91903511dc5db6e8c360ffa330d483b1f638bbca	refs/heads/2_5_1_rna_merge
d1718072ef2d5d921de0c253ccba3af665dbc6ac	refs/heads/JAL-1199-Stk_writing
96f10f96255b4e9bb88601ce01adbf5faf16544c	refs/heads/JAL-1260_droldan
dbabbe48a455467de19b953d098a9cd943f9c133	refs/heads/JAL-1375_ncbiclient
245c9609dc00df56054b35e76aff48a2dda0be50	refs/heads/JAL-1550_intermine-sequence-annotation-client
67473776389cd0a6024aa3e401819e503970082c	refs/heads/JAL-1562_help-documentation-system-refactoring
44f7d3f329e2607a05b7b8b177edb4432e526502	refs/heads/JAL-1601-direct-jpred4-rest-service
0b1c761dfaa8242f122cf868e8897a06ec6eb727	refs/heads/JAL-1956_featureStyles
607cd66d3ccb056b773d9c32271ebf08e06a451c	refs/heads/JAL-2571
e760e4772fc65a111dbb91358281dd182b53b3d0	refs/heads/JAL-2739_2.10.2b1
bf3afd12ede3a18ddb4843a100b075285c9fa92c	refs/heads/JAL-3253-applet-113cc13-2019.08.28-js-optimizations
6200addf078b7f7ace90597dc056dafc7fc602c1	refs/heads/JAL-3253-applet-SwingJS-omnibus
b56e5883749812e770d2337f66d397ae14075612	refs/heads/JAL-3253-applet-test
b87512d6e28a2a93ea2f08dcfbee320856c5c8de	refs/heads/JAL-3253_applet_omnibus-BH
c565b24f5a866bad10eda5050e6e942819d687ac	refs/heads/JAL-3315_getdown_1_8_6_update
c843dbd309a13ac1b576d76b33e2a0a5d3a227bc	refs/heads/JAL-3368_JavaScript_colors
f300e30df117ff4be7d1df5c781161efd0285e5f	refs/heads/JAL-3437_load_project
171426bbaca3ec0ff275e54981c917cbca2f012a	refs/heads/JAL-3866_RNAalifold-slivka-client
dc2e21ef0092f0e79c1837fc76a81710bc74e3a0	refs/heads/JAL-3878_web_services_overhaul
52eaee0814ad21a395b6e76bfb05511b4fc766ae	refs/heads/JAL-3878_ws-overhaul-3
cf04d0714f5d7686f47201d42d63df80b4ebf10d	refs/heads/JAL-4152-typed-singleton-provider
ff3fcbec0f1f62d99eeaa96c7e312cb426da43f5	refs/heads/JAL-4154-platform-specific-constants
f244cdf6267fd446edc039d49428fa8eabcca42c	refs/heads/JAL-429_phylip-file-support
88ec5ec9e697a1a5ee9e2c3ede3e248e1a6d918e	refs/heads/JAL-4442_cant_quit_jalview_on_windows_11
52750109fdb60b7b8d936d4624a8a39d5a722fb2	refs/heads/JAL-4474_jalview.ps1_not_working
e2b7673f7157b2c8cfa45ba774b115c9b3670946	refs/heads/JalScape/JAL-1332
f20ff42eac30f33cb69635ba3217a6224dbeb555	refs/heads/Jalview-BH/JAL-3026
41c22f3101808e56063007b4eef09c1a9181a30e	refs/heads/Jalview-BH/JAL-3026-JAL-3063-JAXB
6ec871abfdeca0c40d2821bbff4839dbfb28d121	refs/heads/Jalview-BH/JAL-3048_dialogs
2cbf9d005db462396fa1dc0750aa63a2e6cd0735	refs/heads/Jalview-BH/JAL-3048_exportSettingsrefactor
54ba1050fb7ef47d3e58f0c0ed52d3e4629ba5f4	refs/heads/Jalview-JS/20190123
521951df7d677995b8e142fd0a3c3061df5d2781	refs/heads/Jalview-JS/JAL-3253-applet
dbbc1013d01d733adc88e7a22ce8a230ae8178ca	refs/heads/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML
1f8ac77d7dd4280fa4349e63c5b4ef0c1dfaf9b7	refs/heads/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly
c844fbda900f095b00a72be43ebf2a068b5050bc	refs/heads/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e
45cdb111f9dec2c4a6b50045e3138b23929f1581	refs/heads/Jalview-JS/JAL-3560-bh-temp
1fb9dd2acf85b18385a90376c991555b7421a0a4	refs/heads/Jalview-JS/JAL-3560_bob_temp
549a0f817a1a3addc064cbb3d8f4fe8d51058c3c	refs/heads/Jalview-JS/JAL-3563-sync-TestNG-test-bob
c700a0ef78467620d38bbeec43bd3b31b08ec257	refs/heads/Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg
cfa118f7383e300235afb04ec0e093bf4e50b928	refs/heads/Jalview-JS/demo
650bca3ef095d09a5354240e7d2bafb6fc524122	refs/heads/Jalview-JS/develop
ce270fef5a3e00b57f0b2077800796c3654ac68f	refs/heads/Jalview-JS/develop-JAL-3559
f3213c0763f9a1d1b911ad5d64074b971f5b8e8b	refs/heads/Jalview-JS/develop-updated-gradle
47933804578c000492a8f6f84a45d7bc6000315b	refs/heads/Jalview-JS/develop-working
7702e684eb32a5719f4da2a99b09319c077af07f	refs/heads/Jalview-JS/develop.JAL-3445-BSML-reader
32c41447d98ef79a9e82c4947d8776f3b0220323	refs/heads/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync
c0f918667cb58c5fdd6bc344db7cd50dd5cf5d43	refs/heads/Jalview-JS/develop.JAL-3446.ctrlDown
9428c0004754fc3376fbbd8023fe71c1336ad2b6	refs/heads/Jalview-JS/developPreFrameEmbedding
0aa289427134d46212cb8fd7e207f714ec0282f3	refs/heads/Jalview-JS/develop_j2s_v3_2_9_j11
2f0f4a60825f566eb793cba837144e2de767a9a6	refs/heads/Jalview-JS/develop_with_gradle_build
0210a246bf503771b40265bda0aeae305ec201ba	refs/heads/Jalview-JS/gradle-minimal
47933804578c000492a8f6f84a45d7bc6000315b	refs/heads/Jalview-JS/gradle_for_eclipse
012a1d2bc849431872a6fd57253d31941e59cc93	refs/heads/Jalview-JS/gradle_with_goomph
9b0bf59c743413e08a272dae04d7347f1163e90b	refs/heads/Jalview-JS/gradle_with_inline_eclipse
59191d7e340d86fc7a294a09fc4e2940bfbef535	refs/heads/Jalview-JS/jim/JAL-3253-JAL-3418
0df0d8560e30bdd32d0f8982c1774fd141835086	refs/heads/Jalview-JS/tasks/JAL-3274-build_details
e30f4e079986a86c88f3510ff5c77f4293d8e8fa	refs/heads/Jalview-JS/update_java2script
9cd3ff27d8a47b2e8b1f3be9ff07d47ea9bc6fd1	refs/heads/Jalview-jJS/JAL-3253-applet-JAL-3436
a18c4df2d9f819b7b38006bcac3e23c14fcd95e5	refs/heads/Pre_R29_develop
ef0377ec8e57164363e74c33d6ede31f85e8ccf7	refs/heads/RNAalifold
447594fbb352e9c1bf1c687edcdda896856b4c0f	refs/heads/Release_2_3_BuildFix
0ec09c85f867015b71e69f1f3782bb4db96f64f4	refs/heads/Release_2_4_branch
f81941152d7100b7cba6c21a9b53f7e09911855c	refs/heads/Release_2_5_Branch
4230b657b444c3667e9c8cc7974730681130ebae	refs/heads/Release_2_6_Branch
2d348a0c5220b0f108d8c029a6503dd8f751b0ff	refs/heads/Release_2_7_Branch
4cf0508ac56ebb01fbd51b547ea9f4a682ca97fb	refs/heads/Release_2_8_0b1_Branch
851862539af88de33410e154cfd0ae5746b49045	refs/heads/Release_2_8_1_Branch
6ca7cf3ba5134086da3fae5397e5404c6f7b0a58	refs/heads/Release_2_8_1_Branch_i18n
6f6f5dd035df25f971ab1191c76bb3bae337e950	refs/heads/Release_2_8_2_Branch
f326c11fa50ef0ab83a31b0d0f9ddb1e66d4ae10	refs/heads/Release_2_8_2_Branch_i18n
dac9672dba85c9bb2d7b7313e015d7561f252fe1	refs/heads/Release_2_8_2b1_Branch
06746783147ba5d514252eeedb43d8fda4d0e358	refs/heads/Release_2_8_Branch
e6dfb718d73b9398701aba29e8c8ffb20bad2b26	refs/heads/Release_2_9_0b1_Branch
cdb598b011f9ab8b33fda92f917c2f96a5e1e577	refs/heads/Release_2_9_Branch
7622ff8a4deb1dfdf960c38883421089c1c0a314	refs/heads/Tcoffee_JAL-1065
c4dd9fbd848d3ffaa88134fb06bed794d69bc6f3	refs/heads/VamJalview
1ac48a3ee02288fe52f16f9637bbaa099594fe4b	refs/heads/WIP_fix_JAL-1423
dce490b7c7c8f2c2021f7dd93ba126af0c6eaf43	refs/heads/alpha/JAL-3066_Jalview_212_slivka-integration
b4a563ef7c7bde6be17d5dba0ef6927b2de555df	refs/heads/alpha/JAL-3362_Jalview_212_alpha
e7e676ca075c5b2832be98b4544364e5d6adc4c1	refs/heads/alpha/JAL-3899_deuniquify_refactor
e46258ec9c1d56a23167aa2ba0ff4778a418d0b5	refs/heads/alpha/Jalview_212_test_merged_buildgradle
e3c3367f89785a5cff5fb3bd419c92ccb4ac13ea	refs/heads/alpha/merge_212_JalviewJS_2112
a848ed8eb380e5f9d915b0d7a062feec4f9d3dad	refs/heads/arnaud/develop
fea21020365d03c17fcdf81e3141fafa77585577	refs/heads/benreview/JAL-3691_for_2_11_2_getdownrebuilds
08a024937b60499b53a60024f9b40402f623ec8d	refs/heads/bug/JAL-1054_broken_test
d5a877fec053515bfd780d289ace37cbb85a357c	refs/heads/bug/JAL-1460_dragndropWindows
ddbcb3e33e1a8d4c644472cfa3d28b193da97064	refs/heads/bug/JAL-147scrollWrappedView
678a8ac35bb269d80cda081bec11e7b403c9811a	refs/heads/bug/JAL-1552dragndroptake2
aa3cf1b48ce4735d980fa5616dfacab458ecefe2	refs/heads/bug/JAL-1552dragndropurl
d4a9ea73ba6f86fdcb69e08529f38600db3a99fc	refs/heads/bug/JAL-1608createGroups
c21161c142574cc7677d3b0666f58d25082b3cf2	refs/heads/bug/JAL-1643_File-chooser-improvement
06f52ec5772e4345648f174d0213ac15c058d168	refs/heads/bug/JAL-1644_Finder-logic-improvement
bca294a4376fbe2087f03ca2c44bd591edc61aed	refs/heads/bug/JAL-1697_browse-local-structures
a49a5c83b2616e58475c57a37b9a5127d1551a64	refs/heads/bug/JAL-1698_Append-Structures
d71500a42803f307500c16250b40f0fc31e74aad	refs/heads/bug/JAL-1712annotationsWithFlanking
0b964c7c950cfdf444261be06a88a4db5a5bd2f5	refs/heads/bug/JAL-1803_JAL-2157
efe59a09e1a7606cb837fd562bdffc44d45b9206	refs/heads/bug/JAL-1819_isNaN
