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JAL-3878 Use annotations from the representative sequence in the new alignment.
[jalview.git]
/
src
/
jalview
/
viewmodel
/
2021-11-22
Mateusz Warowny
JAL-3878 Create pollable task and executor it can be...
tree
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commitdiff
2021-07-09
Mateusz Warowny
JAL-3690 Remove references to old AlignCalcManager.
bug/JAL-3849_aacon-parameters
tree
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commitdiff
2020-12-14
Jim Procter
Merge branch 'Jalview-JS/develop' into merge_js_develop
tree
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commitdiff
2020-10-26
Mateusz Waronwy
JAL-3690 - introduce shutdown method that cleans up...
tree
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commitdiff
2020-10-21
Mateusz Warowny
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager
tree
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commitdiff
2020-06-10
BobHanson
Bamboo text #35 - simpler logic; avoids impossible...
tree
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commitdiff
2020-06-10
BobHanson
Bamboo test #3 The problem is not threading. It is...
tree
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commitdiff
2020-06-10
BobHanson
Bamboo test 2 -- threads and stacktrace
tree
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commitdiff
2020-06-10
BobHanson
So close! Bamboo test
tree
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commitdiff
2020-06-09
BobHanson
JAL-3446 from applet; JAL-3374
tree
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commitdiff
2020-06-02
BobHanson
JAL-3626 from JAL-3253-applet web page embedding
tree
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commitdiff
2020-05-18
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
tree
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commitdiff
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
tree
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commitdiff
2020-04-23
Jim Procter
Merge branch 'develop' into alpha/JAL-3362_Jalview_212_...
tree
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commitdiff
2020-04-21
Jim Procter
JAL-367 code tidy
tree
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commitdiff
2020-04-16
gmungoc
JAL-3567 report mapped location for virtual features...
tree
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commitdiff
2020-04-07
gmungoc
JAL-3210 fudge for JalviewJS to avoid IntervalStore...
tree
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commitdiff
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2020-03-06
gmungoc
JAL-3187 unit test for findComplementFeaturesAtResidue
tree
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-08-13
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
tree
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commitdiff
2019-08-07
gmungoc
JAL-3187 (fudge) look in both alignments for stored...
feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-07-03
tva
JAL-2629 can now filter by sequence e-value or bit...
tree
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commitdiff
2019-06-14
gmungoc
JAL-3302 transfer visible 'linked' features to Chimera
tree
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commitdiff
2019-06-11
gmungoc
JAL-3187 CDS has same dataset sequence as transcript
tree
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-06-05
tva
JAL-3285 delete duplicate variables in AlignmentViewpor...
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged features into AlignmentViewport
tree
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commitdiff
2019-06-04
Jim Procter
Merge branch 'develop' into developtomchmmer
tree
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commitdiff
2019-04-26
gmungoc
JAL-3226 removal of superseded changes
tree
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commitdiff
2019-04-23
hansonr
[JAL-3226] problem that JavaScript (or Java) may consol...
tree
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commitdiff
2019-04-18
hansonr
Adds check for gap padding to disallow fast paint upon...
tree
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commitdiff
2019-04-18
hansonr
Corrects incorrect calls to ViewportRanges.setEndSeq()
tree
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commitdiff
2019-04-18
hansonr
explicit Hashtable objects
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
tree
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commitdiff
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-03-11
gmungoc
Merge branch 'develop' into merge/JAL-3127
tree
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commitdiff
2019-03-11
gmungoc
JAL-3201 restore group colours correctly from project
feature/JAL-2250colourAllGroups
tree
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commitdiff
2019-03-11
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
tree
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commitdiff
2019-03-04
gmungoc
Merge branch 'bug/JAL-3099alignmentVisibleWidth' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-2791exportFilteredFeature' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-3139colocatedFeatures' into develop
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-3158selectionBroadcasts' into...
tree
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commitdiff
2019-02-26
gmungoc
JAL-3201 group colour schemes distinct instances
tree
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commitdiff
2019-02-21
gmungoc
JAL-3187 handle no mapping / complement features withou...
tree
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commitdiff
2019-02-19
gmungoc
JAL-3187 hacks to get peptide variant in to Jmol hover...
tree
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commitdiff
2019-02-18
gmungoc
JAL-3187 reset ViewStyle on Cancel in FeatureSettings
tree
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commitdiff
2019-02-18
gmungoc
JAL-3187 'on top' optional for complementary features
tree
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commitdiff
2019-01-22
gmungoc
JAL-3187 clunky sort by renderorder in findComplementFe...
