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JAL-2435 tidy code
[jalview.git]
/
src
/
jalview
/
gui
/
2017-01-05
gmungoc
JAL-2374 fix popup out by one and multiple groups bugs
tree
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commitdiff
2017-01-05
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-05
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-05
gmungoc
JAL-2373 set state of Above PID, By Conservation in...
tree
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commitdiff
2017-01-05
gmungoc
JAL-2371 tests added
tree
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commitdiff
2017-01-04
gmungoc
JAL-2371 CollectionColourScheme wraps ColourSchemeI
tree
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commitdiff
2016-12-29
gmungoc
JAL-2630 first pass groovy colour scheme (with slight...
tree
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commitdiff
2016-12-23
gmungoc
JAL-2360 removed UserDefinedColours.userColourSchemes
tree
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commitdiff
2016-12-22
gmungoc
JAL-2360 fix bug that prematurely created a SequenceGroup
tree
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commitdiff
2016-12-22
gmungoc
JAL-2360 structure viewers now using ColourMenuHelper...
tree
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commitdiff
2016-12-21
gmungoc
JAL-2360 set new/loaded colour scheme name correctly
tree
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commitdiff
2016-12-21
gmungoc
JAL-2360 ColourMenuHelper now builds and selects items...
tree
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commitdiff
2016-12-21
gmungoc
JAL-2360 fix incorrect action on Cancel user defined...
tree
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commitdiff
2016-12-20
gmungoc
JAL-2360 testRegisterColourScheme to demonstrate a...
tree
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commitdiff
2016-12-20
gmungoc
JAL-2360 ColourSchemes holds configured schemes, AlignF...
tree
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commitdiff
2016-12-19
gmungoc
JAL-2361 select colour menu item by matching its name...
tree
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commitdiff
2016-12-16
kiramt
JAL-2316 Added database name column to URL links table...
tree
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commitdiff
2016-12-16
gmungoc
JAL-2346 ensure view updates when annotation options...
tree
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commitdiff
2016-12-16
gmungoc
Merge branch 'develop' into bug/JAL-2346annotationChoice
tree
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commitdiff
2016-12-16
gmungoc
JAL-2360 getColour() renamed to getColourScheme(),...
tree
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commitdiff
2016-12-16
gmungoc
JAL-2360 refactoring for JalviewColourScheme enum,
tree
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commitdiff
2016-12-15
kiramt
JAL-2316 Changes following review.
tree
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commitdiff
2016-12-13
kiramt
Merge branch 'develop' into features/JAL-2316
tree
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commitdiff
2016-12-13
gmungoc
JAL-2361 adding items to applet colour menus, TCoffee...
tree
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commitdiff
2016-12-12
gmungoc
JAL-2361 extract methods to (re-)build colour menu
tree
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commitdiff
2016-12-12
gmungoc
JAL-1544 backgroud -> background
tree
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commitdiff
2016-12-12
kiramt
JAL-2316 Added GUI checks for duplicate link ids
tree
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commitdiff
2016-12-12
kiramt
JAL-2316 Unit test update to UrlLinkTableModel and...
tree
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commitdiff
2016-12-12
kiramt
JAL-2316 Added jalview.urls.* packages
tree
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commitdiff
2016-12-09
kiramt
JAL-2316 Unit test updates and associated minor changes...
tree
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commitdiff
2016-12-09
gmungoc
JAL-1895 suppress RNA interaction colour option
tree
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commitdiff
2016-12-08
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-12-08
gmungoc
JAL-2359 add Window menu entry only after all danger...
tree
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commitdiff
2016-12-07
gmungoc
JAL-2344 handle null format, simplify JalviewFileChoose...
tree
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commitdiff
2016-12-07
kiramt
JAL-2316 Restructure identifiers.org download
tree
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commitdiff
2016-12-05
gmungoc
JAL-2346 JAL-1553 pull-up / push-down of fields and...
tree
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commitdiff
2016-12-05
kiramt
JAL-2316 Added UrlProvider factories. Tidied up labelling.
tree
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commitdiff
2016-12-05
gmungoc
JAL-1753 JAL-1596 JAL-1933 ensure AWT updates are on...
tree
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commitdiff
2016-12-05
kiramt
JAL-2316 Adjusted unit tests. Tidied UrlLinkProviderI...
tree
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commitdiff
2016-12-02
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-12-02
gmungoc
Unit tests added, minor refactoring
tree
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commitdiff
2016-12-02
kiramt
JAL-2316 GUI updates to Connections tab in Preferences...
tree
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commitdiff
2016-12-01
gmungoc
JAL-2346 unused method removed
tree
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commitdiff
2016-12-01
gmungoc
JAL-2346 save annotation id instead of label with annot...
tree
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commitdiff
2016-12-01
gmungoc
JAL-2346 restore choice of annotation for colouring...
tree
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commitdiff
2016-11-30
Jim Procter
Merge branch 'features/JAL-2320_closeChimeraAction...
tree
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commitdiff
2016-11-29
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-29
gmungoc
JAL-2344 FileFormat.isStructureFile replaces
tree
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commitdiff
2016-11-28
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2016-11-28
tcofoegbu
Merge branch 'features/JAL-2326_JOptionPane-refactoring...
