JAL-2422 general pull-up/removal of common or unused fields and methods
[jalview.git] / src / jalview /
2020-02-21 gmungocJAL-2422 general pull-up/removal of common or unused...
2020-02-20 gmungocJAL-2422 pull-up refactoring of structure commands...
2020-02-04 gmungocJAL-2422 fixed stopProgressBar (broken in pull up refac...
2020-02-04 gmungocJAL-2422 pull up refactoring in preparation for Chimera...
2020-01-31 gmungocJAL-2422 temporary hacks removed; use hex colours for...
2020-01-31 gmungocJAL-2422 more responsive Chimera/X path prompts in...
2020-01-30 gmungocJAL-2422 save/restore ChimeraX session
2020-01-28 gmungocJAL-2422 ChimeraX added to Preferences
2020-01-14 gmungocJAL-2422 proof of concept adaptations for ChimeraX...
2019-12-13 gmungocJAL-2422 'label' command to highlight ChimeraX residue...
2019-12-13 gmungocJAL-2422 write Jalview features to ChimeraX via command...
2019-12-13 gmungocJAL-2422 basic proof of concept of ChimeraX opened...
2019-09-26 gmungocJAL-2481 remove code duplication left by merge
2019-09-26 gmungocJAL-3441 action double-click in Feature Type column...
2019-08-23 gmungocJAL-3141 correct cast of spinner value
2019-08-22 gmungocJAL-3187 case-insensitive codon variant calculation
2019-08-21 gmungocJAL-3187 minor code tidying, todo removal
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans...
2019-08-07 gmungocJAL-3187 (fudge) look in both alignments for stored... feature/JAL-3187linkedFeatures
2019-08-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-07-31 gmungocJAL-3389 add .py to restored Chimera session filename...
2019-07-31 gmungocMerge branch 'bug/JAL-3388structureChooserSorting'...
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId()
2019-07-30 gmungocJAL-3388 correct class for column 0 Ref Sequence bug/JAL-3388structureChooserSorting
2019-07-29 gmungocJAL-3386 correct wrapped width calculation for headless...
2019-07-29 gmungocJAL-3377 more reused of SeqCanvas.computeWrappedGeometry
2019-07-29 gmungocJAL-3377 add seq-annotations gap to cheight not to...
2019-07-29 gmungocJAL-3377 Javadoc added for getWrappedHeight()
2019-07-29 gmungocJAL-3377 corrected wrapped widths height for IdCanvas
2019-07-29 gmungocJAL-3377 include seq-annotation spacing in getWrappedHe...
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into
2019-07-26 gmungocJAL-1793 only decode specific special characters in...
2019-07-26 gmungocJAL-3376 capture VCF POS, ID, QUAL, FILTER as feature... features/JAL-3375vcfValidation
2019-07-26 gmungocJAL-3375 format validate VCF Integer and Float fields
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data
2019-07-16 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-07-16 gmungocJAL-2987 tolerate null double values when formatting...
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-07-08 gmungocJAL-3187 derived peptide variants tweaks and tests
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant...
2019-07-05 gmungocJAL-1793 apply URL decoding when saving VCF attribute...
2019-07-02 Jim ProcterJAL-3111 JAL-3280 hide the version check preference...
2019-07-02 Jim ProcterMerge branch 'develop' into tasks/JAL-3311_removeVamsasMenu
2019-07-01 Ben SoaresJAL-3333 removed unused variable
2019-07-01 Ben SoaresJAL-3333 using floats for smoother weighting
2019-06-29 Ben SoaresJAL-3333 Sorry couldn't resist adding a bit of weightin...
2019-06-29 Ben SoaresJAL-3333 Title text now appears instantly. Altering...
2019-06-28 Ben SoaresMerge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceIn...
2019-06-28 Ben SoaresJAL-3333 changed RGB model. Tested in mojave and Windo...
2019-06-28 Jim ProcterMerge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceIn...
