FishEye: changeset 1156f593e261b3c082e56d783c756aefb08d4d0b

jprocter <Jim Procter>

committed

1156f59

17 years and 1 month ago

updated build strategy and checking for portability.

1a204eb

master + 657 more

2_5_1_rna_merge
JAL-1199-Stk_writing
JAL-1260_droldan
JAL-1375_ncbiclient
JAL-1550_intermine-sequence-annotation-client
JAL-1562_help-documentation-system-refactoring
JAL-1956_featureStyles
JAL-2571
JAL-2739_2.10.2b1
JAL-3253-applet-113cc13-2019.08.28-js-optimizations
JAL-3253-applet-SwingJS-omnibus
JAL-3253-applet-test
JAL-3253_applet_omnibus-BH
JAL-3315_getdown_1_8_6_update
JAL-3368_JavaScript_colors
JAL-3416_different_look_and_feel_on_linux
JAL-3437_load_project
JAL-3866_RNAalifold-slivka-client
JAL-3878-ws-overhaul
JAL-3878_web_services_overhaul
JAL-3878_ws-overhaul-3
JAL-3927_ws_preferences_dialog_fix
JAL-3954_ebi_phmmer
JAL-429_phylip-file-support
JalScape/JAL-1332
Jalview-BH/JAL-3026
Jalview-BH/JAL-3026-JAL-3063-JAXB
Jalview-BH/JAL-3048_dialogs
Jalview-BH/JAL-3048_exportSettingsrefactor
Jalview-JS/20190123
Jalview-JS/JAL-3253-applet
Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML
Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly
Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e
Jalview-JS/JAL-3560-bh-temp
Jalview-JS/JAL-3560_bob_temp
Jalview-JS/JAL-3563-sync-TestNG-test-bob
Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg
Jalview-JS/demo
Jalview-JS/develop
Jalview-JS/develop-JAL-3559
Jalview-JS/develop-updated-gradle
Jalview-JS/develop-working
Jalview-JS/develop.JAL-3445-BSML-reader
Jalview-JS/develop.JAL-3446.SequenceFeatureAsync
Jalview-JS/develop.JAL-3446.ctrlDown
Jalview-JS/developPreFrameEmbedding
Jalview-JS/develop_j2s_v3_2_9_j11
Jalview-JS/develop_with_gradle_build
Jalview-JS/gradle-minimal
Jalview-JS/gradle_for_eclipse
Jalview-JS/gradle_with_goomph
Jalview-JS/gradle_with_inline_eclipse
Jalview-JS/jim/JAL-3253-JAL-3418
Jalview-JS/tasks/JAL-3274-build_details
Jalview-JS/update_java2script
Jalview-jJS/JAL-3253-applet-JAL-3436
Pre_R29_develop
RNAalifold
Release_2_3_BuildFix
Release_2_4_branch
Release_2_5_Branch
Release_2_6_Branch
Release_2_7_Branch
Release_2_8_0b1_Branch
Release_2_8_1_Branch
Release_2_8_1_Branch_i18n
Release_2_8_2_Branch
Release_2_8_2_Branch_i18n
Release_2_8_2b1_Branch
Release_2_8_Branch
Release_2_9_0b1_Branch
Release_2_9_Branch
Tcoffee_JAL-1065
VamJalview
WIP_fix_JAL-1423
alpha/JAL-3066_Jalview_212_slivka-integration
alpha/JAL-3362_Jalview_212_alpha
alpha/JAL-3899_deuniquify_refactor
alpha/merge_212_JalviewJS_2112
arnaud/develop
benreview/JAL-3691_for_2_11_2_getdownrebuilds
bug/JAL-1460_dragndropWindows
bug/JAL-147scrollWrappedView
bug/JAL-1552dragndroptake2
bug/JAL-1552dragndropurl
bug/JAL-1608createGroups
bug/JAL-1643_File-chooser-improvement
bug/JAL-1644_Finder-logic-improvement
bug/JAL-1697_browse-local-structures
bug/JAL-1698_Append-Structures
bug/JAL-1712annotationsWithFlanking
bug/JAL-1803_JAL-2157
bug/JAL-1819_isNaN
bug/JAL-1841rnaSecStr
bug/JAL-1858fastPaintHighlights
bug/JAL-1889serverTestSuite
bug/JAL-1988_quit_window_focus
bug/JAL-1994_Jalviewlite-json-parser-in-browsers
bug/JAL-2023_cdsProjectError
bug/JAL-2034contextchange