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 unit tests updated and errors caught
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 findFeaturesAtResidue answer in render order...
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
tree
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commitdiff
2019-01-18
gmungoc
JAL-3187 basic first version for tooltips only (renderi...
tree
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commitdiff
2018-11-28
gmungoc
JAL-3158 additional calls to reset 'selection changed...
bug/JAL-3158selectionBroadcasts
tree
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commitdiff
2018-10-23
gmungoc
JAL-3139 check group visibility when removing 'redundan...
bug/JAL-3139colocatedFeatures
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
2018-09-27
gmungoc
JAL-2791 method that tests all conditions for feature...
tree
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commitdiff
2018-09-10
gmungoc
JAL-3099 use Alignment.getVisibleWidth() where wanted
bug/JAL-3099alignmentVisibleWidth
tree
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commitdiff
2018-07-20
gmungoc
JAL-3048 revised AlignExportSettings dialog with respon...
tree
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commitdiff
2018-07-09
gmungoc
JAL-3060 extract FeatureEditor class
task/JAL-3060featureEditor
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1950 JAL-2937 allow copy of sequences from group...
tree
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commitdiff
2018-05-07
gmungoc
JAL-1767 JAL-2647 hide 'Input Data..' for PCA loaded...
tree
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commitdiff
2018-05-04
gmungoc
JAL-1767 refactorings to enable faithful restore of...
tree
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commitdiff
2018-04-27
gmungoc
JAL-1767 refactoring and tidying of RotatableCanvas...
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 rename run method (as not a Runnable)
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 code tidying/documentation (non-functional...
tree
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commitdiff
2018-04-25
gmungoc
JAL-1767 minor field tidying prior to functional changes
tree
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commitdiff
2018-04-18
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-04-18
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-04-18
gmungoc
JAL-2593 render 'duplicate' features if transparency...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2939 field/method naming more consistent
tree
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commitdiff
2018-03-30
gmungoc
JAL-2939 remove commented out code
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 pull up set/IsNormalise[HMM]SequenceLogo
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 no need to recalc HMM annotation for show...
tree
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commitdiff
2018-03-21
gmungoc
JAL-2629 tweaks to Information annotation updating
tree
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commitdiff
2018-03-16
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-03-07
gmungoc
JAL-2629 storage and lifecycle of alignment/group HMM...
tree
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commitdiff
2018-03-01
gmungoc
JAL-2629 revising hmmer annotation updating (wip)
tree
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commitdiff
2018-02-28
gmungoc
JAL-2629 some tidying of Hmmer commands (wip)
tree
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commitdiff
2018-02-27
Jim Procter
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
tree
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commitdiff
2018-02-22
Jim Procter
Merge branch 'bug/JAL-2666' into releases/Release_2_10_...
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy unit tests, constants etc
tree
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commitdiff
2018-02-21
Jim Procter
Merge branch 'bug/JAL-2778again' into releases/Release_...
tree
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commitdiff
2018-02-20
gmungoc
JAL-2629 removed SequenceI.get/setLastPosition and...
tree
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commitdiff
2018-02-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-02-09
gmungoc
JAL-2666 fix failure to scroll split alignment of height 1
tree
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commitdiff
2018-02-06
kiramt
Merge branch 'develop' into feature/JAL-2759
feature/JAL-2759
tree
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commitdiff
2018-01-26
kiramt
JAL-2778 tightened up use of resetAlignmentDims
tree
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commitdiff
2018-01-19
kiramt
JAL-2759 Changes to getVisibleSequenceStrings after...
tree
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commitdiff
2018-01-18
kiramt
JAL-2759 change subtractVisibleColumns and removal...
tree
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commitdiff
2018-01-16
kiramt
JAL-2759 Moved alignment annotation code out of HiddenC...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Changed VisibleColsCollection constructor...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Rename findColumnPosition and adjustForHiddenC...
tree
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commitdiff
2018-01-10
gmungoc
JAL-1793 update spike branch to latest
tree
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commitdiff
2018-01-10
gmungoc
JAL-2791 ignore feature type visibility in getColor()
tree
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commitdiff
2017-12-08
gmungoc
JAL-2843 FeatureRenderer.getFeatureFilters returns...
tree
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commitdiff
2017-11-23
gmungoc
JAL-2808 update spike to latest (filter range tooltip...
tree
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commitdiff
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