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JAL-3127 updated colours menu and tree view documentation
[jalview.git]
/
src
/
jalview
/
2018-10-16
Jim Procter
JAL-3127 reinstate ability to set sequence ID colour...
tree
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commitdiff
2018-10-16
Jim Procter
JAL-3127 use AlignViewportI.addGroup to create & propag...
tree
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commitdiff
2018-10-16
Jim Procter
JAL-3127 use AlignViewportI.addGroup() to add group...
tree
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commitdiff
2018-10-16
Jim Procter
viewport flag to indicate when structure view needs...
tree
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commitdiff
2018-10-09
Jim Procter
JAL-3127 Colour sequences by ID - need to check that...
tree
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commitdiff
2018-10-09
Jim Procter
JAL-3127 TODO - resolve reference to Viewport for group...
tree
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commitdiff
2018-10-09
Jim Procter
JAL-3127 pass reference to AlignViewportI when creating...
tree
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commitdiff
2018-09-20
gmungoc
JAL-2843 help text for colour by attribute, feature...
tree
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commitdiff
2018-09-19
gmungoc
JAL-3120 preserve plain colour value when changing...
tree
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commitdiff
2018-09-19
Jim Procter
JAL-2808 JAL-3026 deleted all commented out tab code...
tree
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commitdiff
2018-09-19
gmungoc
JAL-2808 JAL-3032 drop tabbed layout for Colours and...
tree
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commitdiff
2018-09-11
Jim Procter
Merge branch 'develop' into releases/Release_2_11_Branch
tree
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commitdiff
2018-09-09
Jim Procter
JAL-3106 normalise extension before checking if it...
tree
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commitdiff
2018-09-07
Jim Procter
JAL-3107 update any group associated annotation rows...
tree
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commitdiff
2018-09-07
Jim Procter
JAL-2988 if selected file is null (On Java 10/OSX ...
tree
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commitdiff
2018-09-07
Jim Procter
JAL-2988 workaround: overload getSelectedFile() because...
tree
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commitdiff
2018-09-07
Jim Procter
JAL-3106 use .jvp as default
tree
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commitdiff
2018-09-07
Jim Procter
JAL-3105 fix for focus transfer after window closed...
tree
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commitdiff
2018-09-06
Jim Procter
JAL-3091 code committed in error (failed patch for...
tree
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commitdiff
2018-09-06
Jim Procter
JAL-3091 release notes for JAL-3104
tree
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commitdiff
2018-09-06
Jim Procter
JAL-3105 reallocate quality and consensus annotation...
tree
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commitdiff
2018-09-06
Jim Procter
JAL-2854 compute visible annotation panel height and...
tree
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commitdiff
2018-09-05
Jim Procter
Merge branch 'bug/JAL-3076ensemblGeneId' into develop
tree
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commitdiff
2018-09-05
Jim Procter
Merge branch 'bug/JAL-3065_DH_keyPair_Exception_nogroov...
tree
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commitdiff
2018-09-05
Jim Procter
JAL-3065 - amended commit 4906697ab6e5a79fbce3baae89f7...
bug/JAL-3065_DH_keyPair_Exception_nogroovysettings
tree
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commitdiff
2018-09-03
Jim Procter
Merge branch 'patch/VAqua_saveload_update_JAL-2988...
tree
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commitdiff
2018-09-03
gmungoc
Merge branch 'trialMerge' into releases/Release_2_10_5_...
tree
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commitdiff
2018-09-03
gmungoc
JAL-3076 fetch Ensembl sequence as JSON instead of...
tree
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commitdiff
2018-09-03
Jim Procter
Merge branch 'bug/JAL-3065_DH_keyPair_Exception' into...
tree
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commitdiff
2018-09-03
Jim Procter
JAL-3076 clarify javadoc handling single sequence respo...
bug/JAL-3076ensemblGeneId
tree
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commitdiff
2018-08-31
Jim Procter
JAL-3095 account for sequence start when highlighting...
tree
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commitdiff
2018-08-31
Jim Procter
Merge branch 'bug/JAL-3061_RNA_secondary_structure_anno...
tree
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commitdiff
2018-08-31
Jim Procter
Merge branch 'releases/Release_2_10_5_Branch' of source...
tree
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commitdiff
2018-08-31
Jim Procter
java doc and fix for JAL-3095 - region of trimmed RNA...
tree
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commitdiff
2018-08-31
gmungoc
JAL-3003 remove redundant call to drawSelectionGroup
tree
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commitdiff
2018-08-30
Jim Procter
JAL-3092 make sure base pair counter is always moved...
tree
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commitdiff
2018-08-28
gmungoc
JAL-3059 use correct border colour for groups
tree
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commitdiff
2018-08-28
gmungoc
JAL-3003 draw selection group outline on main graphics...
tree
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commitdiff
2018-08-28
gmungoc
JAL-247 comment to clarify wrapped print algorithm
tree
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commitdiff
2018-08-28
gmungoc
JAL-247 print/export wrapped uses common code to draw...
tree
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commitdiff
2018-08-28
gmungoc
JAL-3087 include full alignment height in repeating...
tree
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commitdiff
2018-08-28
gmungoc
JAL-247 draw/print sequence ids now uses common code...
tree
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commitdiff
2018-08-27
Ben Soares
JAL-3061 / JAL-3053
tree
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commitdiff
2018-08-22
Jim Procter
JAL-2988 workaround for jalview save as dialogs - clear...
tree
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commitdiff
2018-08-15
gmungoc
JAL-3080 remove tree partition if no groups created
feature/JAL-3080clearTreeGroups
tree
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commitdiff
2018-08-14
gmungoc
JAL-3078 reset Tree font (only!) on Cancel
bug/JAL-3078cancelTreeFont
tree
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commitdiff
2018-08-10
gmungoc
JAL-3018 updated to Ensembl REST 7.0
tree
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commitdiff
2018-08-10
gmungoc
JAL-3076 refactor for more efficient scan of 'gene...