4ed0cd5f8477ba52a9f5b19b021f8f6183f9dd61	refs/heads/bug/JAL-1841rnaSecStr
3f8f40c6d29cd368cd4b20185d8a769ce8da0555	refs/heads/bug/JAL-1858fastPaintHighlights
2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1	refs/heads/bug/JAL-1889serverTestSuite
0d37fef8a89c67845c14f2383e89003c9a2c5b62	refs/heads/bug/JAL-1988_JAL-3772_improved_quit_handling
d7ed5404a518dfe4a3699ac299b5e644b27dd05e	refs/heads/bug/JAL-1994_Jalviewlite-json-parser-in-browsers
b06dd5c7f0f1a8d7b75fdf165b7d990681f2e2e5	refs/heads/bug/JAL-2023_cdsProjectError
aa3f68f34c3128308d561b321168fb755539f999	refs/heads/bug/JAL-2034contextchange
d5ada7fd50053719348ac1301f45b54970616a87	refs/heads/bug/JAL-2044jmolModelBinding
323209e10678fb37fb1f6ac5321f5032ac8c1ff9	refs/heads/bug/JAL-2154projectMappings
b45b78bfc90750c57a947ba64e47d43de36100f1	refs/heads/bug/JAL-2210_hack_for_Release_2_10
30b2b47cbdfa35b127b0fb09e911815cddd9ed7b	refs/heads/bug/JAL-2245enaXmlChange
3eb959d7f16b64260b8bec08d49b28ffc9670517	refs/heads/bug/JAL-2253
a38d7808b759178025820c8d220a37d1442a57b3	refs/heads/bug/JAL-2255_seq-fetcher-broken-on-linux
18565b7cf82c50da2d6266f885fa6ebef929db79	refs/heads/bug/JAL-2256
a54d99a6637c6d2ea2ada774a49d496ab0b374ee	refs/heads/bug/JAL-2262_dnd-for-local-structure-files
6631ee3334607cc5e0b670191f9df048c157325a	refs/heads/bug/JAL-2272cmdClickGroupEdit
e950d7035158d0dca7bcc466aecfb32450d4bd52	refs/heads/bug/JAL-2277_html-output-wrapped-mode
4f30cce34289ac0c2dee7b65218f8b98a6a63172	refs/heads/bug/JAL-2277_refactorPrintUnwrapped
f7061cf12f703969bf3e22fc7e37f5712b9df10a	refs/heads/bug/JAL-2281JAL-2282
62eb39691722aae525b9aa5c65b38af87ffbcf24	refs/heads/bug/JAL-2282
14f83a93e915f830be2c795ae51798a74eaf797d	refs/heads/bug/JAL-2283consColourEnabled
4aac664cf4bf4e3ed4b18db0c45c6a1c2f1b7368	refs/heads/bug/JAL-2308
86e844061a6202e657f2a6886c5ce0057952995a	refs/heads/bug/JAL-2309
b87940a9a7912d334d0c646c38e658a1a55be769	refs/heads/bug/JAL-2314
462d0235e87b52a930d0930094c32c541bff86a3	refs/heads/bug/JAL-2317_jmol_chimera-chain-factorisation
eb5043c4c5932b46aa018e37ae42bd011405cd87	refs/heads/bug/JAL-2323disulfideOverview
1e103edb54d2b8c206bde10399e488426c4b651d	refs/heads/bug/JAL-2339helpBullets
b644ff46e2ed0a6cecdb2945600254791d275d4a	refs/heads/bug/JAL-2346annotationChoice
9b717f5894d6df63a55ab46a97f4de2e1cc18e9e	refs/heads/bug/JAL-2358phantomChimera
517dab88dfe59707fe225eac761d3c46719a72eb	refs/heads/bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu
331cd27699e0303dd42fd01e293f5fae9445e125	refs/heads/bug/JAL-2386groupConservationColouring
9eabd6dffd6d19b2826b887a5def80351b9bceed	refs/heads/bug/JAL-2399textColour
7592eb537b8a6ed0c69d263955f12a592bf8de8f	refs/heads/bug/JAL-2420revealAllMenu
d54f8d3b0bf910b99991441485fd5d42acf1df7d	refs/heads/bug/JAL-2424getVisibleContigs
3d2b5edf9ea33c6ebbde4717ccc14f03554fb6f0	refs/heads/bug/JAL-2431splitFrameNewView
ef0a35a8dff8c0cc6ffa634c2b01cdca61f74b3d	refs/heads/bug/JAL-2436featureRendererThreading
95443a95c1282c050fe1f28a4ddcaf3f0f75dfb4	refs/heads/bug/JAL-244_interactingpngexportnotwysiwig
71b7dc2dbc920391e3209bde9e915dd3436871f3	refs/heads/bug/JAL-2461
68396d959a624822e59b6210184df8c98732107a	refs/heads/bug/JAL-2479unitteststoNetworkGroup
1173ed15c801a5f16abcb12e05ff913628593639	refs/heads/bug/JAL-247autoIdWidthSeqMarker
ddae5cd17183675eb4a1cb7ad49048193caaf1a0	refs/heads/bug/JAL-247pngShowHiddenSeqMarks
f40c312c2886853668ad7651461d8a1b8600e659	refs/heads/bug/JAL-2491
95702b58b4a81f53147aa5e4add078f965966437	refs/heads/bug/JAL-2507_rnasecstrstockholm
cd126a7085c5ebcfc8c05378c71bd862abc4fd91	refs/heads/bug/JAL-2510amendFeatures
5d9994e09150d0a3e6c49cef59a5a9c242b16290	refs/heads/bug/JAL-2511idAlignment
e63ac3b8efdb9be3a6a94ea36a3642d7a0d615bf	refs/heads/bug/JAL-2512
5078a67d8357697791d2e71f9df95a46e762aa2e	refs/heads/bug/JAL-2515
342037486db348e0d40faf044b8111ddb06c222e	refs/heads/bug/JAL-2517cancelAppletColour
968c3bcde941e502fcf7d497343600f4f58f6c9a	refs/heads/bug/JAL-2536
4b41478373a5c4b90a106af7351ace054f476c67	refs/heads/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release
c3d92b4b7a6cb00f9e596dbb7cd6c8508da5c252	refs/heads/bug/JAL-2547tooltipOnGap
fedf8a87b0e465e6e5ce55a51a123d4a2d477959	refs/heads/bug/JAL-2551
bda14302200fc3bcfe66dc513bd030cba10a3681	refs/heads/bug/JAL-2576
736a572a7f2ef47988a37d01992ff03045bfdb24	refs/heads/bug/JAL-2577
7a449f227cd532d24c214521cb7657420fdba694	refs/heads/bug/JAL-2578
5c796f726aa87b2ce057852bfb9e8d9195c68c73	refs/heads/bug/JAL-2586
e8de20ca6781f6152fdd3cef89122a5a654e3496	refs/heads/bug/JAL-2589gapColour
54dd5d7c3c4384ef383ead7cf3d150ac5fddb3da	refs/heads/bug/JAL-2591
11b2e9b16c3bb93d8788c2bc5d5654f6163402e6	refs/heads/bug/JAL-2592userDefinedScheme
834dcc21a8a324b092285c1295df9392654d526b	refs/heads/bug/JAL-2597
d738273bebedaea35a9e4a5acbe5e681f9fbae67	refs/heads/bug/JAL-2600resizeflicker
c371d7d1dcac5bd74a3f693c656d8cff3168a57f	refs/heads/bug/JAL-2617mappedStopCodon
de5b6551176b63d930db8fbd62efe3434de0a420	refs/heads/bug/JAL-2621
bb27d9c1cc4d5c31df6bae6c469178b2b700e119	refs/heads/bug/JAL-2630gradColourUpdateOverview
230930d6c4a972216f28dfd34c071bf3e83d8010	refs/heads/bug/JAL-2634
4dd40d33a5becefd51c31a426f2501b21029f82c	refs/heads/bug/JAL-2665
345ebd023e398df875d769f85061551888cd71e6	refs/heads/bug/JAL-2665-2.10.2b
e67951a5b302b6a73cccd4b35e6ec1bdda31dde3	refs/heads/bug/JAL-2665-2.10.3
5d149a2e764fcf28b153bd31134a7263d6b3cd2f	refs/heads/bug/JAL-2666
2ca31c294c758a1f7e6c314ff671ddd03f937e60	refs/heads/bug/JAL-2673
0512e7b6771e736d05c3b777760502e3368df56b	refs/heads/bug/JAL-2673_mergewithproblem
1bfb581512684bc3bcbb108405d5db0e795cbc6f	refs/heads/bug/JAL-2691_nomultimermapping
fb06722c6787ed41809827a0ddfb9cc6e9c7324d	refs/heads/bug/JAL-2704gapColourFading
09af5cd382fe2ce9f5ce1a9641615552c96fed51	refs/heads/bug/JAL-2721fastPaintNPE
32c56f877253fa8917d4f4640ed65d6e63376dac	refs/heads/bug/JAL-2722
68f3676bed58ab5f4fdfbd71dcaf4e1ed61d380f	refs/heads/bug/JAL-2728splitFrameDivision
445fed6ffadf67619312eef879720009f4e1f910	refs/heads/bug/JAL-2740
4440154511df719a41ddc7e3a7f24c012ec305a2	refs/heads/bug/JAL-2750
cef8dbc4cf7c8b47864b11aad36596901003639a	refs/heads/bug/JAL-2757_uniprotftsbadquery
98558735e9208afa98bb155bd5350ad0a680ca24	refs/heads/bug/JAL-2772pdbArrayBounds
cbbb5ab209dac86be8439435c9a4fc58371b5429	refs/heads/bug/JAL-2776toggleGroupColour
0168e4a2e558279d5a0523961e8c377732bb964f	refs/heads/bug/JAL-2778again
2e9f692c73eebcd3f09f4762bc86acb5b5058202	refs/heads/bug/JAL-2784
bb620cae1e4c44ae9efaf975c7bbbc63b0558db3	refs/heads/bug/JAL-2791exportFilteredFeature
b37c5048ef9edc96ad514bd1d05932721a1afa2e	refs/heads/bug/JAL-2791selectVisibleFeatures
f941283dbf6f88b3a3973cbea908f8bdef387a3c	refs/heads/bug/JAL-2811
e249a4950d0e7f3c5ea905f3c1c02baebd92b708	refs/heads/bug/JAL-2821
642efeed2ec89ac027f4a9f21393669e61632282	refs/heads/bug/JAL-2827
24774f02cc21b562b62479e149a226dd1a8c3e5e	refs/heads/bug/JAL-2829deleteCharsWithGaps
aace9d05c0870c703bfdfb28c1608213cee019bf	refs/heads/bug/JAL-2830_editManglesDatasetSequence
195b605509007fa22622c277eb106ae6e994bfb0	refs/heads/bug/JAL-2831
66e2ef1a1a7767b8ca8d40f108f29e9036166236	refs/heads/bug/JAL-2837
9b5106c49c8fa0a7269f38ad1825851eb8ba5b85	refs/heads/bug/JAL-2839findWithHidden
16eb01c0d83f94f2c1065b6688166d8624529fa2	refs/heads/bug/JAL-2842
ac8b34acc63ae60f009b195375eb0d70d18f3c72	refs/heads/bug/JAL-2846
8d455fca935d22c72ac32afc39633eb485da9d38	refs/heads/bug/JAL-2848resetColoursAmendFeatures
f5cadfa2a55d78a08268a0df9a7c3f64d1c43e8a	refs/heads/bug/JAL-2851
aa885913f06fc3885c818370544f43474a14f402	refs/heads/bug/JAL-2859_uniprottowrongpdbid
da8227037b89968cfd923ae3707743f2c0369d20	refs/heads/bug/JAL-2864nullOverviewCanvas
a958faf67348b6360f735e51b9b23c24976014cf	refs/heads/bug/JAL-2865removeGC
94202c5a8e9ddccf471659d63025f6174811df7f	refs/heads/bug/JAL-2876byLabelThreshold
0defe3aeb990d75fd672e882edbe9e8156b34414	refs/heads/bug/JAL-2899
6750995f850bda7402e9b69bd4cb55713cdf9d4d	refs/heads/bug/JAL-2907stockholmGapChar