bug/JAL-2044jmolModelBinding
bug/JAL-2154projectMappings
bug/JAL-2210_hack_for_Release_2_10
bug/JAL-2245enaXmlChange
bug/JAL-2253
bug/JAL-2255_seq-fetcher-broken-on-linux
bug/JAL-2256
bug/JAL-2262_dnd-for-local-structure-files
bug/JAL-2272cmdClickGroupEdit
bug/JAL-2277_html-output-wrapped-mode
bug/JAL-2277_refactorPrintUnwrapped
bug/JAL-2281JAL-2282
bug/JAL-2282
bug/JAL-2283consColourEnabled
bug/JAL-2308
bug/JAL-2309
bug/JAL-2314
bug/JAL-2317_jmol_chimera-chain-factorisation
bug/JAL-2323disulfideOverview
bug/JAL-2339helpBullets
bug/JAL-2346annotationChoice
bug/JAL-2358phantomChimera
bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu
bug/JAL-2386groupConservationColouring
bug/JAL-2399textColour
bug/JAL-2420revealAllMenu
bug/JAL-2424getVisibleContigs
bug/JAL-2431splitFrameNewView
bug/JAL-2436featureRendererThreading
bug/JAL-2461
bug/JAL-2479unitteststoNetworkGroup
bug/JAL-247autoIdWidthSeqMarker
bug/JAL-247pngShowHiddenSeqMarks
bug/JAL-2491
bug/JAL-2507_rnasecstrstockholm
bug/JAL-2510amendFeatures
bug/JAL-2511idAlignment
bug/JAL-2512
bug/JAL-2515
bug/JAL-2517cancelAppletColour
bug/JAL-2536
bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release
bug/JAL-2547tooltipOnGap
bug/JAL-2551
bug/JAL-2576
bug/JAL-2577
bug/JAL-2578
bug/JAL-2586
bug/JAL-2589gapColour
bug/JAL-2591
bug/JAL-2592userDefinedScheme
bug/JAL-2597
bug/JAL-2600resizeflicker
bug/JAL-2617mappedStopCodon
bug/JAL-2621
bug/JAL-2630gradColourUpdateOverview
bug/JAL-2634
bug/JAL-2665
bug/JAL-2665-2.10.2b
bug/JAL-2665-2.10.3
bug/JAL-2666
bug/JAL-2673
bug/JAL-2673_mergewithproblem
bug/JAL-2691_nomultimermapping
bug/JAL-2704gapColourFading
bug/JAL-2721fastPaintNPE
bug/JAL-2722
bug/JAL-2728splitFrameDivision
bug/JAL-2740
bug/JAL-2750
bug/JAL-2757_uniprotftsbadquery
bug/JAL-2772pdbArrayBounds
bug/JAL-2776toggleGroupColour
bug/JAL-2778again
bug/JAL-2784
bug/JAL-2791exportFilteredFeature
bug/JAL-2791selectVisibleFeatures
bug/JAL-2811
bug/JAL-2821
bug/JAL-2827
bug/JAL-2829deleteCharsWithGaps
bug/JAL-2830_editManglesDatasetSequence
bug/JAL-2831
bug/JAL-2837
bug/JAL-2839findWithHidden
bug/JAL-2842
bug/JAL-2846
bug/JAL-2848resetColoursAmendFeatures
bug/JAL-2851
bug/JAL-2859_uniprottowrongpdbid
bug/JAL-2864nullOverviewCanvas
bug/JAL-2865removeGC
bug/JAL-2876byLabelThreshold
bug/JAL-2899
bug/JAL-2907stockholmGapChar
bug/JAL-2920_uniprotvariantfeature
bug/JAL-2924nullTooltip
bug/JAL-2934proportionalScrolling
bug/JAL-2983negativeSliderMin
bug/JAL-2991_exporttosvgwrapview
bug/JAL-2992panelHeight
bug/JAL-3002fastPaintWrapped
bug/JAL-3003epsWithSelection
bug/JAL-3049colourCellTooltip
bug/JAL-3059groupBorder
bug/JAL-3065_DH_keyPair_Exception_nogroovysettings
bug/JAL-3072scrollThread
bug/JAL-3075
bug/JAL-3076ensemblGeneId
bug/JAL-3078cancelTreeFont
bug/JAL-3082selectRegex
bug/JAL-3083cancelAnnotationColour
bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way
bug/JAL-3097blankExtraColumns
bug/JAL-3099alignmentVisibleWidth
bug/JAL-3103_browser_launcher_problems_macos_and_linux
bug/JAL-3120restoreFeatureColour
bug/JAL-3139colocatedFeatures
bug/JAL-3141_Messages_discrepancy_fix
bug/JAL-3154tableColumnDrag
bug/JAL-3158selectionBroadcasts
bug/JAL-3161annotationTooltipRange
