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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / project / Jalview2XML.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-11-01 James ProcterMerge branch 'develop' into patch/JAL-4281_idwidthandan... commit | commitdiff
2023-10-23 James ProcterMerge branch 'develop' into improvement/JAL-4124_dont_d... commit | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... commit | commitdiff
2023-09-08 James ProcterJAL-4281 store/restore ID width and manual adjustment... commit | commitdiff
2023-09-08 James ProcterJAL-4282 make sure font is updated in alignPanel before... commit | commitdiff
2023-09-05 James ProcterJAL-629 use JalviewStructureDisplayI in place of Struct... commit | commitdiff
2023-09-01 Ben SoaresJAL-629 Save structure frames in project files when... commit | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options commit | commitdiff
2023-09-01 James ProcterJAL-4124 need to repaint alignFrames imported from... commit | commitdiff
2023-09-01 James ProcterJAL-4124 matrix is saved in dataset, with forward refer... commit | commitdiff
2023-08-29 James ProcterJAL-4124 Dataset holds list of MatrixType instances... commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-07-18 James Procterexploring making PAE storage in projects more efficient commit | commitdiff
2023-05-22 James ProcterJAL-1551 spotless commit | commitdiff
2023-05-19 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to... commit | commitdiff
2023-05-14 James ProcterJAL-2349 store/restore mappable contact matrix in proje... commit | commitdiff
2023-03-20 James ProcterJAL-4134 override default hasTree so PAE tree is saved! commit | commitdiff
2023-03-17 James ProcterJAL-4134 store/restore Newick tree for PAE annotation row commit | commitdiff
2023-03-15 James ProcterJAL-4134 JAL-3855 store/restore groups, tree and thresh... commit | commitdiff
2023-02-23 James ProcterJAL-4133 update validChar width when font is changed... commit | commitdiff
2023-02-22 James ProcterJAL-4133 store/restore alignment view’s charWidth and... commit | commitdiff
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised... commit | commitdiff
2023-02-16 James ProcterJAL-1713 don’t close an automatically created overview... commit | commitdiff
2023-02-13 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... commit | commitdiff
2023-02-10 James ProcterFix for JAL-4126 - don’t automatically create a thresho... commit | commitdiff
2023-01-31 James ProcterJAL-1713 update from Jalview 2.11.3 develop commit | commitdiff
2022-11-08 Ben SoaresJAL-1988 JAL-3772 Fixes highlighted by tests commit | commitdiff
2022-10-25 Ben SoaresJAL-3772 silly NPE error fixed commit | commitdiff
2022-09-26 Ben SoaresJAL-1988 JAL-3772 linked undostack to saved changes... commit | commitdiff
2022-09-23 Ben SoaresJAL-1988 property based fake delay whilst saving projec... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... commit | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... commit | commitdiff
2022-02-07 Jim ProcterMerge branch 'feature/JAL-1713_overviewInProject' into... commit | commitdiff
2022-02-07 Jim ProcterJAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTit... bug/JAL-3785autoOverviewTitle commit | commitdiff
2022-01-17 Ben Soaresclose filehandles straight after parse, without setting... commit | commitdiff
2022-01-11 Ben Soaresclose filehandles straight after parse, without setting... commit | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2021-08-30 Jim ProcterJAL-3863 add canonical DBRefEntry flag to Jalview project commit | commitdiff
2020-12-19 gmungocJAL-1713 restore project with no Overview, regardless... commit | commitdiff
2020-12-17 gmungocJAL-1713 close and replace auto-opened Overview with... commit | commitdiff
2020-12-13 gmungocJAL-1713 renamed method to OverviewPanel.get/setFrameBo... commit | commitdiff
2020-12-12 gmungocJAL-1713 JAL-3119 JAL-3785 refactored get/set Overview... commit | commitdiff
2020-12-10 gmungocJAL-1713 read/set OverviewPanel geometry on parent... commit | commitdiff
2020-12-10 gmungocJAL-1713 save Overview title in project, don't save... commit | commitdiff