10cb8ffc129d24c1a4bc506199d2e144ec99c038	refs/heads/bug/JAL-2920_uniprotvariantfeature
440a51fb7671e735cbf877500f4931987f23f692	refs/heads/bug/JAL-2924nullTooltip
3ba561cc50d627d9426285993988d3d99c2232f8	refs/heads/bug/JAL-2934proportionalScrolling
0f9e00ed49ec59c268db6f15ac0f3feb562770db	refs/heads/bug/JAL-2991_exporttosvgwrapview
31ebae5b435a9bfaab6fdbe9eb2c86ba8ef00589	refs/heads/bug/JAL-2992panelHeight
9b8a7cae41e5d0e2dfcd806319ca2d301dd133c5	refs/heads/bug/JAL-3002fastPaintWrapped
ae84c1dc2deb8aa70c9d6ef90b2f56e152a5790c	refs/heads/bug/JAL-3003epsWithSelection
8334a9d216c71bd0960ea01e2991c26382a139b7	refs/heads/bug/JAL-3049colourCellTooltip
00e9d8ee88dbf637ff3bac98c1e0b038625f7437	refs/heads/bug/JAL-3059groupBorder
d5e758fa924437e30dc65b80a46cafcf4691da2f	refs/heads/bug/JAL-3065_DH_keyPair_Exception_nogroovysettings
08a853afa3f76ec24a175e37bff43dc18ef781b1	refs/heads/bug/JAL-3072scrollThread
013692af798bd65da3b5cc39cb24a0aaca54e613	refs/heads/bug/JAL-3075
ef84f77ebe6c73e67e8ec789b02f41891715ebdd	refs/heads/bug/JAL-3076ensemblGeneId
68de2395c5eff963b717e41ef0230084336522a6	refs/heads/bug/JAL-3078cancelTreeFont
d8720fc191cba996c440171ef8e07462ef9f7035	refs/heads/bug/JAL-3082selectRegex
c56d96f3544cd3b4e0a7d36a8eba04f767eaf57a	refs/heads/bug/JAL-3083cancelAnnotationColour
7d30c031f338d9866e2564d86dfa746423d65f40	refs/heads/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way
92e13307a132894d5133db15bb127afa872cdc45	refs/heads/bug/JAL-3097blankExtraColumns
92c2fd083f7f5844693878f946441d75241f13bb	refs/heads/bug/JAL-3099alignmentVisibleWidth
e42eed3a0089a8a064560df4cf17a5021fd1e16a	refs/heads/bug/JAL-3120restoreFeatureColour
ef7d9bed59341ba8a035dc4578cd9c62b655286b	refs/heads/bug/JAL-3139colocatedFeatures
470b622223b227bdbd4af3151f9d002a95bb1f52	refs/heads/bug/JAL-3141_Messages_discrepancy_fix
1177ddadfb3c0197acc16f228790e56de4a2025d	refs/heads/bug/JAL-3154tableColumnDrag
f1f528a731ee18c62c4f1944ea3eda41960f16f9	refs/heads/bug/JAL-3158selectionBroadcasts
14208707a204bf8f7f2f714eebfdfd937094b943	refs/heads/bug/JAL-3161annotationTooltipRange
8018b976d0b8bd10994ff64f590832d1091e4558	refs/heads/bug/JAL-3162featureStartLtEnd
06476b6d02ef690bf684905cba39eb7b5db7525b	refs/heads/bug/JAL-3164complementOverview
63dc4eb11b8a7129326134f4d9a041823372778c	refs/heads/bug/JAL-3166npeAllRowsHidden
8488bc9805734461d015552f1447a607412fc550	refs/heads/bug/JAL-3171_maintain_datasets_across_views
bb4e715f6a6681100b7b43562211cf690118ee8a	refs/heads/bug/JAL-3178nonposFeatureExport_take2
14d6afdf47982b050cab51431d01588620723e8c	refs/heads/bug/JAL-3183groupColourOverwritten
e0fead054f258a000aad3f6a053d8a2aaeb92aa0	refs/heads/bug/JAL-3184restoreGroupVisibility
63cead20b09743e899a22cb89f1c09e4d41cc8c0	refs/heads/bug/JAL-3195idResolution
46242d05bbdd0ad5c77230436b189d904e303f35	refs/heads/bug/JAL-3201groupClustal
cd578c5f56a88269077e547ed22f3b5f4bd033cb	refs/heads/bug/JAL-3202zerosInProfile
5bad8435fd8ef2481b42814d876c12d4f52f0620	refs/heads/bug/JAL-3212columnSelectionWithHidden
904dafed30e4da63436e5303851c735a88ea1a4f	refs/heads/bug/JAL-3215hydroColours
961e285f3c6769a3d68152a7784d85f6e814cafb	refs/heads/bug/JAL-3218scalePanelPopups
90a413a8cf57d937a8529651a2c688ba3fe4784c	refs/heads/bug/JAL-3235sortPropertiesJava9
f29373e1a61c59573c822f1476c13b054264796a	refs/heads/bug/JAL-3235sortPropertiesJava9-2
93fa1f2cb39ea3ffcf142ab35a77917e2b3d1bbf	refs/heads/bug/JAL-3239monospacedEps
6853a22b51420bcea0fe12932d8850ffb30d9844	refs/heads/bug/JAL-3244jmolWindows
940d306aecea7dfca8c55cc4beee938a95de43df	refs/heads/bug/JAL-3286duplicatePdbQuery
cbdf701c27664c48d6b8cbb21c95c9994c5e97b6	refs/heads/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame
9fa3368723ed450b77baeb02c5eaec33f7668965	refs/heads/bug/JAL-3288splitFrameMenusJava11
94c90874868e68016e7521e4f28738b3f5436dde	refs/heads/bug/JAL-3296changeStartInvalidateCursor
afa061b7ecd1bc011096d9f2879448185874fcd3	refs/heads/bug/JAL-3330_backpropagateEnsemblFeatureColours
416f3bcbd98380f18b8ea5b5124e088e81387cb8	refs/heads/bug/JAL-3341unitTestFails
3f086e4f77ae2baed4b6290bce9cfd964fbc9446	refs/heads/bug/JAL-3365_extendedDSSP_via_stockholm
4abe263f327773456c984373a8387e4d8c3be5a9	refs/heads/bug/JAL-3365_failing_per_sequence_ss_tests
68e4922642155902049847769a23ff0fecba5100	refs/heads/bug/JAL-3388structureChooserSorting
d0a3c7594380d978b0d3bf3cbdba55a016b9d920	refs/heads/bug/JAL-3412idWidthDiscrepancy
1dc587cd6751c722615c0da18e06a2ac5f7276f3	refs/heads/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException
ef331671d007dc298187e064b7568e0a87c1585a	refs/heads/bug/JAL-3477_memory_max_allocation
81fa75d3be89d74c209d9c8d83c70a53329cb587	refs/heads/bug/JAL-3487-splash-JS
4ffa5161216adc501b127408f1596f507b9c7b92	refs/heads/bug/JAL-3489mapChainsFromFile
5574cf40bdcaf7ca99ba0611ed76824e7fb12cd9	refs/heads/bug/JAL-3490findSpanHiddenGaps
75b8a1f5fc598fce03b4304c5e165c2ef6855389	refs/heads/bug/JAL-3502wrappedScale
2bc2eea0112451e462f90fd0a07e82ca7d20f689	refs/heads/bug/JAL-3509hideResnum
1e096be5d77acc09902b3ada8eeb82a55cd6535c	refs/heads/bug/JAL-3523_cwd_not_preserved
bde972cad13060894eadcb189afc9fa3d8ec265a	refs/heads/bug/JAL-3536getCrossrefTwice
fc59e4fa8e496692052905f4427fe03cc118dbf2	refs/heads/bug/JAL-3541_cloverReport_gradle_task_fails
cee7f3931f46066e9f81a1cac7d29083e49de8d4	refs/heads/bug/JAL-3561_translatefileformats
d7f669694da3aefe896e649e2ba52f68ae5b790b	refs/heads/bug/JAL-3574filterByPOS
476a45a4f966195404f7b118c6e25f0bbc7f3bfd	refs/heads/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs
7baccbacc20ff22336ca8c94935f6124b5e5a135	refs/heads/bug/JAL-3612_overviewFeatureOrdering
4c5a5acfdbbca27883389d46b52c0e4cc5881b30	refs/heads/bug/JAL-3613emblCDSTracking
54770bcd7db9bcac27cf211246e029660d6a3f15	refs/heads/bug/JAL-3648graphDragRelease
48f5f04700dcb49463b20303c2075292f9d4d1d3	refs/heads/bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
708cc06af06aa2912319ad736bcfecb62081de39	refs/heads/bug/JAL-3700_mapSequenceSelection
0c85e43a68ad2de5318b6e3f09bd743b7933a890	refs/heads/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI
548ca3e0a4a049bf0c0743efcdc6bdb2a0c6112a	refs/heads/bug/JAL-3705saveProteinId
62c6e630bd24574d279417dd6b4ee921b5537131	refs/heads/bug/JAL-3706virtualStopCodon
8b4fb6dae17a6f34412b1ca6953e9923a9dc7c19	refs/heads/bug/JAL-3725overlappingVirtualFeatures
23e240e0e174b189d6561a5cb5c5f8dfaf3ad83b	refs/heads/bug/JAL-3744_read_gzip_file_in_jalviewjs
7addf95ae5d9d395bf535ee843238add6497f96c	refs/heads/bug/JAL-3751_revisited
e35961e7ec71dc750e181300f4b099508ed82ad5	refs/heads/bug/JAL-3751overlappingCDS
8e28da69f3e2efb3b510bbd0f08032b01a727646	refs/heads/bug/JAL-3760_protsTreatedAsNucleotides
4512cdb02fc0660c87e3bacf489f299623c3d33b	refs/heads/bug/JAL-3761_locateInFromTo
4bd3d60110787a65e53b5c1b9d4f10ddb7025090	refs/heads/bug/JAL-3765_Find_bugs_in_21112
a26b3456e3547547d052f1c5437255bd8690dd7d	refs/heads/bug/JAL-3774_splitFrameFinder
f90b9284525e774e2d2f53811954235513f20cbc	refs/heads/bug/JAL-3779setGroupProperties
7b32d373b60d0af55481cfd6d377b2cc1ec035c0	refs/heads/bug/JAL-3785autoOverviewTitle
818739945b29ef80bae395f0341055b844608ad0	refs/heads/bug/JAL-3788_autoOverviewClustal
8bcec0698d13dede379ac8079d544d2da50e106c	refs/heads/bug/JAL-3806_mappingCoversCDS_reprise
cb628aab46f9027e71b71203b322f96710e09990	refs/heads/bug/JAL-3806_mappingCoversSequence
4d71acba1cc4999e8e4061ec3e9ae55e1b37084e	refs/heads/bug/JAL-3806_without_shared_DS_for_2_11_2
b6bd3fa646b6728cd59c8d0de91270ab6c70f86f	refs/heads/bug/JAL-3807_jpred-with-slivka
7b64243974c397a651fab57090dba203b332e406	refs/heads/bug/JAL-3809_ws_params_dialog_fix
37713035750521ec4a22eba221e810465623b0c0	refs/heads/bug/JAL-3810_annotation_ws_stopping_abruptly
e691bab6155dcc19e5d6ed552ba97138cd0c7b50	refs/heads/bug/JAL-3818_jmolDeadlock
0b438477b16470202bddfecb54e0587036b37202	refs/heads/bug/JAL-3849_aacon-parameters
c7a72b43db4b03f2146e1cd7c41ac2e59fac1e0c	refs/heads/bug/JAL-3972_VAqua_for_Java11