bug/JAL-3162featureStartLtEnd
bug/JAL-3164complementOverview
bug/JAL-3166npeAllRowsHidden
bug/JAL-3171_maintain_datasets_across_views
bug/JAL-3178nonposFeatureExport_take2
bug/JAL-3183groupColourOverwritten
bug/JAL-3184restoreGroupVisibility
bug/JAL-3195idResolution
bug/JAL-3201groupClustal
bug/JAL-3202zerosInProfile
bug/JAL-3212columnSelectionWithHidden
bug/JAL-3215hydroColours
bug/JAL-3218scalePanelPopups
bug/JAL-3235sortPropertiesJava9
bug/JAL-3235sortPropertiesJava9-2
bug/JAL-3239monospacedEps
bug/JAL-3244jmolWindows
bug/JAL-3286duplicatePdbQuery
bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame
bug/JAL-3288splitFrameMenusJava11
bug/JAL-3296changeStartInvalidateCursor
bug/JAL-3330_backpropagateEnsemblFeatureColours
bug/JAL-3341unitTestFails
bug/JAL-3365_extendedDSSP_via_stockholm
bug/JAL-3365_failing_per_sequence_ss_tests
bug/JAL-3388structureChooserSorting
bug/JAL-3412idWidthDiscrepancy
bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException
bug/JAL-3477_memory_max_allocation
bug/JAL-3487-splash-JS
bug/JAL-3489mapChainsFromFile
bug/JAL-3490findSpanHiddenGaps
bug/JAL-3502wrappedScale
bug/JAL-3509hideResnum
bug/JAL-3523_cwd_not_preserved
bug/JAL-3536getCrossrefTwice
bug/JAL-3541_cloverReport_gradle_task_fails
bug/JAL-3561_translatefileformats
bug/JAL-3574filterByPOS
bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog
bug/JAL-3612_overviewFeatureOrdering
bug/JAL-3613emblCDSTracking
bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown
bug/JAL-3648graphDragRelease
bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
bug/JAL-3700_mapSequenceSelection
bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI
bug/JAL-3703_saving_a_file_in_Windows_10_fails
bug/JAL-3705saveProteinId
bug/JAL-3706virtualStopCodon
bug/JAL-3725overlappingVirtualFeatures
bug/JAL-3744_read_gzip_file_in_jalviewjs
bug/JAL-3751_revisited
bug/JAL-3751overlappingCDS
bug/JAL-3753_resources_duplicated_in_jalview_jar
bug/JAL-3760_protsTreatedAsNucleotides
bug/JAL-3761_locateInFromTo
bug/JAL-3765_Find_bugs_in_21112
bug/JAL-3774_splitFrameFinder
bug/JAL-3779setGroupProperties
bug/JAL-3785autoOverviewTitle
bug/JAL-3788_autoOverviewClustal
bug/JAL-3806_mappingCoversCDS_reprise
bug/JAL-3806_mappingCoversSequence
bug/JAL-3806_without_shared_DS_for_2_11_2
bug/JAL-3807_jpred-with-slivka
bug/JAL-3809_ws_params_dialog_fix
bug/JAL-3810_annotation_ws_stopping_abruptly
bug/JAL-3818_jmolDeadlock
bug/JAL-3849_aacon-parameters
bug/JAL-3850_gradle_7_build_failure_no_SimpleHttpFileServerFactory
bug/JAL-3885_sequence_fetched_not_displaying_PFAM_Seed
bug/JAL-3962_awt_dll_problem
bug/JAL-3972_VAqua_for_Java11
bug/JAL-3973_source_tarball_not_building
bug/JAL-3980_JAL-3981_tooltips_sequence_details
bug/JAL-3997_NPE_in_wrapped_mode
bug/JAL-797
bug/JAL-914multipleHelpScreens
bug/JAL-98consensusMemory
bug/Jal-1696_disable-pdb_id-field-settings
bug/r2_11_2/JAL-3904_structureviewermenu
bugs/JAL-2777_whitespaceChain
bugs/JAL-2780_JAL-2781_pdbnegativenums
bugs/JAL-2922
bugs/JAL-3009_blockingNetworkThreads
cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport
cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat
