master
+ 170 more
- JAL-3253-applet-113cc13-2019.08.28-js-optimizations
- JAL-3253-applet-SwingJS-omnibus
- JAL-3253-applet-test
- JAL-3253_applet_omnibus-BH
- 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
- Jalview-BH/JAL-3026
- Jalview-BH/JAL-3026-JAL-3063-JAXB
- 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
- alpha/JAL-3066_Jalview_212_slivka-integration
- 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-3103_browser_launcher_problems_macos_and_linux
- bug/JAL-3162featureStartLtEnd
- bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame
- bug/JAL-3365_extendedDSSP_via_stockholm
- bug/JAL-3365_failing_per_sequence_ss_tests
- bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException
- bug/JAL-3487-splash-JS
- bug/JAL-3523_cwd_not_preserved
- bug/JAL-3541_cloverReport_gradle_task_fails
- bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog
- bug/JAL-3612_overviewFeatureOrdering
- bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown
- bug/JAL-3648graphDragRelease
- bug/JAL-3700_mapSequenceSelection
- bug/JAL-3703_saving_a_file_in_Windows_10_fails
- bug/JAL-3705saveProteinId
- 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-3761_locateInFromTo
- bug/JAL-3785autoOverviewTitle
- bug/JAL-3788_autoOverviewClustal
- 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-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/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
- develop
- doc/JAL-3746_Release_2_11_2
- feature/JAL-1713_overviewInProject
- feature/JAL-2422ChimeraX
- feature/JAL-3117_overviewFocusAlignment
- feature/JAL-3144noJTree
- feature/JAL-3190jalviewjsChimera
- feature/JAL-3390hideUnmappedStructure
- feature/JAL-3442colourCaching
- feature/JAL-3443findColorAsInt
- feature/JAL-3551Pymol
- feature/JAL-3576intervalStore_1_2
- feature/JAL-3615gzipXfam
- feature/JAL-3624siftsInJS
- feature/JAL-3690_callback-based-web-services
- feature/JAL-3692enaEndpoint
- 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-3417_sdppred_calcs
- features/JAL-3638_jumptonextindel
- features/JAL-3641_phredfromfastq
- 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
- improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option
- improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store
- improvement/JAL-3420_match_jvl_icon_with_new_website_jvl_icon
- improvement/JAL-3503_startup_preferences
- 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
- issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop
- jalview-headless
- merge/Ben_trying_out_JSdevelop_with_develop
- merge/JAL-3210_developToJSDevelop
- 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-3840_2_11_2
- patch/JAL-3874_newJmolAndGradleDedup
- patch/JAL-3976_3dbeaconsnull
- patch/JAL-4008_jabaws_2_2_1_patch
- patch/JAL-4024_jumpScrollHang
- patch/for2.11.2/JAL-3821_ena_rna_moltype
- releases/Release_2_11_2_Branch
- spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data
- spike/JAL-3622_Scanner_swingjs_J212_merge
- spike/JAL-3690_with_patched_j2s_v3_2_9_plugin
- spike/JAL-3781_2d_scaling
- spike/try_spotless_JAL-3438
- task/JAL-3089annLabelsPopup
- task/JAL-3210_ben_testing_jalviewJS_building
- 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_Uninstall_Old_Jalview_application_for_develop_branch
- task/JAL-3911_getdown_improvements
- task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup
- task/r2_11_2/JAL-3871_Jmol_dedup
- update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more