be1bafa0439c091e51d7a6aa2084fd201f8c24f4	refs/heads/bug/JAL-3978_copy_bin_dir_to_getdownArchiveBuild_task
569a95435f50f9537f9d49dcc796a3c8f918cae1	refs/heads/bug/JAL-3980_JAL-3981_tooltips_sequence_details
ea7aa18440e6140ec7485e6cefdfb1dffb945580	refs/heads/bug/JAL-3997_NPE_in_wrapped_mode
1b33d2e45c7cedc0c58b7f78fbf35a742b1a1a05	refs/heads/bug/JAL-4001_fix_About_Jalview_not_appearing
e4c2a9483a41740a85c95ffbf014e23f9afe79f6	refs/heads/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq
68d58f205b96505c393bcf699db43dd586901233	refs/heads/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
360177d2c0f4550de2be90b5f9536b991123e16f	refs/heads/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0
c1f6935d26ee154d9c1769fe0ae24107d7431412	refs/heads/bug/JAL-4072_zip_slip_vulnerability_in_getdown
768df7afff3cb5ecb636cf324f5965f0aeb1b9a4	refs/heads/bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol
3acfdb3ddd5e3b785fd0880bcebc9e267a717bbe	refs/heads/bug/JAL-4125_flatlaf_quithandler_external_structureviewers_not_closed
a327fd39320e482fad4b57f256f3e3c8ebcf015b	refs/heads/bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
e6e897ddf845d4e79ff5e6c7afddf66766c7d31d	refs/heads/bug/JAL-4128_resizing_overview_with_solid_drags_causes_exception
c764fbfdffe3a52349038c957d7a73b8e22e9985	refs/heads/bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux
6c89ed59f96a34f51b1cb06592c75583986295ea	refs/heads/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such
f4865ea9ed6053ddd96a6157b124642488153a21	refs/heads/bug/JAL-4229_varna_helix_mapping_offby1
d2858ba11088212f756b4a2d09eb20f32fa9874c	refs/heads/bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error
80d58b8bdf6ca4cc38af10df2fcc9c05eb21dd00	refs/heads/bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
49c595b1a5d841a27e6c01367da99d278152b976	refs/heads/bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog
a2d271cc24be4411224b296c9130b372fc8086c7	refs/heads/bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message
ed6ea3eca75d7750869faae2b10588fffd007e99	refs/heads/bug/JAL-4277_dirname_substitution_always_absolute
67f21ba986462faaa66c606709463fff6c29c116	refs/heads/bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpaint_or_paint
df2cec95b7f3cc69f976c495c1cbc3fab18eb351	refs/heads/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
aabbea350930b8c2904e4f1544f0d786e7d59792	refs/heads/bug/JAL-4290_headless_alignment_figure_with_sse
f8392b9f693b70051bd96540e9bd67477ef34160	refs/heads/bug/JAL-4298_java_console_causing_hang_at_startup
bca92e34b044bba83a9e5a0284cd18b4029d0167	refs/heads/bug/JAL-4302_treeheightrendererbroke
72e63582d51fbaa0cc5a3963abc96814f984039b	refs/heads/bug/JAL-4313-make-visible-annot-fix
bfe2ce7ec6dc0598f06b91d0e380e6fe36e30e47	refs/heads/bug/JAL-4313_cme_in_tests
56d72101b0584635cf539d5413db27abc8deb575	refs/heads/bug/JAL-4334_unknownstartenduniprotfeatures
d40eec66396ecc2590d76e24110d94da5e59f6c9	refs/heads/bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square
65d394e306a91a2b0a7d7490615dede3d7b9a085	refs/heads/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
69827911885f6e7ed824b5e6f2f802e0a23c25f0	refs/heads/bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately
0041b370235a60faada5dde14f7fd7e0cd881e4d	refs/heads/bug/JAL-4369_uniprot_in_jalviewJS
fc3c0910b7086411d72104c0a2cf4b8b45a95015	refs/heads/bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch
5366f4b373ba3fbfd8fa5d591e79d34f04381296	refs/heads/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port
2cb06b103be32e40c74a0510789ea073adc73ca3	refs/heads/bug/JAL-4375_annotation_not_redrawn_correctly_when_scrolling_left-right_via_trackpad_in_wrap_mode
f194e85e7f9cd2062989b1487b2a294c5faa0986	refs/heads/bug/JAL-4375_annotation_not_redrawn_correctly_when_scrolling_left-right_via_trackpad_in_wrap_mode_2114_needs_splitting
a187bcd7ecb0cf1b43af64450a5e0b0d35c87027	refs/heads/bug/JAL-4389-web-services-prefs-panel
be7117b5da70a06cc8bdd2f327faac1355db93d3	refs/heads/bug/JAL-4397_failing_idWidth_tests
5640ec0623c6d1205e62f9fe15292f32bfdab7d9	refs/heads/bug/JAL-4407_no_sec_str_from_draganddrop_to_msa
83043201cd0a00131ec745674ec486d6dcbf5d18	refs/heads/bug/JAL-4416_sview_not_shown_for_local_strucfile
fe6e1a5e8e7b69ed17cbe917250acf41c2eb12a3	refs/heads/bug/JAL-4421_customise_volume_name_of_DMG_installers
13190d3a1ce589bfb7bd24e81e2c8660a88ff161	refs/heads/bug/JAL-4427_HTML_code_in_sequence_ID_text
ee3e6523e7e1e274b56cf2d29f50e029e199a993	refs/heads/bug/JAL-4437_one_channel_build_cant_launch_builds_from_other_channel
2eb618d01fe32876a15108b267a26d9eeba221ac	refs/heads/bug/JAL-4456_cannot_change_double_click_settings_for_links
efcc858be7c5023e58786f8117092b5879e573d7	refs/heads/bug/JAL-4460_alignment_save_as_format_not_registering
004bcce3b9afea926ffe15514ce3080186a71d2b	refs/heads/bug/JAL-4467_getdownArchive_task_fails
72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9	refs/heads/bug/JAL-4477_unmapped_filename_characters
85dead08e22e1ed61738f045b58349c18b8131b2	refs/heads/bug/JAL-4482_gradle_task_linkCheck_fails
4aa30fa9dd69fe01111355dda8b970a6ad9fca4c	refs/heads/bug/JAL-4492_gradle_build_not_excluding_classes
2de98d293f03069b1585e64b27666b2e3e801137	refs/heads/bug/JAL-4513_JvCacheableInputBoxTest_flaky_on_build_server
56b390641b07da301f3591785141ff09a261b22d	refs/heads/bug/JAL-797
634afceda19c45e6d9790bfc23294a647b237fbc	refs/heads/bug/JAL-914multipleHelpScreens
75d5069a8e8942343a999fe4d474079856fbc5d3	refs/heads/bug/JAL-98consensusMemory
8fc9f1cacf08e1a4b229cf2709d058a4bcca72a1	refs/heads/bug/Jal-1696_disable-pdb_id-field-settings
05e40b4dd4e216024024fb921d797917d74daa76	refs/heads/bug/r2_11_2/JAL-3904_structureviewermenu
d5c825f47c13faafe6330906ae31fe2ad78bb22f	refs/heads/bugs/JAL-2777_whitespaceChain
277430ec004bfec081efa4d7a2fd9690d80fc01f	refs/heads/bugs/JAL-2780_JAL-2781_pdbnegativenums
e7928abb87528410a82902124a19cbd7ff95d3d6	refs/heads/bugs/JAL-2922
10fee0d88f1f9abdfbaae35c59f6d5aeefae9495	refs/heads/bugs/JAL-3009_blockingNetworkThreads
eb26f5aa7a1961c0e1fb5e14f12e880a651b38fa	refs/heads/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport
e99c06994dd1e8e0d1740b7eaa89cd2c63861e89	refs/heads/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat
80edaa84d6d9beac9f0d2c71b50b7b56fd393427	refs/heads/codereviews/JAL-1990_IProgressIndicator_jalview.structure
544bd63f8e2c0122da4f309bdc415162fc1da737	refs/heads/develop
747167089ecf8d6afc70d417f5a20352e029bd95	refs/heads/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged
ce63feae60026b5815c18b133447d0f265d4cf8a	refs/heads/development/Release_2_12_Branch
b16a3f9999681fee83f87ba0ecd309d32383f28f	refs/heads/doc/JAL-2494_JAL-2828_mergefindAnnotation
214ad7e089fdf9cde66ac5e5d56d498101bbe2c3	refs/heads/doc/JAL-3746_Release_2_11_2
b115893996b4607564e163855427abd59ce956fb	refs/heads/doc/JAL-4090_Release_2_11_3_0
e7bfd7141229e93961d676431233487da4e7789b	refs/heads/documentation/JAL-4418_2_11_4_0_docs
52af9a567a4c6009f24b8a9de6e3b43c8d718658	refs/heads/experiment/JAL-4386_JAL-4435_with_HSB_colours
cfb973824e06936f2f3b2c4cf9605bd687896cf4	refs/heads/experiment/JAL-4386_experimental_string_to_colour_scheme_methods
9e95025ca7a686639c1acdc630db8edde72ffc61	refs/heads/feature/2588
7aa1e482163172b1ea16622eb2195fc8f2039951	refs/heads/feature/JAL-1244stretchStatusMsg
069ab787ab3f2de53f5b24f8af3ea078ff52671b	refs/heads/feature/JAL-1260_genbank_embl_flatfile_import_reloaded
94833478359db02471755ad0e8ee3be05c3393fe	refs/heads/feature/JAL-2087ensemblSpeciesAssist
40d9c9f294735841777e3a387458f1085987571b	refs/heads/feature/JAL-2250colourAllGroups
7af63d41af61d31af8d8790d1483ed474050bdf2	refs/heads/feature/JAL-2422ChimeraX
77f0b8285c6711ad803832553f28b03ea8366efb	refs/heads/feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
7bbe4d3a4369a952ef5ca086ce5846dd4cad6866	refs/heads/feature/JAL-2527
21be5363b2f7b61aade8a4b4caf54da28d8cd82a	refs/heads/feature/JAL-2553ensemblGenomes