codereviews/JAL-1990_IProgressIndicator_jalview.structure
critical/JAL-3933_log4j_update_for_develop_branch
critical/JAL-3933_log4shell_mitigation
develop
doc/JAL-2494_JAL-2828_mergefindAnnotation
doc/JAL-3746_Release_2_11_2
feature/2588
feature/JAL-1244stretchStatusMsg
feature/JAL-1260_genbank_embl_flatfile_import_reloaded
feature/JAL-1713_overviewInProject
feature/JAL-2087ensemblSpeciesAssist
feature/JAL-2250colourAllGroups
feature/JAL-2422ChimeraX
feature/JAL-2527
feature/JAL-2553ensemblGenomes
feature/JAL-2587
feature/JAL-2611
feature/JAL-2613
feature/JAL-2664
feature/JAL-2674take2
feature/JAL-2738GeneLocus
feature/JAL-2745ebiHttps
feature/JAL-2759
feature/JAL-2873ensemblSpeciesQuery
feature/JAL-2909bamfiles
feature/JAL-2909bamfiles_features
feature/JAL-2994chimeraPath
feature/JAL-3080clearTreeGroups
feature/JAL-3081customAnnOrder
feature/JAL-3093wrappedModeTooltips
feature/JAL-3117_overviewFocusAlignment
feature/JAL-3121gffAttributeMap
feature/JAL-3127_seqidChainshading
feature/JAL-3143ensemblJSON
feature/JAL-3144noJTree
feature/JAL-3148structureColourSchemes
feature/JAL-3169cancelOverwrite
feature/JAL-3180colourAnnotationMenu
feature/JAL-3181linkOrdering
feature/JAL-3187linkedFeatures
feature/JAL-3187viewstyleFlags
feature/JAL-3190jalviewjsChimera
feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting
feature/JAL-3205symmetricCalc
feature/JAL-3251biotypedMappings
feature/JAL-3364splitFrameImage
feature/JAL-3390hideUnmappedStructure
feature/JAL-3400viewChainsMenu
feature/JAL-3442colourCaching
feature/JAL-3443findColorAsInt
feature/JAL-3468featureDescriptionEllipsis
feature/JAL-3469clinvarVCF
feature/JAL-3499featuresFileMotifs
feature/JAL-3515-slivka-preferences
feature/JAL-3551Pymol
feature/JAL-3576intervalStore_1_2
feature/JAL-3615gzipXfam
feature/JAL-3624siftsInJS
feature/JAL-3686_slivka_client_js_update
feature/JAL-3690_callback-based-web-services
feature/JAL-3692enaEndpoint
feature/JAL-3719_gapColourInAlignmentView
feature/JAL-3719_gapColourInAlignmentView_2.11.2
feature/JAL-3730ensemblPingRetries
feature/JAL-3851_prototype_comms_for_jbrowse2
feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop
feature/JAL-3874_add_source_jars_to_eclipse
feature/JAL-3982_mouseover_highlighting_viaJAL-3860
feature/JAL-984splitAdjuster
feature/intervalStoreJ
feature/r2_11_2/JAL-3808_gff2_exonerate
features/JAL-1264_showHideAnnotations
features/JAL-1270_JUnit-to-TestNG
features/JAL-1469_svg-output-for-figure-export
features/JAL-1479_SIFTS-mapping
features/JAL-1499
features/JAL-1499_MEGA
features/JAL-1541_BioJsMSAViewer-export-option
features/JAL-1550_intermine-sequence-annotation-client
features/JAL-1553_improvement-select-column-by-annotation-row-query-interface
features/JAL-1553_select-columns-by-annotation
features/JAL-1563_uniprot-free-text-search
features/JAL-1601_jpred4rest
features/JAL-1605_html-svg-export
features/JAL-1641_JSON
features/JAL-1641_JSON-File-format
features/JAL-1667_PDBe_Search_API
features/JAL-1705_ensembl
features/JAL-1725chimeraListener
features/JAL-1740_BioJsAutoUpdater
features/JAL-1740_Decoup-BioJS
features/JAL-1759jmolUpdate
features/JAL-1767pcaInProject
features/JAL-1780_export-settings_flatfile
