master
+ 254 more
- JAL-3253_applet_omnibus-BH
- JAL-3315_getdown_1_8_6_update
- JAL-3416_different_look_and_feel_on_linux
- 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
- Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg
- 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/develop_j2s_v3_2_9_j11
- Jalview-JS/develop_with_gradle_build
- Jalview-JS/gradle_for_eclipse
- Jalview-JS/update_java2script
- alpha/JAL-3066_Jalview_212_slivka-integration
- alpha/JAL-3362_Jalview_212_alpha
- alpha/JAL-3899_deuniquify_refactor
- alpha/Jalview_212_test_merged_buildgradle
- alpha/merge_212_JalviewJS_2112
- arnaud/develop
- benreview/JAL-3691_for_2_11_2_getdownrebuilds
- bug/JAL-1988_JAL-3772_improved_quit_handling
- bug/JAL-247autoIdWidthSeqMarker
- bug/JAL-2830_editManglesDatasetSequence
- bug/JAL-2934proportionalScrolling
- bug/JAL-2983negativeSliderMin
- bug/JAL-3103_browser_launcher_problems_macos_and_linux
- bug/JAL-3178nonposFeatureExport_take2
- bug/JAL-3212columnSelectionWithHidden
- 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-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-4072_zip_slip_vulnerability_in_getdown
- bug/r2_11_2/JAL-3904_structureviewermenu
- cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport
- cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat
- critical/JAL-3933_log4j_update_for_develop_branch
- critical/JAL-3933_log4shell_mitigation
- develop
- doc/JAL-3746_Release_2_11_2
- feature/JAL-1260_genbank_embl_flatfile_import_reloaded
- feature/JAL-1713_overviewInProject
- feature/JAL-2422ChimeraX
- feature/JAL-3117_overviewFocusAlignment
- feature/JAL-3121gffAttributeMap
- feature/JAL-3187linkedFeatures
- feature/JAL-3187viewstyleFlags
- feature/JAL-3251biotypedMappings
- feature/JAL-3364splitFrameImage
- feature/JAL-3390hideUnmappedStructure
- feature/JAL-3400viewChainsMenu
- 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/r2_11_2/JAL-3808_gff2_exonerate
- features/JAL-1953_Archeopteryx_with_Jalview_2_11_2
- features/JAL-2909_bamImport_2_11_2
- features/JAL-3010ontologyFeatureSettings
- features/JAL-3187_uitweaks
- features/JAL-3375vcfValidation
- features/JAL-3417_sdppred_calcs
- features/JAL-3638_jumptonextindel
- features/JAL-3641_phredfromfastq
- features/JAL-4034_improve_3dbeacons_button_and_ux
- features/JAL-4061_and_JAL-4062_findselectfeatures
- features/JAL-4071_visibleFeaturesCounter
- features/JAL-518_justify_seqs_in_region
- features/JAL-722alignmentProperties
- 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
- improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option
- 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
- improvement/JAL-4023_snotation_for_trees
- improvement/JAL-4064_M1_native_JRE_bundled_in_DMG
- issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop
- jims/work_on_2_12/JAL-3664_hmmer_ux
- merge/Ben_trying_out_JSdevelop_with_develop
- merge/JAL-3210_developToJSDevelop
- merge/JAL-3285_mchmmer_with_211_develop
- 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-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_task/JAL-3763_newDatasetForCds
- patch/JAL-1236_customClustalHeader
- 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/JAL-4024_jumpScrollHang
- patch/JAL-4036_uniprot_fts_legacy_endpoint
- patch/Release_2_11_1_Branch_patch_JAL-3490
- patch/for2.11.2/JAL-3821_ena_rna_moltype
- patch/r2_11_1_branch_JAL-3703_closing_files
- releases/Release_2_11_1_4_debianpatches
- releases/Release_2_11_1_Branch
- releases/Release_2_11_2_Branch
- releases/Release_2_11_Branch
- spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data
- 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/JAL-4047/JAL-4048_columns_in_sequenceID
- spike/JAL-4055_retire_JDesktop
- spike/clinvar
- spike/javier_noseqhack
- spike/try_spotless_JAL-3438
- story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window
- 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/JAL-4059_updateJmolandSwingJS
- task/r2_11_2/JAL-3871_Jmol_dedup
- tasks/JAL-3070_wsinterfaces
- tasks/JAL-3311_removeVamsasMenu
- testbuild/JAL-3412_getIdWidth_test
- testing/JAL-3577_jalviewversion_autoset_fixed
- trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker
- update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more