2d137c4d89286572fba9e1f81eee9b35e4ca4a97	refs/heads/feature/JAL-2587
88bc41a8d340988625001b2828625c1a668cadd9	refs/heads/feature/JAL-2611
44b924cfd6b3aab4e7fa279062aab20e88c3b591	refs/heads/feature/JAL-2613
3f03cc818538d68c829869c6341112c44cf648d9	refs/heads/feature/JAL-2664
822ee0479afcc500c72f16b7fa972dc99c8bf5d5	refs/heads/feature/JAL-2674take2
dc3dd2e76d340b0577259c4e9d64372a1c126aee	refs/heads/feature/JAL-2738GeneLocus
390c4abf37f2d87285d0e17f2c34c67820de06ff	refs/heads/feature/JAL-2745ebiHttps
8c5cefb3ac80bd094a8dab7ce6735a11583b1772	refs/heads/feature/JAL-2759
916c073172d5e374f7375ec718420455472dfcb3	refs/heads/feature/JAL-2873ensemblSpeciesQuery
6f516287c0c9fa3e3f13c8e0c9b95dd99045d22a	refs/heads/feature/JAL-2909bamfiles
429bbdae3d5229ec1b92ec59f4b5a25bcfcf13f8	refs/heads/feature/JAL-2909bamfiles_features
d99f77c85d5694808788ec662d50427ab3770da2	refs/heads/feature/JAL-2994chimeraPath
6f153aac5d457ab69f994d71df1cf30b69d07af5	refs/heads/feature/JAL-3080clearTreeGroups
9e66ffdd391a2467fd6821abf9f8f0ca66e5a18d	refs/heads/feature/JAL-3081customAnnOrder
6c37aee46593060e9b5d0d0a864a73039817570c	refs/heads/feature/JAL-3093wrappedModeTooltips
812efb59846c842cd8d3ac16690cf6d762d88579	refs/heads/feature/JAL-3117_overviewFocusAlignment
f89d8403d91ec95d00196bf5f922e2be82ad5c90	refs/heads/feature/JAL-3121gffAttributeMap
c5b363c47e896e47fe5b6d3b64abbdf47bd6f94a	refs/heads/feature/JAL-3127_seqidChainshading
fb0359bd129a8f615f59817424bce2cc0d8fb71d	refs/heads/feature/JAL-3143ensemblJSON
181cd6607ecd631aa5972582ff1d99c5bea75b23	refs/heads/feature/JAL-3144noJTree
87cac19ea40aecf1ddaa23dac531531d7f29b481	refs/heads/feature/JAL-3148structureColourSchemes
d7527de9d963ee1869b0c7545be3d9213cdd0c6d	refs/heads/feature/JAL-3169cancelOverwrite
1aa2f97dbda5915fee0871270495596afc2c1011	refs/heads/feature/JAL-3180colourAnnotationMenu
bfb35471fbb8dd6cc4252b9a12b81057922e8f5e	refs/heads/feature/JAL-3181linkOrdering
5ce7f678c611cdb0d60a578b81680493cb649824	refs/heads/feature/JAL-3187linkedFeatures
dff427de0ee64e80b4e67b092159fc081df73fcd	refs/heads/feature/JAL-3187viewstyleFlags
58b30fcf2ee02b59666655a5bdf99d6e660b2e70	refs/heads/feature/JAL-3190jalviewjsChimera
712030864564b9fbd1405d2e3d8cdb67481b3cac	refs/heads/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting
187269da0130408d24901c88acb10c217f6284f9	refs/heads/feature/JAL-3205symmetricCalc
879ce4991c4ab61bfe995995e23286e98e5fb955	refs/heads/feature/JAL-3251biotypedMappings
ede65e4bb4c184f93f794c1d3aa05521355e4bb9	refs/heads/feature/JAL-3364splitFrameImage
2043c7f197d747c97536289f5fdad72065961dfa	refs/heads/feature/JAL-3390hideUnmappedStructure
4faf17681ecb23497054f58147ea7201dfb4c031	refs/heads/feature/JAL-3400viewChainsMenu
353cb52722490edcba2c13b18836b6d37c5455de	refs/heads/feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_native_libraries
6b3a4a1b636be96f2bc46a8a454dd6ce3d280021	refs/heads/feature/JAL-3442colourCaching
e9b3b4078647e40fcdb23d5f0814c05954cf730f	refs/heads/feature/JAL-3443findColorAsInt
b9cd85ce07264ecb77d6c9943f37372f66124983	refs/heads/feature/JAL-3468featureDescriptionEllipsis
f501ebf56839e4115d9d48d20a6c936856dc0e37	refs/heads/feature/JAL-3469clinvarVCF
136f41377900e9e70d9d083664e898a255af74dd	refs/heads/feature/JAL-3481_conservation_gap_threshold_preferences
acc51b96b52db925f7ab71342c6024ef0e8f4b5b	refs/heads/feature/JAL-3499featuresFileMotifs
b08aa323c3e2fcacbe28b003d2d2a3c027d19b31	refs/heads/feature/JAL-3515-slivka-preferences
ca4ed63aacf92872319f2bf64225c2742c338184	refs/heads/feature/JAL-3551Pymol
2ac00907dd4b7777add99046c57c0945d2d2f653	refs/heads/feature/JAL-3576intervalStore_1_2
06c84c2db67300554884a60f8c844c08028f800e	refs/heads/feature/JAL-3615gzipXfam
3acad896ec7aabf1df54556a2959c00bf50eff0f	refs/heads/feature/JAL-3624siftsInJS
b9a24a3b7bacdc1f653b5de8b696e0892fa8f5c5	refs/heads/feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
71c5a29a58e5505aaf7d63a8c9f1bea3ae93d629	refs/heads/feature/JAL-3686_slivka_client_js_update
e23c809d6cd203187c5f65efd03741ec4cb637be	refs/heads/feature/JAL-3690_callback-based-web-services
511a2a91507d3bafe876660789e7a06d3b7d6e56	refs/heads/feature/JAL-3692enaEndpoint
f76e980eed78557acf0749bd390a1aa8c4625d65	refs/heads/feature/JAL-3719_gapColourInAlignmentView
45e607ef30f3e6cb3db68ae26c33be650c99833c	refs/heads/feature/JAL-3719_gapColourInAlignmentView_2.11.2
fc07a043c80a393765160ce7e672e9fdb4719599	refs/heads/feature/JAL-3730ensemblPingRetries
e239a325b544039d7b2c210492f4706f66ba57c0	refs/heads/feature/JAL-3851_prototype_comms_for_jbrowse2
f3fdf76ef87665cb4d0ff812283128dd3294b870	refs/heads/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop
9a3fbb958e7b83e448f34eaadd32a9667bd444ca	refs/heads/feature/JAL-3874_add_source_jars_to_eclipse
5d60cda87940311cfff2679e6f0e96890d3e1fd6	refs/heads/feature/JAL-3954-ebi-phmmer
631b4913d708d2ccc3c1ad6b1650f507e7008601	refs/heads/feature/JAL-3982_mouseover_highlighting_viaJAL-3860
6b4319fb38bc15ddce1d91aac65be0b3448007cb	refs/heads/feature/JAL-4159_pasimap
1a2a4ce555a75c3c0cf2929ee346ff13e883c3c6	refs/heads/feature/JAL-4159_pasimap_JAL-4423_alt_msa_source
4c2789fc5d5f3ccc8ef55d833d3c87dcb45956c2	refs/heads/feature/JAL-4162_Read_and_write_Relaxed_PHYLIP_format
0c90355de2854b4ba6f30c1c162f9cb0c712351a	refs/heads/feature/JAL-4227_Rfam2020_sslines
8e2023f3b7c46fac1c4c6b10058bfb146355cc85	refs/heads/feature/JAL-4274_configurable_bitmap_export_preferences
fa25baa61ac89d1bba5eccf6fe3df85928191706	refs/heads/feature/JAL-4307_hetatm_showhide
f6d1305378fa256a42caf7d284b13d5a084bc471	refs/heads/feature/JAL-4315_fc_draganddrop
a323332f89e44b7a3b8b1aee27ce6e12c22f44ca	refs/heads/feature/JAL-4386_JAL-4435_coloured_lines_for_providers
39291a3fa3b81f3a82111b067ffd51c87b14fe8d	refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels
03ba07a5429bb19cc81bbfd44d240e002481877b	refs/heads/feature/JAL-4386_JAL-4435_trees_from_annotations_on_alignment_2114_update
2940d9c01539dd10962eb201ec7f0cb0eb905be9	refs/heads/feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
f40edd5d97571d331bd03489ef67858bbb2595bf	refs/heads/feature/JAL-4446_cancellable_pasimap_etal
f3e21a7b9556252fd1ede2c8323a64320842db79	refs/heads/feature/JAL-4476_reformat_ss_consensus_annotation_labels
b7175b93f334b38b41eb5cf53bd4f45983ba7c53	refs/heads/feature/JAL-629_--output_-_means_output_to_STDOUT
74d24ffdac9ac6f852ea19654669a6c2562375fc	refs/heads/feature/JAL-984splitAdjuster
daae26d77ca41f38972dfcada536e95bdfb5c753	refs/heads/feature/intervalStoreJ
3efc24bc7b7855ff135fa96e35ab1004eaeb4f5e	refs/heads/feature/r2_11_2/JAL-3808_gff2_exonerate
32973e4c3a37dd4485c4190f45bbf43017af40df	refs/heads/features/JAL-1264_showHideAnnotations
c93b9ad2ebfab4cad4608a8890132918589576be	refs/heads/features/JAL-1270_JUnit-to-TestNG
b8810711642d8473325c8a3d3e76cc5c3c9b5bbd	refs/heads/features/JAL-1469_svg-output-for-figure-export
49f0437d385ee4c6dbe701180a4ba704da76b5f8	refs/heads/features/JAL-1479_SIFTS-mapping
6a495a81e764c82f9fdfb6b3f990b962a5b85286	refs/heads/features/JAL-1499
4a85628075aa27923821a910758c9b9d69cb1708	refs/heads/features/JAL-1499_MEGA
6407c5a12a5768eace1b7fd25cea265601b494c3	refs/heads/features/JAL-1541_BioJsMSAViewer-export-option
8b392a6c4542bc83a1267a168b296876d48dfb86	refs/heads/features/JAL-1550_intermine-sequence-annotation-client
61d7d669232e22adc47cac9fe8dd9db291d382fe	refs/heads/features/JAL-1553_improvement-select-column-by-annotation-row-query-interface
f73031db2e38bfe6e3f1cd42f91b0f9b0130071a	refs/heads/features/JAL-1553_select-columns-by-annotation
174606cd2bcaed91adb0a39639e8905fa9a8a6d2	refs/heads/features/JAL-1563_uniprot-free-text-search
5117f0d57f8ee5a531a630677ae0e1fdaeb725d9	refs/heads/features/JAL-1601_jpred4rest
81edd609f9841a84d5799d221277d45413a177cf	refs/heads/features/JAL-1605_html-svg-export
fa49359cbca59fe30b2bc13283510b99afe4317e	refs/heads/features/JAL-161_JAL-4173_nhx_tags_in_stockholm
0bec946ff94726b35e8b0c8508c42d3cec59ee37	refs/heads/features/JAL-1641_JSON
