FishEye: changeset 3fade83499e769d08529a9da301b64af33795610

Ben Soares

committed

3fade83

2 years and 5 months ago

JAL-3252 tgz unpacking no longer needed by getdown. Unfinished code and dependency on apache-commons-compress removed. Documentation mention… Show more

JAL-3252 tgz unpacking no longer needed by getdown. Unfinished code and dependency on apache-commons-compress removed. Documentation mentioning common-compress updated.

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91b9975

master + 185 more

JAL-3253_applet_omnibus-BH
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-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/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_quit_window_focus
bug/JAL-3103_browser_launcher_problems_macos_and_linux
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-3412idWidthDiscrepancy
bug/JAL-3523_cwd_not_preserved
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/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-3390hideUnmappedStructure
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
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-4034_improve_3dbeacons_button_and_ux
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-3280_Migrate_the_VersionChecker_service_to_build_properties
improvement/JAL-3289_new_launch_screens
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-3449_add_install4j_installer_getdown_versions_to_jalview_console.2
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
issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop
jims/work_on_2_12/JAL-3664_hmmer_ux
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-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
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-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
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

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