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JAL-4059 fix that boolean for non-value query string args
[jalview.git]
/
src
/
jalview
/
project
/
Jalview2XML.java
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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commitdiff
2023-11-01
James Procter
Merge branch 'develop' into patch/JAL-4281_idwidthandan...
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2023-10-23
James Procter
Merge branch 'develop' into improvement/JAL-4124_dont_d...
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diff to current
2023-10-19
Ben Soares
JAL-4305 Isolate and unify the Jalview object from...
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diff to current
2023-09-08
James Procter
JAL-4281 store/restore ID width and manual adjustment...
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2023-09-08
James Procter
JAL-4282 make sure font is updated in alignPanel before...
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diff to current
2023-09-05
James Procter
JAL-629 use JalviewStructureDisplayI in place of Struct...
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diff to current
2023-09-01
Ben Soares
JAL-629 Save structure frames in project files when...
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commitdiff
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diff to current
2023-09-01
Ben Soares
JAL-629 Fix --structureimage and options
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diff to current
2023-09-01
James Procter
JAL-4124 need to repaint alignFrames imported from...
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diff to current
2023-09-01
James Procter
JAL-4124 matrix is saved in dataset, with forward refer...
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diff to current
2023-08-29
James Procter
JAL-4124 Dataset holds list of MatrixType instances...
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diff to current
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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diff to current
2023-07-18
James Procter
exploring making PAE storage in projects more efficient
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diff to current
2023-05-22
James Procter
JAL-1551 spotless
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diff to current
2023-05-19
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
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commitdiff
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diff to current
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
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diff to current
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
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diff to current
2023-05-18
James Procter
JAL-4134 column grouping model and methods moved to...
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diff to current
2023-05-14
James Procter
JAL-2349 store/restore mappable contact matrix in proje...
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diff to current
2023-03-20
James Procter
JAL-4134 override default hasTree so PAE tree is saved!
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2023-03-17
James Procter
JAL-4134 store/restore Newick tree for PAE annotation row
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diff to current
2023-03-15
James Procter
JAL-4134 JAL-3855 store/restore groups, tree and thresh...
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diff to current
2023-02-23
James Procter
JAL-4133 update validChar width when font is changed...
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diff to current
2023-02-22
James Procter
JAL-4133 store/restore alignment view’s charWidth and...
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2023-02-22
James Procter
JAL-3858 persist PAE matrix (only so far) as serialised...
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2023-02-16
James Procter
JAL-1713 don’t close an automatically created overview...
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2023-02-13
James Procter
Merge branch 'develop' into feature/JAL-1713_overviewIn...
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diff to current
2023-02-10
James Procter
Fix for JAL-4126 - don’t automatically create a thresho...
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diff to current
2023-01-31
James Procter
JAL-1713 update from Jalview 2.11.3 develop
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diff to current
2022-11-08
Ben Soares
JAL-1988 JAL-3772 Fixes highlighted by tests
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diff to current
2022-10-25
Ben Soares
JAL-3772 silly NPE error fixed
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diff to current
2022-09-26
Ben Soares
JAL-1988 JAL-3772 linked undostack to saved changes...
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commitdiff
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diff to current
2022-09-23
Ben Soares
JAL-1988 property based fake delay whilst saving projec...
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commitdiff
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diff to current
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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diff to current
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
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diff to current
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
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2022-02-07
Jim Procter
Merge branch 'feature/JAL-1713_overviewInProject' into...
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2022-02-07
Jim Procter
JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTit...
bug/JAL-3785autoOverviewTitle
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2022-01-17
Ben Soares
close filehandles straight after parse, without setting...
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diff to current
2022-01-11
Ben Soares
close filehandles straight after parse, without setting...
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diff to current
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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diff to current
2021-08-30
Jim Procter
JAL-3863 add canonical DBRefEntry flag to Jalview project
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2020-12-19
gmungoc
JAL-1713 restore project with no Overview, regardless...
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2020-12-17
gmungoc
JAL-1713 close and replace auto-opened Overview with...
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2020-12-13
gmungoc
JAL-1713 renamed method to OverviewPanel.get/setFrameBo...
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2020-12-12
gmungoc
JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview...
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2020-12-10
gmungoc
JAL-1713 read/set OverviewPanel geometry on parent...
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2020-12-10
gmungoc
JAL-1713 save Overview title in project, don't save...