b6e04973b3b7b0ea9c7f75cd88e496aef082366d	refs/heads/features/JAL-1641_JSON-File-format
a624bae1db1ec7edde062bacfe3890c1e018209f	refs/heads/features/JAL-1667_PDBe_Search_API
07eba26e68b83d767aac0af12c18db5eafe90db4	refs/heads/features/JAL-1705_ensembl
bb82c9968358436e350e1ba03700ca4a16663161	refs/heads/features/JAL-1725chimeraListener
64fb69927bb37d8773a75b684a3e7ab3f0c5c212	refs/heads/features/JAL-1740_BioJsAutoUpdater
91818aa43666f34bbbd41df9b91659d736b73403	refs/heads/features/JAL-1740_Decoup-BioJS
fb4518e1dcb44b61a42f7656b0b23f05171f8c40	refs/heads/features/JAL-1759jmolUpdate
55d8ed2824ef1e2f5a8ea30f43d14980119f8c43	refs/heads/features/JAL-1767pcaInProject
2e2e6d269fbaa505151fe777374f41111f2910d5	refs/heads/features/JAL-1780_export-settings_flatfile
d2ad79a5a6edf4c1dbbbc2f454579864dcf1e3b8	refs/heads/features/JAL-1781annotationXmlIds
c93b9ad2ebfab4cad4608a8890132918589576be	refs/heads/features/JAL-1782_JUnit-to-TestNG
af14381c1d151fbc755528c29bb6530b44c9e191	refs/heads/features/JAL-1793VCF
14b9c2563a9c79ac462bf700192e386249ba062c	refs/heads/features/JAL-1807java2Script
8c7fd90d480e2671e0fa251ada3c89fa1d18862a	refs/heads/features/JAL-1812_JAL-2083_groovyBinding
167ce32fb49494a4d6ae03ffdb430f05f4d93f76	refs/heads/features/JAL-1856dbRefFetcherMessages
6936b57e5469c796a998d661a7a07648832ccf70	refs/heads/features/JAL-1912_biojson-per-sequence-annotation
8449dcdc681745be31669b83c91ca74a91f85b41	refs/heads/features/JAL-1919_mmCIF-Support
b940a47e88bb6606cd5a0ace5f7be1192567fb38	refs/heads/features/JAL-1933_occupancy
b09158307712372752e22a0e766b3a5b9b9e15df	refs/heads/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2
c6492a740f2fbd1a2611f669e6a618335a7858b2	refs/heads/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch
55ab1d6dc5b9b6ae410f5e7709e5560988e60ecf	refs/heads/features/JAL-1978_msagrid
ee0f6c877392ffc2018ae1a832042fbd364730ab	refs/heads/features/JAL-2039_Offer_cached_structurefiles_immediately
3e98c1348b037f0972367245a524f182029a9686	refs/heads/features/JAL-2040_JAL-2137_phyre2
baa11f60d8ed1ce99b054e11cc0fecc586f8e92e	refs/heads/features/JAL-2055alternateFeatureColours
408b2821c8daf99245bf6358d06760701d90ddd8	refs/heads/features/JAL-2068groovyAnnotationWorker
f2b03e9fecf41886ebf5f747fd4be02edf042bee	refs/heads/features/JAL-2094_colourInterface
de6f16e01ddb7846dc67f8f7a71ed6862d7aa986	refs/heads/features/JAL-2103
4eb1ed22600411fe5b6e9ac93084b45429ccfad6	refs/heads/features/JAL-2110_crossRefDuplications
d734217a33aa6bfa39a4ac207592b4696ffdc48d	refs/heads/features/JAL-2113_emblXml1.2
b8cd52fe7bed59130e5b080acfd42c3ef2effdbb	refs/heads/features/JAL-2136_phyre2_integration
c51dbe7933683b64548f5353e67561d2b5e377f7	refs/heads/features/JAL-2136_phyre2_integration_updated
7fadc8dc33be5781fac68507b08a9e387ddb5761	refs/heads/features/JAL-2177_update_jmol_to_14.6.4_2016.10.26
b342c421914723ac1b3403280cb8bc346011326e	refs/heads/features/JAL-2253ensemblGenomes
fdeeb42848df5648feab5acc978a44e667785a1e	refs/heads/features/JAL-2284_export-biojsmsa-via-cli
c5cece0a9d56e59293c8e6497b5afa6e26842646	refs/heads/features/JAL-2295setChimeraAttributes
01f25e260a8c336119462420a1c2a11512293b41	refs/heads/features/JAL-2316
ee778ac34b35c8d8fef03f1f3a58efb7d5be650a	refs/heads/features/JAL-2320_closeChimeraAction
5f4e1e4c330b045e9c8bce28ee132a0fca3834d8	refs/heads/features/JAL-2326_JOptionPane-refactoring
2b6a2fdd887521f16ec777aab3126d6209f2a0a6	refs/heads/features/JAL-2344FileFormatI
9a4238fddebd328b1c0ffb94d089fdffebc4f184	refs/heads/features/JAL-2351jmolExchange
17cdbbba31b43aa92793c30629e586ef0012af72	refs/heads/features/JAL-2379pcaMemory
3c75c089a56859ec8e7f674d7054e82af41e4b77	refs/heads/features/JAL-2388hiddencolumnschanges
2a35abbd49049cce7f7bb1abb0543e444e72485c	refs/heads/features/JAL-2393customMatrices
229d9b7b9a762ac94f580ea4ffe9d0a4bb01f30c	refs/heads/features/JAL-2432_annotbypercent
be762d8d9c71a7aa3121e845c45911c7192b7827	refs/heads/features/JAL-2446NCList
124aa4823768a2c745a5e41f2ebfe13ab77bbea4	refs/heads/features/JAL-2447experimentalFlag
61ba3fbbcf553e5945051ae4f7ab185ddd2e6dca	refs/heads/features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
c82a1b264834640075607a75372711dd199f24db	refs/heads/features/JAL-2473_set-minimium-dimensions
e4496f5b27c5a01a1cc494653bd3f9f49080d544	refs/heads/features/JAL-2476dropFiles
f063821ed0be9c1581af74643a1aa5798731af65	refs/heads/features/JAL-250_hideredundantseqs
2e6299399bd798ad2959a2b80fd3ac2d2a1374df	refs/heads/features/JAL-2523httpRetries
88694463a2aea303694231603b61970f72a5a259	refs/heads/features/JAL-2526sequenceCursor
79501a7433d7fd26f958b8574e2147e011433224	refs/heads/features/JAL-2549_updateJABAWSto220
8ec596f7eef1aec80c0daf94441dfb88cd070a4f	refs/heads/features/JAL-2609fastPaintWrapped
3d37855b16fa12dcd4e1351610b1240cbd8600d0	refs/heads/features/JAL-2620alternativeCodeTables
4c6cd08af580ff73cfce39bec34ae4658a4b4b34	refs/heads/features/JAL-2754findFeaturesByColumn
f47e7c2da5a0542cd0020c727abb3dc05f8442e5	refs/heads/features/JAL-2758_shorteruniprot
106a3890f956e2aa7780b2985f4326655912a558	refs/heads/features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
7b0ba470199c1a023da41d54ebd81f39a837ea2d	refs/heads/features/JAL-2814ftsHelp
b4ebd059827a953d3d54b14ff08eefc99825be5d	refs/heads/features/JAL-2885UniprotHttps
70f98ab214fefd664892e8c8ec44811d820a802d	refs/heads/features/JAL-2909_bamImport2_11
0f216582318763932198af826f95c11cf3d3cd38	refs/heads/features/JAL-2909_bamImport_2_11_2
083fb85bfa1be57c30db0ac1cb9f5f8ad08d1060	refs/heads/features/JAL-2944_openStructuresInSelectedView
6a05eb3f55d97e685f0c723822384633d5636778	refs/heads/features/JAL-3010ontologyFeatureSettings
25008f6fd7150baf5626e878affebcd111bcf695	refs/heads/features/JAL-3020attributeValuePrompting
c0a7ff7df2df7483f96428206ed40fac728a81f5	refs/heads/features/JAL-3085_gnupdf
5dc249708303dd777f4570bb66335150a8beab07	refs/heads/features/JAL-3187_uitweaks
91d83d4836ba3f8c6c395d46d607faf693946e66	refs/heads/features/JAL-3375vcfValidation
3459a8a691cb22508d7067f240b7254e588e77d3	refs/heads/features/JAL-3417_sdppred_calcs
4e2f6c0857eff90e30d4b64540ce4b7265053bc9	refs/heads/features/JAL-345_selectFromFind
c605461a165b7d3ac4af8e0c4d7928f469ffe06b	refs/heads/features/JAL-34_comparing_msas
c86b3bf029c0a54ffc24e5f8c4a4275b5db7e144	refs/heads/features/JAL-3638_jumptonextindel
a59756286e7f58d7ccd639b149bbeeecd7409995	refs/heads/features/JAL-3641_phredfromfastq
a939b4c646235d460df3b7b9377ef8d8569caaff	refs/heads/features/JAL-3858_PAEsInProjects
f05e348630e97e1d86d222bd22bab09d6bf0fb06	refs/heads/features/JAL-3895_alphafoldcolours
8dbe9206561daac950b4154da519d7aad4cfeaee	refs/heads/features/JAL-3914_modelqualityscores_v2115
0a00266f602cde16fddd1b297279cf9b2c13a708	refs/heads/features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4
23d35876a0c39c603fb95f3764df46c4cfd1fb5a	refs/heads/features/JAL-4061_and_JAL-4062_findselectfeatures
29f7e24d4261af7af91dd5d1192fc5640997e754	refs/heads/features/JAL-4071_visibleFeaturesCounter
8b46f39580d6fe338c3dc15375863067bca2b543	refs/heads/features/JAL-4134_treeviewerforcolumns
0ccaf35f7e6a5cc62d4f433b39d574d0aa4b2d26	refs/heads/features/JAL-4134_use_annotation_row_for_colours_and_groups
7fd29d4a8927f1c5e59aab981531ab0f303b0214	refs/heads/features/JAL-4219_extended_fasta_rna_ss
0a648fa578eef83e9f17a1d581aba8fcf9a393da	refs/heads/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps
840c90a082ffc6f29a512501337c4e4397ad604f	refs/heads/features/JAL-4257_adjustablegapparams_nw
c1aa510c36a5c12a76bfebcaa57157f3d82e8d76	refs/heads/features/JAL-4366_foldseek_3di_viewing
f6be36d7152321642e41db9d8bdbd2580431541e	refs/heads/features/JAL-4489_cluster_pca_and_pasimap
30bbab8b2e223cc7a28c69556092d405c8dc48f7	refs/heads/features/JAL-4489_clustering_and_pca_pasimap_views
116f0a097d2eb368760877c42b87c5cebcb56df2	refs/heads/features/JAL-518_justify_seqs_in_region
4dc159c9f47284ecfd253840dded4772af7be954	refs/heads/features/JAL-629_with_threads_NOT_PASSING_TESTS