features/JAL-1781annotationXmlIds
features/JAL-1782_JUnit-to-TestNG
features/JAL-1793VCF
features/JAL-1807java2Script
features/JAL-1812_JAL-2083_groovyBinding
features/JAL-1856dbRefFetcherMessages
features/JAL-1912_biojson-per-sequence-annotation
features/JAL-1919_mmCIF-Support
features/JAL-1933_occupancy
features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch
features/JAL-1978_msagrid
features/JAL-2039_Offer_cached_structurefiles_immediately
features/JAL-2040_JAL-2137_phyre2
features/JAL-2055alternateFeatureColours
features/JAL-2068groovyAnnotationWorker
features/JAL-2094_colourInterface
features/JAL-2103
features/JAL-2110_crossRefDuplications
features/JAL-2113_emblXml1.2
features/JAL-2136_phyre2_integration
features/JAL-2136_phyre2_integration_updated
features/JAL-2177_update_jmol_to_14.6.4_2016.10.26
features/JAL-2253ensemblGenomes
features/JAL-2284_export-biojsmsa-via-cli
features/JAL-2295setChimeraAttributes
features/JAL-2316
features/JAL-2320_closeChimeraAction
features/JAL-2326_JOptionPane-refactoring
features/JAL-2344FileFormatI
features/JAL-2351jmolExchange
features/JAL-2379pcaMemory
features/JAL-2388hiddencolumnschanges
features/JAL-2393customMatrices
features/JAL-2432_annotbypercent
features/JAL-2446NCList
features/JAL-2447experimentalFlag
features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
features/JAL-2473_set-minimium-dimensions
features/JAL-2476dropFiles
features/JAL-250_hideredundantseqs
features/JAL-2523httpRetries
features/JAL-2526sequenceCursor
features/JAL-2549_updateJABAWSto220
features/JAL-2609fastPaintWrapped
features/JAL-2620alternativeCodeTables
features/JAL-2754findFeaturesByColumn
features/JAL-2758_shorteruniprot
features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
features/JAL-2814ftsHelp
features/JAL-2885UniprotHttps
features/JAL-2909_bamImport2_11
features/JAL-2909_bamImport_2_11_2
features/JAL-2944_openStructuresInSelectedView
features/JAL-3010ontologyFeatureSettings
features/JAL-3020attributeValuePrompting
features/JAL-3085_gnupdf
features/JAL-3187_uitweaks
features/JAL-3375vcfValidation
features/JAL-3417_sdppred_calcs
features/JAL-345_selectFromFind
features/JAL-3638_jumptonextindel
features/JAL-3641_phredfromfastq
features/JAL-518_justify_seqs_in_region
features/JAL-653_JAL-1766_htslib_refseqsupport
features/JAL-653_gffalignments
features/JAL-653_rebased_gffalignments
features/JAL-666_exportoverview
features/JAL-722alignmentProperties
features/JAL-728alternateQuality
features/JAL-845linkedProteinDnaEditing
features/JAL-845splitPaneMergeDevelop
features/JAL-857_dynamic-example-files
features/JAL-892varnaToProject
features/hmmer
features/hmmer_statistics
features/mchmmer
features/mchmmer_merge_JAL-1950
features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767
features/r2_11_2/JAL-3829_3dbeacons
features/r2_11_2/JAL-3922_jmolSelectionHighlighting
features/r2_11_2_alphafold/JAL-2349_JAL-3855
features/r_2_11_2_JAL-819_undeleteAutoAnnotation
features/sequenceFeatureRefactor
groovy/JAL-2074_upgradeto2.4.4
hack/JAL-1617_workaround
imp/JAL-2774
imp/JAL-2775
improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_properties