2019-06-28 Ben SoaresJAL-3333 Smooth rotation of image now too
2019-06-28 Ben SoaresJAL-3333 added height to rotating image preferred size
2019-06-28 Jim ProcterJAL-3330 apply Ensembl feature settings when showing... bug/JAL-3330_backpropagateEnsemblFeatureColours
2019-06-28 Ben SoaresJAL-3333 Replaced title text rendered in animated image...
2019-06-26 Jim ProcterJAL-3334 fix - always load full SO to resolve the seque...
2019-06-26 Jim ProcterJAL-3111 get rid of nasty tab characters
2019-06-26 Jim ProcterJAL-3332 test to check for duplicate db sources and...
2019-06-26 Jim ProcterJAL-3330 javadoc
2019-06-24 Jim ProcterJAL-3330 merge styles onto originating view after fetch...
2019-06-24 Jim ProcterJAL-3330 dbreffetcher: record any feature display model...
2019-06-24 Jim ProcterJAL-3330 merge styles onto originating views when show...
2019-06-24 Jim ProcterJAL-3330 mergeFeatureStyles - needs test coverage
2019-06-19 Ben SoaresMerge branch 'merge/JAL-3310_and_JAL-3300' into develop
2019-06-19 Ben SoaresJAL-3321 Last pieces of the getdown-launcher.jar upgrad...
2019-06-19 Jim ProcterMerge branch 'develop' into documentation/JAL-3111_rele...
2019-06-18 gmungocJAL-3313 don't double count mapped codons
2019-06-18 Jim ProcterMerge branch 'bug/JAL-2830_editManglesDatasetSequence...
2019-06-18 Ben SoaresMerge branch 'develop' into merge/JAL-3310_and_JAL...
2019-06-18 gmungocJAL-3187 javadoc
2019-06-18 Jim ProcterMerge branch 'bug/JAL-3286duplicatePdbQuery' into develop
2019-06-18 gmungocJAL-3304 option to export linked features also for...
2019-06-18 Ben SoaresJAL-3312 Fixed SHIFT-CMD/SHIFT-CTRL Key combinations...
2019-06-18 gmungocJAL-3304 option to export linked features in Jalview...
2019-06-18 gmungocJAL-3187 i18n show linked features checkboxes
2019-06-18 gmungocJAL-3305 mirror popup menu column selections in split...
2019-06-17 Ben SoaresJAL-3310 JAL-3300 two getdown fixes merged
2019-06-17 gmungocJAL-2792 JAL-3187 linked features (if shown) in Feature...
2019-06-17 gmungocJAL-3187 update alignAs code and unit tests for 'shared...
2019-06-17 gmungocJAL-3187 add sequence to feature details table (and...
2019-06-17 Jim ProcterJAL-3311 remove menus and documentation relating to... tasks/JAL-3311_removeVamsasMenu
2019-06-14 Ben SoaresJAL-3295 pre-merged code with JAL-3295 branch which...
2019-06-14 Ben SoaresJAL-3278 A system.out.println turned into a cache.log...
2019-06-14 Jim ProcterJAL-3111 report build type and commit in stdout from...
2019-06-14 Jim ProcterJAL-3299 JAL-3280 javadoc on BuildDetails bean
2019-06-14 gmungocJAL-3302 transfer visible 'linked' features to Chimera
2019-06-13 gmungocJAL-3303 ignore deletions when computing peptide variants
2019-06-13 Jim ProcterMerge branch 'bug/JAL-3295_CMD_select_not_working_in_se...
2019-06-13 gmungocJAL-3143 recognise lnc_RNA as transcript
2019-06-12 Ben SoaresJAL-3295 Fixed CMD-select of sequences in alignment...
2019-06-11 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-11 gmungocJAL-3143 also parse "phase" from JSON response if present
2019-06-11 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-11 gmungocJAL-3288 fixes for gain/lose focus
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript
2019-06-07 gmungocJAL-3187 save and restore flags for show complement...
2019-06-07 gmungocJAL-3187 change fields to local variables
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-07 gmungocMerge branch 'bug/JAL-3288splitFrameMenusJava11' into...
2019-06-07 gmungocJAL-3187 Viewport schema attributes for showComplementF...
2019-06-07 gmungocJAL-3251 added optional attributes Sequence.biotype...
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