a8a60500f1be9c3e02976f2193eb62ff5a302220	refs/heads/features/JAL-653_JAL-1766_htslib_refseqsupport
2a9991ef1eb02d97e9c8ed1644f292117ae6f600	refs/heads/features/JAL-653_gffalignments
2ce465aaa3047e1ef758a26af2fbfcf8626b4a69	refs/heads/features/JAL-653_rebased_gffalignments
39f46f6adedc1b0a1553e9dd3133582aa63ff4de	refs/heads/features/JAL-666_exportoverview
48a66195bf4aee8b2c479d3bbbf4c1fb8b824f5a	refs/heads/features/JAL-722alignmentProperties
878897fd12216b10828d6ff387f5450029d8b017	refs/heads/features/JAL-728alternateQuality
95ceead3cb4ea5aa5260e1fd4ab53658b64866e1	refs/heads/features/JAL-845linkedProteinDnaEditing
b04bbad58a8dd34fe773dfeb758e71e64606ed9e	refs/heads/features/JAL-845splitPaneMergeDevelop
bcc6651c0d31d68ce84435cebcb4e6b858594f87	refs/heads/features/JAL-857_dynamic-example-files
516cbeec2ab5eb61f1767720258d896920f2db4d	refs/heads/features/JAL-892varnaToProject
4490c246e02057d0e539233c2ef348ca561c8688	refs/heads/features/hmmer
7717b24f1e894ad268121890c479848c53df64b0	refs/heads/features/hmmer_statistics
e0fd9965a1ffacf4ac034a79e7cb5f7e898ff69f	refs/heads/features/mchmmer
1903e771d3dae79e9a57fcc1147efd37e8a51421	refs/heads/features/mchmmer_merge_JAL-1950
091704be1e1e54b7990e8e6a10f7c0fd12d33416	refs/heads/features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767
27dc4596d13971e00f04578d469c5e3eb604757f	refs/heads/features/r2_11_2/JAL-3829_3dbeacons
7d6652012194b95cbe89cf96c990450f68e277f5	refs/heads/features/r2_11_2/JAL-3922_jmolSelectionHighlighting
a8c998b5e5debd0dc8a17daa8005a1cc3ca07078	refs/heads/features/r2_11_2_alphafold/JAL-2349_JAL-3855
0c876c3cb4c877ef6cc68e3a182bbae3b96e016c	refs/heads/features/r2_11_2_alphafold/JAL-629
79362a91b9005d5391ee9f1621cb7c09f4c5b179	refs/heads/features/r_2_11_2_JAL-819_undeleteAutoAnnotation
b13f521553582ef2fbfd7815ae25e23284babdea	refs/heads/features/sequenceFeatureRefactor
73204ed7001df8ec4fc431934333bb3cfc6c90f3	refs/heads/groovy/JAL-2074_upgradeto2.4.4
57af23f63ef752b8530bd7eae9722d04fd537368	refs/heads/hack/JAL-1617_workaround
f3d0dc3395aff566e8005e6a6a9a13bf795c14a4	refs/heads/imp/JAL-2774
4687e1243f51bd09334792b8a7ce518a5aa07de7	refs/heads/imp/JAL-2775
759d755e2a451b2167b2df8345887379a7f648d7	refs/heads/improvement/JAL-3289_new_launch_screens
99f12fbfb7363175e43de3cb4c48750e71bb5023	refs/heads/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files
4d93d7d9bd4b514f5f2f010238946fc92137ecc2	refs/heads/improvement/JAL-3393_DMG_Finder_window_improvements
3ade835a89217d9714e278334ff3eaaef9272311	refs/heads/improvement/JAL-3393_Improved_DMG_background_image_beta_strand
0b165691fd3a7bb1d22438350157691a5d0bc2f9	refs/heads/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store
b2d6230c6cce0eb7ad58cfb29afc0620ac2b935e	refs/heads/improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file
fedea1822d5623bfe841cebf01f39bfc00577868	refs/heads/improvement/JAL-3416_FlatLaf_3.2
432842b2544071500b05978f4e0e177f6819a0cb	refs/heads/improvement/JAL-3416_FlatLaf_3.2.1
7f0c5c453a345a700b9e19caebaf7a3b55783759	refs/heads/improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf
7496d38ebe9d2c3ddd1d2f1bacf95c2381b63264	refs/heads/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task
56f4324f197ac20954ce304d103ff26f1dda58e2	refs/heads/improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2
54f3ce881faa9a1dedd39493da180e9378e8de3b	refs/heads/improvement/JAL-3474_lots_of_.cvsignore_files
e77b677c404d0850fab45aecac341abc64d8766d	refs/heads/improvement/JAL-3543_dont_report_null_versions_in_java_console
4b4f8f64b569ca51b56062fa34be5e5d8bebc1cc	refs/heads/improvement/JAL-3594_BG_and_UoD_logos_added
61d76e280b86f0d3cfc2fe298af449ca2cc28410	refs/heads/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen
c5a59615bd078dc444f95fbf165fdae8037b29f5	refs/heads/improvement/JAL-3594_logos_for_jalview_test
f52c6d390a8bbc118582f3ba3ca06170bf9d5e48	refs/heads/improvement/JAL-3783_upgrade_to_groovy-4
7f6ee29107c9ef22cc6de42e6986a71a7e5b099c	refs/heads/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text
7817ebe14e236eec069a16abbc16fc9d07e0913d	refs/heads/improvement/JAL-3826_gradle_configuration_for_intellij_idea
c4820a850ccb7171fd29206655bc327af7226e6b	refs/heads/improvement/JAL-3830_remove_dock_icon_in_headless_mode
082e1cf48b2af3f53e64d0074fa7efe718a0ef5e	refs/heads/improvement/JAL-3847_add_dependencies_reported_by_gradle_7
9e4c993bfeb431474dbbe24b147503ec7526e6d8	refs/heads/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions
08cb80a354f055421234d7e2fd5c9f6293e53226	refs/heads/improvement/JAL-3848_slivka_0.8
959eb0c3ea53b293548ca23908fa1866c804eed5	refs/heads/improvement/JAL-3848_slivka_0.8_updated_jslib
3f5088fe082c479c0de91f897ed26a5adf540f98	refs/heads/improvement/JAL-4014_gecos_colour_schemes
20b5e49eaffdbc56b9d0274200a12204e362d5b1	refs/heads/improvement/JAL-4023_snotation_for_trees
cb0b037507bc9b4f1134c4886fec9b564a7508d9	refs/heads/improvement/JAL-4054_Upgrade_to_install4j10
931bd79285961f259c0c6b9bcfc4166465054423	refs/heads/improvement/JAL-4064_Addition_of_macOS_AARCH64_native_DMG
50caa2bce4379ecdb02a2c0eccc44078487f2f0b	refs/heads/improvement/JAL-4111_suffixed_DEVELOP_channels
a30c93041b5dddb591cd5c62302ffe2aeca858d7	refs/heads/improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews
b036a71275c547ea3875298480a9a61b36f80eae	refs/heads/improvement/JAL-4193_cl_arg_prevent_startup_file
e7205ce1559cfce568839e1168ab522f0744adb6	refs/heads/improvement/JAL-4206_improve_JalviewFileChooser_for_flatlaf
c79c2ba103f2b2c4c8b22c870614334c340997a0	refs/heads/improvement/JAL-4212_remove_macos_test_java_icons
60800519ae6ffc67e1a7011d0a71a868b17984e7	refs/heads/improvement/JAL-4217_added_a_timeout_to_tests
167b079862998eb6857942b4d235d4c3dae8a5e5	refs/heads/improvement/JAL-4245-return-null-from-getRootDataset
c209e4de401c4c8ff1b566b2ae8158a116ee9f72	refs/heads/improvement/JAL-4250_secondary_structure_annotation_antialias
3613fa2821de21019a4b45ea3eec562a5a730c71	refs/heads/improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
24148ee604dd03ceaeab63c123f3afc5cc2a57a7	refs/heads/improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters
00295142757dcaa892733bc104547e41f5078814	refs/heads/improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
a04a7992b1055fa52f5031ef9d10d2228ee78899	refs/heads/improvement/JAL-4308_smalleridtooltip
ae8edbda04dc4fabab67c71fe65c4b091b4b8073	refs/heads/improvement/JAL-4381_dynamic_value_colouring_of_annotations
0a9d2d927d759106beb2b7622f7b58c245140abd	refs/heads/improvement/JAL-4409_implement_extra_schemes_in_getdown
82ffdea414be32b2fee43828940c0af3c0f17801	refs/heads/improvement/JAL-4461_select_format_from_extension
9e54c643f2bcf3e3c22685e6fadaa28e470fd97a	refs/heads/improvement/JAL-4469_handling_uniprot_versioned_accesion_ids
c6c46de559211c83d7e8bdf450d17628ae534af4	refs/heads/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop
73e4b463a2257168a1155a96deb0a18a0e4ce162	refs/heads/improvement/JAL-629_Apply_alignment_options_to_all_globbed_files
2319ef1a410ce35bf2ef1800fd0be4e779ee44eb	refs/heads/issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop
49aba3947cbe082a083b0a5422e36e527b9227a4	refs/heads/j2s/develop
eb40ed78f348375efcd74b5a683bdc2380b3bd61	refs/heads/j2s/develop-bh
4231d40261fef32ce4570a6bbad0d35df44e8baf	refs/heads/j2s/develop-bh-2
c07eb2c5794833bd0241000d6844d783fe10cb82	refs/heads/j2s/develop-jim
c07eb2c5794833bd0241000d6844d783fe10cb82	refs/heads/j2s/develop-mungo
55cae9b50608f760cbf6ae2627e1d79d16746186	refs/heads/j2s/develop-toc
8f66f871d7e0c6db502106a5668f4fdaf1448f2a	refs/heads/jalview-headless
06b709e1b942293188d561999a3c0d1042633868	refs/heads/jims/JAL-3130_Java11_Gradle_publishing
a16e52efe8a069302d4aaa8230ed0dc2e592bcf4	refs/heads/jims/JAL-4386_from_renia
85e30a861f26369f9be8cffa4a1345c79092a895	refs/heads/jims/JAL-4420_review_redo
1e75445b3e45bb22baebbcd215137df1c1aef34f	refs/heads/jims/bug/JAL-4298_java_console_causing_hang_at_startup