improvement/JAL-3289_new_launch_screens
improvement/JAL-3384_Redirect_stdout_and_stdin_to_files
improvement/JAL-3393_DMG_Finder_window_improvements
improvement/JAL-3393_Improved_DMG_background_image_beta_strand
improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store
improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file
improvement/JAL-3420_match_jvl_icon_with_new_website_jvl_icon
improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task
improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2
improvement/JAL-3474_lots_of_.cvsignore_files
improvement/JAL-3503_startup_preferences
improvement/JAL-3543_dont_report_null_versions_in_java_console
improvement/JAL-3594_BG_and_UoD_logos_added
improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen
improvement/JAL-3594_logos_for_jalview_test
improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text
improvement/JAL-3826_gradle_configuration_for_intellij_idea
improvement/JAL-3830_install4j9_macos_setup_application
improvement/JAL-3830_macOS_bundle_wrapper
improvement/JAL-3847_add_dependencies_reported_by_gradle_7
improvement/JAL-3848_slivka_0.8
improvement/JAL-3848_slivka_0.8_updated_jslib
improvement/JAL-4014_gecos_colour_schemes
issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop
j2s/develop
j2s/develop-bh
j2s/develop-bh-2
j2s/develop-jim
j2s/develop-mungo
j2s/develop-toc
jalview-headless
jims/JAL-3130_Java11_Gradle_publishing
jims/work_on_2_12/JAL-3664_hmmer_ux
kjvdh/features/CipresWebservices
kjvdh/features/PhylogenyViewer
kjvdh/features/PhylogenyViewer_tabbedsupport
kjvdh/features/testing
merge/Ben_trying_out_JSdevelop_with_develop
merge/JAL-1563_uniprot-free-text-search
merge/JAL-2136_phyre2_integration
merge/JAL-3187_JAL-3010
merge/JAL-3210_developToJSDevelop
merge/JAL-3285_mchmmer_with_211_develop
merge/JAL-845_JAL-1640
merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch
merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services
merge/Jalview-JS_develop_with_develop_build.gradle_gradle.properties_utils_install4j
merge/develop_JAL-1780_JAL-653_JAL-1892
merge/develop_JAL-3521_minimal_build.gradle_file
merge/develop_JAL-3725
merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch
merge/develop_bug/JAL-2154projectMappings
merge/develop_feature/JAL-3141_backupfiles_for211
merge/develop_task/JAL-3763_newDatasetForCds
merges/JAL-2906_update2_11_from_2_10_4
mungo_develop
patch/JAL-1236_customClustalHeader
patch/JAL-1791_timestamp
patch/JAL-2068_JAL-2169_multiviewannotworker
patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles
patch/JAL-2321_addsecstrForDroppedPDBFile
patch/JAL-2694_maptoallchainsworkaround
patch/JAL-2732
patch/JAL-2755_UniprotEnsemblSubnameWorkaround
patch/JAL-2914_relaxedGFFpragmas
patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars
patch/JAL-3561_JAL-3660_fileformatexport_CLI
patch/JAL-3562_fixAlignmentPanelTest
patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1
patch/JAL-3692enaEndpointFlatfile
patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3
patch/JAL-3794_X_is_a_dna_rna_base_too
patch/JAL-3821_ena_rna_moltype
patch/JAL-3840_2_11_1_4
patch/JAL-3840_2_11_2
