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JAL-2630 first pass groovy colour scheme (with slight refactoring)
[jalview.git] / src /
2016-12-29 gmungocJAL-2630 first pass groovy colour scheme (with slight... tree | commitdiff
2016-12-23 gmungocJAL-2360 removed UserDefinedColours.userColourSchemes tree | commitdiff
2016-12-23 gmungocJAL-2120 JAL-2360 remove obsolete PDBViewer tree | commitdiff
2016-12-22 gmungocJAL-2360 fix bug that prematurely created a SequenceGroup tree | commitdiff
2016-12-22 gmungocJAL-2360 structure viewers now using ColourMenuHelper... tree | commitdiff
2016-12-21 gmungocJAL-2360 set new/loaded colour scheme name correctly tree | commitdiff
2016-12-21 gmungocJAL-2360 ColourMenuHelper now builds and selects items... tree | commitdiff
2016-12-21 gmungocJAL-2360 comment only tree | commitdiff
2016-12-21 gmungocJAL-2360 tidy up, simplify isApplicableTo test tree | commitdiff
2016-12-21 gmungocJAL-2360 no RNAHelices colouring for groups tree | commitdiff
2016-12-21 gmungocJAL-2361 Blosum is enabled for peptide tree | commitdiff
2016-12-21 gmungocJAL-1421 add types to Map tree | commitdiff
2016-12-21 gmungocJAL-2360 fix incorrect action on Cancel user defined... tree | commitdiff
2016-12-21 gmungocJAL-2360 tidy spelling and file contents order only tree | commitdiff
2016-12-21 gmungocJAL-2360 Javadoc and test cases for findAnnotation tree | commitdiff
2016-12-20 gmungocJAL-2360 testRegisterColourScheme to demonstrate a... tree | commitdiff
2016-12-20 gmungocJAL-2360 ColourSchemes holds configured schemes, AlignF... tree | commitdiff
2016-12-19 gmungocJAL-2360 amended toAppletParameter() for reproducible... tree | commitdiff
2016-12-19 gmungocJAL-2361 select colour menu item by matching its name... tree | commitdiff
2016-12-16 Jim ProcterJAL-2360 report line number when threshold cannot be... tree | commitdiff
2016-12-16 gmungocJAL-2360 added UserColourScheme.toAppletParameter+test... tree | commitdiff
2016-12-16 gmungocJAL-2360 getColour() renamed to getColourScheme(),... tree | commitdiff
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type... tree | commitdiff
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum, tree | commitdiff
2016-12-14 gmungocJAL-2360 added check for null annotations array tree | commitdiff
2016-12-13 gmungocJAL-2365 test for lightgray, darkgray not lightGray... tree | commitdiff
2016-12-13 gmungocJAL-2360 code formatting only and if-else changed to... tree | commitdiff
2016-12-13 gmungocJAL-2361 adding items to applet colour menus, TCoffee... tree | commitdiff
2016-12-12 gmungocJAL-2361 extract methods to (re-)build colour menu tree | commitdiff
2016-12-12 gmungocJAL-2360 simplify nucleotide flag, remove setter tree | commitdiff
2016-12-12 gmungocJAL-1544 backgroud -> background tree | commitdiff
2016-12-12 gmungocJAL-2362 return correct lower-case colour; Javadoc... tree | commitdiff
2016-12-12 gmungocJAL-2632 corrected lookup of residue colour tree | commitdiff
2016-12-09 gmungocJAL-2105 updated for reviewed REST version 4.8 tree | commitdiff
2016-12-09 gmungocJAL-1895 suppress RNA interaction colour option 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
2016-11-30 Jim ProcterMerge branch 'features/JAL-2320_closeChimeraAction... tree | commitdiff
2016-11-30 gmungocJAL-2344 use ".cif" for saved mmCIF file (and refactor... 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
2016-11-22 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-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
2016-11-14 tcofoegbuJAL-2322 Refactored unified architecture for data ... tree | commitdiff
2016-11-11 tcofoegbuJAL-2277 Refactored out duplicated method - printUnwrap... 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 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
2016-11-08 gmungocJAL-2301 made T hydrophobic as per the cited conservati... tree | commitdiff
2016-11-08 tcofoegbuJAL-2292 updated method calls tree | commitdiff
2016-11-08 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-11-08 tcofoegbuJAL-2292 renamed method and improved implementation... tree | commitdiff
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