2020-12-10 gmungocJAL-1713 save/restore Overview in project (todo: restor... commit | commitdiff
2020-11-13 Ben SoaresJAL-3775 Eclipse re-formatting commit commit | commitdiff
2020-11-12 Ben SoaresJAL-3633 ensure check both or https:// for urls commit | commitdiff
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls commit | commitdiff
2020-05-29 gmungocJAL-3551 null pointer defence while structure files... feature/JAL-3551Pymol commit | commitdiff
2020-05-26 gmungocJAL-1761 pattern for structure viewer construction... commit | commitdiff
2020-05-19 gmungocMerge branch 'develop' into feature/JAL-3551Pymol commit | commitdiff
2020-05-15 gmungocJAL-3619 default silently to Jmol if viewerType absent... commit | commitdiff
2020-05-11 gmungocJAL-2422 restore saved ChimeraX session from project commit | commitdiff
2020-04-30 gmungocJAL-3551 save structure viewer session refactorings... commit | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2020-03-09 gmungocMerge branch 'develop' into feature/JAL-2422ChimeraX commit | commitdiff
2020-02-04 gmungocJAL-2422 pull up refactoring in preparation for Chimera... commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... commit | commitdiff
2019-08-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff
2019-07-31 gmungocJAL-3389 add .py to restored Chimera session filename... commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-06-07 gmungocJAL-3187 save and restore flags for show complement... commit | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... commit | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2019-05-02 gmungocJAL-3244 renamed Platform method for clarity bug/JAL-3244jmolWindows commit | commitdiff
2019-04-17 gmungocJAL-3026 fix bug loading Jalview Project (in Java) commit | commitdiff
2019-03-27 hansonrconsolidation of Platform isJS calls commit | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... commit | commitdiff
2019-03-15 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-03-15 gmungocJAL-2964 missed branch for restore link tree to all... commit | commitdiff
2019-03-14 gmungocJAL-3210 JAL-3141 JAL-3056 disable backups in JalviewJS commit | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2019-03-11 gmungocMerge branch 'develop' into merge/JAL-3127 commit | commitdiff
2019-03-11 gmungocJAL-3201 restore group colours correctly from project feature/JAL-2250colourAllGroups commit | commitdiff
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into... commit | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3120restoreFeatureColour' into... commit | commitdiff
2019-02-28 gmungocMerge remote-tracking branch 'origin/feature/JAL-3141_b... commit | commitdiff
2019-02-28 Jim ProcterMerge branch 'feature/JAL-3141_backupfiles_for211'... merge/develop_feature/JAL-3141_backupfiles_for211 commit | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... commit | commitdiff
2019-01-23 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff
2019-01-23 gmungocJAL-3063 correct handling of absent choice element... commit | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... commit | commitdiff
2019-01-20 Ben SoaresJAL-3141 Re-added some changes in Jalview2XML missed... commit | commitdiff
2019-01-18 Jim ProcterMerge branch 'feature/JAL-3063jaxbNoCastor' into featur... commit | commitdiff
2019-01-16 Jim ProcterMerge branch 'feature/JAL-3063jaxbNoCastor' into develop commit | commitdiff
2019-01-11 hansonr(commented out but potentially useful) methods to tap... commit | commitdiff
2018-12-21 gmungocJAL-1767 minimise local variable scope commit | commitdiff
2018-12-20 Jim ProcterJAL-1767 port save/load PCA panel to JAXB - JAL-3063 commit | commitdiff
2018-12-14 Jim ProcterJAL-3171 record mapping between unmarshalled sequence... commit | commitdiff
2018-12-14 Jim ProcterJAL-3171 raise warning when a dataset reference exists... commit | commitdiff
2018-12-14 Jim ProcterJAL-3171 resolve dataset for imported projects via... commit | commitdiff
2018-12-14 Jim ProcterJAL-3171 register existing dataset for new view commit | commitdiff
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... commit | commitdiff
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