patch/JAL-3847_gradleV7andV8Patches
patch/JAL-3874_newJmolAndGradleDedup
patch/JAL-3976_3dbeaconsnull
patch/JAL-4008_jabaws_2_2_1_patch
patch/Release_2_11_1_Branch_patch_JAL-3490
patch/VAqua_saveload_update_JAL-2988
patch/for2.11.2/JAL-3821_ena_rna_moltype
patch/r2_11_1_branch_JAL-3703_closing_files
portforward/JAL-2675_2102b1to2103
release/JAL-1645_r29
releases/Release_2_10_0_Branch
releases/Release_2_10_1_Branch
releases/Release_2_10_2_Branch
releases/Release_2_10_2b1_Branch
releases/Release_2_10_3_Branch
releases/Release_2_10_4_Branch
releases/Release_2_10_5_Branch
releases/Release_2_10_Branch
releases/Release_2_11_1_4_debianpatches
releases/Release_2_11_1_Branch
releases/Release_2_11_2_Branch
releases/Release_2_11_Branch
releases/Release_2_9_1_Branch
reviews/features/JAL-2136_phyre2_integration_withJims
schema/JAL-1764_structureViewAttribute
spike/JAL-1950_hmmer3client
spike/JAL-2778_changelookandfeelOpaqueWindows
spike/JAL-3548_exampleRestServer
spike/JAL-3622_Scanner_swingjs_J212_merge
spike/JAL-3690_with_patched_j2s_v3_2_9_plugin
spike/JAL-3753_helphtmldupes
spike/JAL-3781_2d_scaling
spike/clinvar
spike/javier_noseqhack
spike/phyre2
spike/try_spotless_JAL-3438
spikes/geoff
spikes/jim
spikes/jims_test
spikes/jpred
spikes/kira
spikes/koen
spikes/mungo
spikes/phyre
spikes/thomas
spikes/toch
story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window
task/JAL-1794_jettyExamplesServer
task/JAL-2164_mcviewforoldjalviewprojects
task/JAL-2196pdbeProperties
task/JAL-2562_SequenceI.findPosition
task/JAL-2662
task/JAL-3042_remove_SimpleDocument_dependency
task/JAL-3047_clover2104b1_cherrypick
task/JAL-3047_clovercoverage
task/JAL-3060featureEditor
task/JAL-3068lineartDialog
task/JAL-3089annLabelsPopup
task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS
task/JAL-3193mergeEnsemblGenomes
task/JAL-3210_ben_testing_jalviewJS_building
task/JAL-3243_PDB_free_text_error
task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files
task/JAL-3281_Automatic_installers_download_table_generation
task/JAL-3337-rm-lib-update-sourceDist
task/JAL-3349_Support_cli_JRE_arguments_through_getdown
task/JAL-3394_install4j8_option
task/JAL-3510-update-clover-to-4.4.1
task/JAL-3521_Slimmed_down_build.gradle_for_debian
task/JAL-3577_Jalview_Test_installers
task/JAL-3594_updated--CHANNEL_cosmetics
task/JAL-3763_newDatasetForCds
task/JAL-3789_configurable_j2s_file_for_headless_transpile_with_official_swingjs
task/JAL-3805_Remove_Old_Jalview_Uninstaller_application
task/JAL-3805_Remove_Uninstall_Old_Jalview_application_for_develop_branch
task/JAL-3911_getdown_improvements
task/JAL-3934_update_log4j_again
task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup
task/r2_11_2/JAL-3871_Jmol_dedup
tasks/JAL-3035_remove_dasobert_dependency
tasks/JAL-3067_slivkaprep
tasks/JAL-3070_wsinterfaces
tasks/JAL-3311_removeVamsasMenu
testbuild/JAL-3412_getIdWidth_test
testing/JAL-3577_jalviewversion_autoset_fixed
testpaches/JAL-2719_JAL-1264_testfails
trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker
update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more
vamsasDemo

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