribute with value False tree | commitdiff
2016-11-16 gmungocJAL-2295 don't exclude RESNUM from transfer to Chimera tree | commitdiff
2016-11-14 tcofoegbuJAL-2322 Refactored unified architecture for data ... tree | commitdiff
2016-11-14 gmungocJAL-2296 new code and refactoring for 'copy Chimera... tree | commitdiff
2016-11-14 gmungocJAL-2295 don't copy 'Chimera' features back to Chimera tree | commitdiff
2016-11-14 gmungocJAL-2296 parse Chimera atomspec to AtomSpec tree | commitdiff
2016-11-14 gmungocJAL-2296 report whether SequenceFeature actually added... tree | commitdiff
2016-11-14 gmungocJAL-2295 JAL-2296 skeleton 'attributes to features... tree | commitdiff
2016-11-11 tcofoegbuJAL-2277 Refactored out duplicated method - printUnwrap... tree | commitdiff
2016-11-11 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-11 gmungocJAL-2295 JAL-2269 JAL-2319 mockable SIFTS file, fix... tree | commitdiff
2016-11-11 gmungocJAL-2295 improved integrity of 'isFinishedInit' flag tree | commitdiff
2016-11-11 gmungocJAL-2295 set finishedInit to false before checking... tree | commitdiff
2016-11-11 gmungocJAL-2295 (optionally) return Chimera command reply tree | commitdiff
2016-11-11 gmungocJAL-2295 correct test for Float.isNaN(score) ! tree | commitdiff
2016-11-10 tcofoegbuMerge branch 'develop' into bug/JAL-2317_jmol_chimera... tree | commitdiff
2016-11-10 tcofoegbuJAL-2317 Fixed Chimera command for hiding/showing disti... bug/JAL-2317_jmol_chimera-chain-factorisation tree | commitdiff
2016-11-10 gmungocJAL-2295 additional tests, stronger sanitisation of... tree | commitdiff
2016-11-10 tcofoegbuBugfix to enable accurate chain extraction/association... tree | commitdiff
2016-11-10 gmungocJAL-2320 thread to close Chimera viewer panel if Chimer... features/JAL-2320_closeChimeraAction tree | commitdiff
2016-11-10 gmungocJAL-2320 added getViewer() method to return Chimera... tree | commitdiff
2016-11-09 gmungocJAL-2295 set attributes commands include feature value... tree | commitdiff
2016-11-09 gmungocJAL-2295 single constant for "RESNUM" feature name tree | commitdiff
2016-11-08 gmungocJAL-2295 JAL-1596 method to pass a command script file... tree | commitdiff
2016-11-08 gmungocJAL-2301 made T hydrophobic as per the cited conservati... tree | commitdiff
2016-11-08 gmungocJAL-2295 feature and colour commands refactored to... tree | commitdiff
2016-11-08 gmungocJAL-2295 method added to return a compact mapped range... tree | commitdiff
2016-11-08 gmungocJAL-2295 extracted AtomSpecModel for reuse in Chimera... tree | commitdiff
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for... tree | commitdiff
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