tree
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commitdiff
2016-11-25
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2016-11-25
gmungoc
JAL-2344 use .equals() to compare FileFormatI objects
tree
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commitdiff
2016-11-24
gmungoc
Distinguish text-only output formats and others (.jar...
tree
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commitdiff
2016-11-24
tcofoegbu
JAL-2326 updated references of JOptionPane to JvOptionPane
tree
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commitdiff
2016-11-24
gmungoc
Further tweaks to get tests passing
tree
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commitdiff
2016-11-24
tcofoegbu
JAL-2326 added layer of abstraction between Jalview...
tree
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commitdiff
2016-11-24
gmungoc
FileFormatI further tweaks, clean compile
tree
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commitdiff
2016-11-23
Jim Procter
Merge branch 'bug/JAL-2323disulfideOverview' into develop
tree
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commitdiff
2016-11-23
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-22
tcofoegbu
Merge branch 'bug/JAL-2277_refactorPrintUnwrapped'...
tree
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commitdiff
2016-11-22
gmungoc
JAL-2337 fix: only adjust once for scroll offset
bug/JAL-2277_refactorPrintUnwrapped
tree
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commitdiff
2016-11-22
Jim Procter
Merge branch 'features/JAL-1738_JAL-345_selectionfromhi...
tree
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commitdiff
2016-11-22
Jim Procter
JAL-1738 JAL-345 changed keystroke to ‘B’ (with modifie...
tree
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commitdiff
2016-11-22
gmungoc
JAL-2277 refactored AlignmentPanel.printUnwrapped to...
tree
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commitdiff
2016-11-21
tcofoegbu
JAL-2277 bug fix for mis-alligned graphics output for...
tree
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commitdiff
2016-11-21
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-11-21
tcofoegbu
JAL-2332 bugfix to enable structure chooser opening...
tree
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commitdiff
2016-11-21
gmungoc
Merge branch 'develop' into bug/JAL-2323disulfideOverview
tree
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commitdiff
2016-11-17
gmungoc
JAL-2327 disulfide bond abstracted to SequenceFeature...
tree
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commitdiff
2016-11-16
Jim Procter
Merge branch 'features/JAL-1723_sequenceReport' into...
tree
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commitdiff
2016-11-16
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-15
kiramt
JAL-2316 Moved url providers into own package
tree
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commitdiff
2016-11-15
kiramt
JAL-2316 Refactoring of functionality to provide urls...
tree
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commitdiff
2016-11-14
tcofoegbu
JAL-2322 Refactored unified architecture for data ...
tree
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commitdiff
2016-11-14
gmungoc
JAL-2295 JAL-2296 skeleton 'attributes to features...
tree
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commitdiff
2016-11-14
kiramt
Url links changes - incomplete checkin as battery low
tree
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commitdiff
2016-11-11
tcofoegbu
JAL-2277 Refactored out duplicated method - printUnwrap...
tree
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commitdiff
2016-11-11
gmungoc
JAL-2295 improved integrity of 'isFinishedInit' flag
tree
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commitdiff
2016-11-11
gmungoc
JAL-2295 set finishedInit to false before checking...
tree
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commitdiff
2016-11-10
tcofoegbu
Bugfix to enable accurate chain extraction/association...
tree
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commitdiff
2016-11-10
gmungoc
JAL-2320 added getViewer() method to return Chimera...
tree
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commitdiff
2016-11-07
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-07
gmungoc
JAL-2282 show url links that need checked; remove ...
tree
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commitdiff
2016-11-07
gmungoc
JAL-2295 handle no progress bar message properly
tree
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commitdiff
2016-11-07
gmungoc
JAL-2295 (unoptimised) write Jalview features as Chimer...
tree
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commitdiff
2016-11-04
kiramt
JAL-2315 Clear sequenceURLLinks if all sequence links...
tree
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commitdiff
2016-11-04
kiramt
JAL-2282 Better check for existing url links
tree
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commitdiff
2016-11-04
kiramt
JAL-2282 Message box stays on top at Jalview open;...
tree
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commitdiff
2016-11-04
gmungoc
JAL-966 JAL-1854 removed redundant methods / modifiers...
tree
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commitdiff
2016-11-03
kiramt
JAL-2282 Link menu disabled if there are no valid links
tree
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commitdiff
2016-11-03
kiramt
JAL-2282 If checkbox on warning dialog is unclicked...
tree
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commitdiff
2016-11-03
gmungoc
JAL-2310 don't double-count sequence matches; code...
tree
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commitdiff
2016-11-03
gmungoc
JAL-2295 step 1 new menu item to transfer Jalview attri...
tree
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commitdiff
2016-11-02
Jim Procter
JAL-345 JAL-1738 menu item, AlignFrame action listener...
tree
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commitdiff
2016-11-02
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2282'...
tree
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commitdiff
2016-11-02
gmungoc
JAL-98 JAL-1854 encapsulate 'magic number' threshold...
tree
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commitdiff
2016-11-02
kiramt
JAL-2282 Renamed internal use of sequence id / db acces...
tree
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commitdiff
2016-11-01
tcofoegbu
JAL-2280 refactored and improved structure file identif...
tree
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commitdiff
2016-11-01
kiramt
JAL-2282 Refactor SequenceAnnotationReport to use refac...
tree
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commitdiff
2016-11-01
kiramt
JAL-2282 Changed DB accession id token to $DB_ACCESSION...
tree
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commitdiff
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