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2020-12-10
gmungoc
JAL-1713 save/restore Overview in project (todo: restor...
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commitdiff
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2020-11-13
Ben Soares
JAL-3775 Eclipse re-formatting commit
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diff to current
2020-11-12
Ben Soares
JAL-3633 ensure check both or https:// for urls
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diff to current
2020-09-23
Ben Soares
JAL-3633 ensure check both or https:// for urls
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diff to current
2020-05-29
gmungoc
JAL-3551 null pointer defence while structure files...
feature/JAL-3551Pymol
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2020-05-26
gmungoc
JAL-1761 pattern for structure viewer construction...
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2020-05-19
gmungoc
Merge branch 'develop' into feature/JAL-3551Pymol
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2020-05-15
gmungoc
JAL-3619 default silently to Jmol if viewerType absent...
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2020-05-11
gmungoc
JAL-2422 restore saved ChimeraX session from project
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2020-04-30
gmungoc
JAL-3551 save structure viewer session refactorings...
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diff to current
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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2020-03-09
gmungoc
Merge branch 'develop' into feature/JAL-2422ChimeraX
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2020-02-04
gmungoc
JAL-2422 pull up refactoring in preparation for Chimera...
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2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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diff to current
2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
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2019-08-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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2019-07-31
gmungoc
JAL-3389 add .py to restored Chimera session filename...
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diff to current
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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diff to current
2019-06-07
gmungoc
JAL-3187 save and restore flags for show complement...
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diff to current
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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diff to current
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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diff to current
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
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diff to current
2019-05-02
gmungoc
JAL-3244 renamed Platform method for clarity
bug/JAL-3244jmolWindows
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commitdiff
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diff to current
2019-04-17
gmungoc
JAL-3026 fix bug loading Jalview Project (in Java)
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diff to current
2019-03-27
hansonr
consolidation of Platform isJS calls
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diff to current
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
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diff to current
2019-03-15
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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diff to current
2019-03-15
gmungoc
JAL-2964 missed branch for restore link tree to all...
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diff to current
2019-03-14
gmungoc
JAL-3210 JAL-3141 JAL-3056 disable backups in JalviewJS
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2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
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diff to current
2019-03-11
gmungoc
Merge branch 'develop' into merge/JAL-3127
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diff to current
2019-03-11
gmungoc
JAL-3201 restore group colours correctly from project
feature/JAL-2250colourAllGroups
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diff to current
2019-03-11
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
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2019-03-04
gmungoc
Merge branch 'bug/JAL-3120restoreFeatureColour' into...
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2019-02-28
gmungoc
Merge remote-tracking branch 'origin/feature/JAL-3141_b...
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2019-02-28
Jim Procter
Merge branch 'feature/JAL-3141_backupfiles_for211'...
merge/develop_feature/JAL-3141_backupfiles_for211
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diff to current
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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diff to current
2019-01-23
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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commitdiff
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diff to current
2019-01-23
gmungoc
JAL-3063 correct handling of absent choice element...
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commitdiff
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diff to current
2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
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commitdiff
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diff to current
2019-01-20
Ben Soares
JAL-3141 Re-added some changes in Jalview2XML missed...
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commitdiff
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diff to current
2019-01-18
Jim Procter
Merge branch 'feature/JAL-3063jaxbNoCastor' into featur...
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diff to current
2019-01-16
Jim Procter
Merge branch 'feature/JAL-3063jaxbNoCastor' into develop
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commitdiff
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diff to current
2019-01-11
hansonr
(commented out but potentially useful) methods to tap...
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commitdiff
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diff to current
2018-12-21
gmungoc
JAL-1767 minimise local variable scope
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commitdiff
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diff to current
2018-12-20
Jim Procter
JAL-1767 port save/load PCA panel to JAXB - JAL-3063
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commitdiff
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diff to current
2018-12-14
Jim Procter
JAL-3171 record mapping between unmarshalled sequence...
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commitdiff
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diff to current
2018-12-14
Jim Procter
JAL-3171 raise warning when a dataset reference exists...
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commitdiff
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diff to current
2018-12-14
Jim Procter
JAL-3171 resolve dataset for imported projects via...
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commitdiff
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diff to current
2018-12-14
Jim Procter
JAL-3171 register existing dataset for new view
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commitdiff
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diff to current
2018-12-06
Ben Soares
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
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