Merge branch 'documentation/JAL-2325_release2101' into releases/Release_2_10_Branch
[jalview.git] / src / jalview / schemes /
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns
2016-11-08 gmungocJAL-2301 made T hydrophobic as per the cited conservati...
2016-11-02 gmungocJAL-98 ProfileI interface for Profile
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis...
2016-11-01 gmungocJAL-98 use Integer constants; tests added for propHash...
2016-10-27 gmungocJAL-98 refactor bleachColour() to ColorUtils
2016-10-26 gmungocJAL-2286 modal residue check + commenting
2016-10-26 gmungocJAL-2286 javadoc, refactor, unit tests for threshold...
2016-10-25 gmungocJAL-2286 use constant for fixed colours
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-25 gmungocJAL-98 field comments updated
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-09-29 Jim ProcterJAL-2236 fix: bail if no context available for subgroup
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
2016-06-22 gmungocJAL-2015 fixed bug in copy constructor and added tests
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles
2016-03-15 gmungocJAL-2016 FeatureSettingsI now FeatureSettingsModelI
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-02-25 gmungocJAL-2015 parse/write Jalview feature format pushed...
2016-02-24 gmungocJAL-2015 JAL-1956 rollout of FeatureColourI in place of JAL-1956_featureStyles
2016-02-22 gmungocJAL-1705 first pass at applying preset feature colourin...
2016-02-20 gmungocMerge branch 'JAL-1956_featureStyles' into features...
2016-02-20 gmungocJAL-2016 first draft of pre-set feature colour scheme
2016-02-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h...
2016-01-21 tcofoegbuJAL-1479 JAL-1979 updated the modified-aminoacid triple...
2015-12-22 gmungocJAL-1421 parameterised map constructor used
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-30 tcofoegbuJAL-1912 added support of tcoffee annotation and other...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-09-07 gmungocJAL-1636 translate stop codon as '*', mouseover * as...
2015-09-05 Jim ProcterJAL-1871 choose a new RNA Helices palette when annotati...
2015-09-05 Jim ProcterJAL-1871 don’t change the palette every time an edit...
2015-09-05 Jim ProcterJAL-1871 reinstate random generation of palette when...
2015-09-05 Jim ProcterJAL-1869 make per-sequence RNA helix colours each time...
2015-09-05 Jim ProcterJAL-1233 tidy up and use same RNA helix colours in...
2015-09-05 Jim ProcterJAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection...
2015-09-03 Jim ProcterJAL-1680 JAL-1576 JAL-1233 all conservation and consens...
2015-09-03 Jim ProcterJAL-1576 fix: trigger broadcast of colour change with...
2015-09-03 Jim ProcterJAL-1550 JAL-1551 formatting
2015-09-03 Jim ProcterJAL-1233 JAL-1576 copy constructor to propagate helix...
2015-09-03 gmungocJAL-1828 lookup table to convert MSE to MET when parsin...
2015-07-23 Jim ProcterJAL-1819 use Float.isNaN() to check for NaNs!
2015-05-20 gmungocJAL-1741 nucleotide-aware colour schemes applied to...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2015-01-07 Jim ProcterMerge branch 'develop' into JAL-1483_29dev
2015-01-07 Jim ProcterJAL-1483 register feature similarity model
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-12-05 gmungocMerge branch 'Release_2_8_2_Branch' of local repository...
2014-12-03 gmungocJAL-1609 wip on Chimera colour by sequence
2014-12-01 Jim ProcterJAL-795 hack to ignore black colour in annotation element.
2014-11-24 Jim ProcterJAL-1593 refactor rna helix colours to static singleton...
2014-11-23 Jim ProcterJAL-1593 allow per-sequence shading of RNA helix (store...
2014-11-23 Jim ProcterJAL-1569 test for open/close RNA parenthesis character
2014-11-23 Jim ProcterJAL-1569 formatting
2014-11-14 Jim ProcterMerge branch 'develop' into JAL-1483_featureBasedTreeCalc
2014-11-03 Jim ProcterJAL-795 JAL-674 tweaked logic to avoid black annotation...
2014-10-30 Jim Procterpatch for JAL-795 - use base secondary structure colour...
2014-09-23 darolmarJAL-1355
2014-07-18 j.procter@dundee... JAL-795 take colour from annotation if colour is present
2014-06-13 Jim ProcterMerge branch 'Release_2_8_2_Branch' into JAL-1483_featu...
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-06-04 Jim ProcterJAL-952 fixed unresolved conflict breaking build
2014-06-04 Jim ProcterJAL-952 fixed unresolved conflict breaking build
2014-06-03 Jim ProcterJAL-1512 comment out for 2.8.1 release
2014-06-03 Jim ProcterJAL-1512 fix calculation once again and include score...
2014-06-03 Jim ProcterJAL-1473 make it easier to generate HTML documentation...
2014-06-02 Jim ProcterJAL-1512 rejig buggy conservation-basesd score matrix...
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-05-02 Jim ProcterMerge branch 'JAL-1397' into develop
2014-05-01 Jim Procterremove todo
2014-05-01 Jim ProcterJAL-1092 TODO - allow Jalview/JalviewLite to generate...
2014-05-01 Jim ProcterJAL-1492 JAL-1397 make AnnotatedCollectionI context...
2014-05-01 Jim ProcterJAL-1492 JAL-1397 JAL-643 JAL-969 factory method to...
2014-05-01 Jim ProcterJAL-1492 JAL-1397 JAL-643 JAL-969 modifiable flag on...
2014-05-01 Jim Procterjavadoc
2014-04-29 Jim ProcterJAL-643 - abstracted colourscheme components to allow...
2014-04-27 Jim ProcterMerge branch 'JAL-952_rnahelix' into develop
2014-04-27 Jim ProcterJAL-952 JAL-1268 add RNA Helices and T-Coffee to list...
2014-04-27 Jim ProcterJAL-952 resolve colour scheme as 'RNA Helices'
2014-04-27 Jim ProcterJAL-952 refactor code to select annotation for colourin...
2014-04-25 Jim ProcterMerge branch 'JAL-1177_prop_rnasecstr' into develop
2014-04-25 Jim Procterfix for JAL-1268
2014-04-21 Jim ProcterMerge branch 'jims_marckhacks' into develop
2014-04-21 Jim Procteravoid potential NPE
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