tree
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commitdiff
2018-08-10
gmungoc
JAL-3076 fetch Ensembl sequence as JSON instead of...
tree
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commitdiff
2018-08-03
Ben Soares
JAL-3061
tree
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commitdiff
2018-08-02
Ben Soares
JAL-3053
tree
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commitdiff
2018-07-30
bsoares
Fixed bug ignoring "alpha" extended braces in RNA SS...
tree
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commitdiff
2018-07-17
bsoares
JAL-3065
tree
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commitdiff
2018-06-26
Jim Procter
JAL-3042 don't allow user to change default history...
tree
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commitdiff
2018-06-26
Jim Procter
JAL-3035 - jalview-das is no more !
tree
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commitdiff
2018-06-07
Jim Procter
Merge branch 'bugs/JAL-3009_blockingNetworkThreads...
tree
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commitdiff
2018-06-07
gmungoc
JAL-2755 correct Javadoc and error handling
tree
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commitdiff
2018-06-07
gmungoc
JAL-2920 wrap description in <html/> if it includes...
tree
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commitdiff
2018-06-06
Jim Procter
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into...
tree
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commitdiff
2018-06-06
Jim Procter
JAL-2920 revised TODO for JAL-3025
bug/JAL-2920_uniprotvariantfeature
tree
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commitdiff
2018-06-06
Jim Procter
JAL-2920 don’t output variant/original sequence as...
tree
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commitdiff
2018-06-06
Jim Procter
JAL-1920 JAL-3017 use newline not <br/> in description...
tree
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commitdiff
2018-06-05
Jim Procter
JAL-3009 news reader thread should be in background...
bugs/JAL-3009_blockingNetworkThreads
tree
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commitdiff
2018-06-05
Jim Procter
JAL-3009 Identifiers.Org retrieval on background thread.
tree
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commitdiff
2018-06-04
gmungoc
JAL-3019 correctly form toRange of 'traversed' MapList
tree
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commitdiff
2018-06-04
gmungoc
JAL-3018 updated REST versions to 6.3
tree
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commitdiff
2018-06-04
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
tree
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commitdiff
2018-06-02
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
tree
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commitdiff
2018-05-31
gmungoc
JAL-2808 don't capture or report min-max for mixed...
tree
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commitdiff
2018-05-31
gmungoc
JAL-2808 pre-fill numeric inequality filter with min...
tree
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commitdiff
2018-05-28
gmungoc
Merge branch 'bug/JAL-797' into develop
tree
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commitdiff
2018-05-28
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2018-05-25
Jim Procter
Merge branch 'bug/JAL-2992panelHeight' into releases...
tree
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commitdiff
2018-05-25
Jim Procter
Merge branch 'bug/JAL-1460_dragndropWindows' into relea...
tree
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commitdiff
2018-05-25
gmungoc
JAL-2992 simpler heuristic for available height
bug/JAL-2992panelHeight
tree
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commitdiff
2018-05-25
Jim Procter
Merge branch 'bug/JAL-2991_exporttosvgwrapview' into...
tree
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commitdiff
2018-05-25
Jim Procter
JAL-1460 temp variable for clearer conditional and...
bug/JAL-1460_dragndropWindows
tree
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commitdiff
2018-05-25
Jim Procter
JAL-1460 javadoc
tree
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commitdiff
2018-05-25
gmungoc
JAL-2995 tooltip on fields with double-click to browse...
tree
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commitdiff
2018-05-24
gmungoc
JAL-2997 additional tests
tree
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commitdiff
2018-05-24
Jim Procter
JAL-1460 tidied up the use of windows link file parser
tree
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commitdiff
2018-05-24
Jim Procter
JAL-1460 more complete drag'n'drop debugging info and...
tree
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commitdiff
2018-05-24
Jim Procter
JAL-1460 process .lnk files dragged to Jalview when...
tree
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commitdiff
2018-05-24
Jim Procter
JAL-1460 new data flavor for URLs added belt-and-braces...
tree
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commitdiff
2018-05-23
gmungoc
JAL-2993 AlignFrame listen for keystrokes in OverviewPanel
tree
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commitdiff
2018-05-23
Jim Procter
fix for JAL-2991 - we could do better :/
bug/JAL-2991_exporttosvgwrapview
tree
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commitdiff
2018-05-23
gmungoc
JAL-2997 handle tab-delimited trailing column number...
tree
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commitdiff
2018-05-21
gmungoc
JAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW
bug/JAL-797
tree
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commitdiff
2018-05-21
gmungoc
JAL-2920 use HGVS notation for protein variant feature
tree
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commitdiff
2018-05-11
gmungoc
JAL-2986 corrected findIndex for out of range residue...
tree
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commitdiff
2018-05-10
Jim Procter
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into...
tree
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commitdiff
2018-05-10
Jim Procter
JAL-2920 simplified logic and added corner cases for...
tree
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commitdiff
2018-05-09
gmungoc
JAL-2984 add pdb as sequence(s) if associate structure...
tree
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commitdiff
2018-05-09
Jim Procter
Merge branch 'patch/JAL-2976_vaqua4_fallback' into...
tree
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commitdiff
2018-05-09
Jim Procter
JAL-2976 fixed bad equivalence check and implemented...
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2321 ensure default is ‘parseImmediately=true’
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2321 use configured values for structure derived...
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2321 add secondary structure & temp factor if not...
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2321 use StructureImportSettings singleton settings...
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2321 isParseImmediately() allows the parse() method...
tree
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commitdiff
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