04b337fcf5c6c1ba9578928d2b984be4639ed77e	refs/heads/jims/review_JAL-4409_implement_extra_schemes_in_getdown_failingtestsNetwork
1595128a4bfc730f1e55c347f0a52eb0d491ca92	refs/heads/jims/work_on_2_12/JAL-3664_hmmer_ux
a2756c97c9e2598cd102061b829502dd58f33d07	refs/heads/kjvdh/features/CipresWebservices
914a9aaf5a2eeb3cdedf136c2e6b4b6e4b5d6174	refs/heads/kjvdh/features/PhylogenyViewer
62f2ed464010270830afcfe954647a51dfb5114b	refs/heads/kjvdh/features/PhylogenyViewer_tabbedsupport
02afcdbc87b196aa929bcffabf83e409fd807077	refs/heads/kjvdh/features/forester
9f679c5ef6f4bebc7766c48e61d5d31aee3ff9bf	refs/heads/kjvdh/features/testing
bc1218cc2ea545ecb1106f3bc4ed71919fc0efe4	refs/heads/master
e95c5f895775891d55d9f23d5da64f8ce6bd07bb	refs/heads/merge/Ben_trying_out_JSdevelop_with_develop
a3499f1eaaef8cc03aac19a28f960acd0fd70a04	refs/heads/merge/JAL-1563_uniprot-free-text-search
140b350c1bb78f0d6b46f9fcbfc523a05c32beba	refs/heads/merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
c03aaae74c93db1c8fa0e95258bfbccfe1d3106d	refs/heads/merge/JAL-2136_phyre2_integration
471cfb5b0f6bb249e478f0c02d80eeea6a834383	refs/heads/merge/JAL-244+JAL-629+JAL-3416+JAL-3421+JAL-3820+JAL-3830+JAL-4001+JAL-4160+JAL-4189+JAL-4214+JAL-4242+JAL-4255_Updates_to_these_issues_branches_with_merge_conflicts_resolved-bens_stuff
834b2f0f7bee2c61ab68b285d5e81ff94b425400	refs/heads/merge/JAL-3187_JAL-3010
1b8304d543a0beb003842903ce3a662d4bbe37a7	refs/heads/merge/JAL-3210_developToJSDevelop
5cb4c1540eaca054c26ff42a8319f0dbffb1f8e6	refs/heads/merge/JAL-3285_mchmmer_with_211_develop
809c044d96563eea97b00f2c55d2065480f6cac8	refs/heads/merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
368b868f85fe04076d81e9bf9b799acc750d59eb	refs/heads/merge/JAL-845_JAL-1640
f3d57563c0364d1d44889156e264414fa32b5443	refs/heads/merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch
ab7d77e52196fa14fbfe35c6373c069e4b0ba6f0	refs/heads/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services
06cc168f208017912e21e64cb9d25e1657d83cb4	refs/heads/merge/Jalview-JS_develop_with_develop_build.gradle_gradle.properties_utils_install4j
bccb3f12a82f40bea6836bd7dcb4b45abd45b0be	refs/heads/merge/develop_JAL-1780_JAL-653_JAL-1892
6fa882584a8e33a1c9975391dfe34520940ba8c6	refs/heads/merge/develop_JAL-3521_minimal_build.gradle_file
d2164f857e0729b86b1e0ffa4c858487f0a3298f	refs/heads/merge/develop_bug/JAL-2154projectMappings
116f357c7b1056f7c20dd0f7ecbcb50ea50e4e72	refs/heads/merge/develop_feature/JAL-3141_backupfiles_for211
192935b3270aa3da4a937d72348f1344758c83bc	refs/heads/merge/develop_task/JAL-3763_newDatasetForCds
8764cf9e079a8c7d72d920403ce4db71450183f1	refs/heads/merged_2_11_2_0_to_2_12
9bc0c6be2b195af9fed245e9e7ae27d73196fac8	refs/heads/merges/JAL-2906_update2_11_from_2_10_4
eae8ea788fabd5382a8525c1fc6aab8eadaf6020	refs/heads/mmw/JAL-3878-ws-overhaul
93f8a69a2c710d18f8e0c0ceaa6291dbb2d6e9cc	refs/heads/mmw/JAL-3878_ws-overhaul-3
55b313fa4afcd5daed336266ee15af107d2eb42e	refs/heads/mmw/JAL-3954_ebi_phmmer
ce0b7a6c34cd7b2a46419ac8f303204dca03f816	refs/heads/mmw/JAL-4139-multi-harmony-patch
fbfa316634e1b709b5abc18345bfc65ab4982bef	refs/heads/mmw/JAL-4199-task-execution-update
c5d63bcec264839aa8cbfdf476adf72853d23758	refs/heads/mmw/JAL-4199-web-services-testing
b01f64cc79e6a7b8f101f2e15ed4d84549306bfb	refs/heads/mmw/bug/JAL-4241-annotation-alignment-fix
e8ca44a5b30d7a5dfef4299ac6ea3f15ad763096	refs/heads/mmw/bug/JAL-4241-annotation-alignment-fix-slivka
99df572854b30d78d04658083672cf7e0e04ad88	refs/heads/mungo_develop
4c2789fc5d5f3ccc8ef55d833d3c87dcb45956c2	refs/heads/new_feature/JAL-4019_ambiguous_base_colourscheme
bd14eb7c52101ce6bead70bf6872a7307b79c0e1	refs/heads/patch/JAL-1236_customClustalHeader
0e2dcfdd561f71744858237cb3f8a7e714f2544b	refs/heads/patch/JAL-1791_timestamp
60083c09e41c5685e7afea332b58dbca2cdd61a7	refs/heads/patch/JAL-2068_JAL-2169_multiviewannotworker
1571c1185c5dda26fdee57318c8fab98da263b85	refs/heads/patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles
c9e6efcdf33bcd88bd19a48b2934c28e48892fab	refs/heads/patch/JAL-2292_caseSensitivePAE
a2684be1a91eaa743a5b0efa8be66590d2a80cfb	refs/heads/patch/JAL-2321_addsecstrForDroppedPDBFile
dcbbfa95b35e8316628a92ce3c2ba31c555d3faa	refs/heads/patch/JAL-2694_maptoallchainsworkaround
725f1f4a7e1448349bf7dd5f8efb1370de5b9a3e	refs/heads/patch/JAL-2732
8c09d04c5ec473af68b498295321d58ad58c343d	refs/heads/patch/JAL-2755_UniprotEnsemblSubnameWorkaround
3900c35baa85360e632d91fa9a845d8eb9d727e3	refs/heads/patch/JAL-2914_relaxedGFFpragmas
384b9ce126634ac0c7a9fef5b1788d3fe8fc91cb	refs/heads/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars
be328353173bc1e78f50e10f9a1418ed9f3b80a3	refs/heads/patch/JAL-3561_JAL-3660_fileformatexport_CLI
98d7c6c0436db04ac8fa7d13be472df8546760fe	refs/heads/patch/JAL-3562_fixAlignmentPanelTest
8a491d35239e20cd026fbdbef092783f759ddbc7	refs/heads/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1
d286c3c2ea062ec6bef24ebeb7e8d32dd45365e3	refs/heads/patch/JAL-3692enaEndpointFlatfile
882ed2993331d2ce171a2bbdc7e8729f12ff603b	refs/heads/patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3
4b9650841842bbe1798455d39bde2e6f28e80a2f	refs/heads/patch/JAL-3794_X_is_a_dna_rna_base_too
6121acb3dfdeaf17957bcaf275dbf8e64f629a44	refs/heads/patch/JAL-3821_ena_rna_moltype
227c9c583a110b1581ab1036be289b1f838cf8ea	refs/heads/patch/JAL-3840_2_11_1_4
6cc69d298e6ee55f08aafb1c747507607092beaf	refs/heads/patch/JAL-3840_2_11_2
39a8879cfa185d65e57e123e32691cf31d84013b	refs/heads/patch/JAL-3847_gradleV7andV8Patches
3dc34c42cf456deb5f97622de81e7dcfff1d9840	refs/heads/patch/JAL-3855_fixup_pae
f2134a990625e5d9190daa31b7771fcafff58c96	refs/heads/patch/JAL-3874_newJmolAndGradleDedup
862dbed4080eb694f8c09fbfd81a5cf37eef2928	refs/heads/patch/JAL-3921_jmol_session_save
c9c5cdd4e2859de09b36d76227e0d0dce7aaf98d	refs/heads/patch/JAL-3976_3dbeaconsnull
094b06cac0d0e8f781462027ed2e4af5fe32d7c6	refs/heads/patch/JAL-4008_jabaws_2_2_1_patch
71a3cc0202bd8b731f01e5706372e9bae047d592	refs/heads/patch/JAL-4024_jumpScrollHang
44efe0e8eeb7651580a2b71950811e64de19209d	refs/heads/patch/JAL-4062_sort_and_merge_contiguousregions
278d4b2921b6cb58c3a6c15de0c0a4ed3c66b3f7	refs/heads/patch/JAL-4077_jmolsaveloadwindows
d8f7080f6bd2953aa6a3ac14605464e48c233aa2	refs/heads/patch/JAL-4079_scalability_bottlenecks
f6755cf786d55afa7de610a088cabb3a96f35a65	refs/heads/patch/JAL-4110_stdout_for_tests
456e7b01bf201167e0063d0e8b56d4717322d6c0	refs/heads/patch/JAL-4114_updated_3dbeacons_api
faaea5e75f32c615b8f7d5adbd8468118cfb8c3a	refs/heads/patch/JAL-4119_sifts_ftp_split
f8c699730f0692531c9401733e494a5bd14fa979	refs/heads/patch/JAL-4155_IdCanvas_getAlignPanel_fix
49ff0aa506eb0b2e031fa3e8d16337e0c8cf2508	refs/heads/patch/JAL-4184_description_stockholm
30d40769ea0a8edfd43afb448122cfe2cf396b2a	refs/heads/patch/JAL-4195_calcWorker_for_2_11_2_6
4b031bc957ad1c5512798c6206adac7ed0364331	refs/heads/patch/JAL-4195_cli_eps_export_npe
4a6e033ecbe830a86d77f8910beb90b09522aceb	refs/heads/patch/JAL-4196_structure_viewer_synchronising
a55e4576868379847eebc4f5741ae24a48ef2476	refs/heads/patch/JAL-4213_addref_with_selection
0b2df62f9d5ffe2b2fbfd3652a257f4234a9bf9f	refs/heads/patch/JAL-4222_100s_timeout_on_imagexport
e84c71f1aae017708e17cdb978f57afc4a75e19e	refs/heads/patch/JAL-4222_quit_with_gui_export_cli_args
01454522de50064eb4439153c0584bd19db36e78	refs/heads/patch/JAL-4232-disable-unavailable-services
373ea2f39547c5432fc2922e5d958e1955de14e8	refs/heads/patch/JAL-4260_fix_up_select_via_ruler_in_wrapped
78ec90225e576df0562932c75a61b35640028103	refs/heads/patch/JAL-4281_idwidthandannotHeight_in_project
b4151f8875efd004ab1b4c9501ae8a5b265a36c4	refs/heads/patch/JAL-4298_synchronize_consoledoc
903878e5cd0b225d20fc674063483e74eb46421a	refs/heads/patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources
c81cbfa7472e56c48bcdf068d21a46db29617351	refs/heads/patch/JAL-4317_enablefeaturewhenadjustingstyle
3f848bf2699737ea0daea99f4b5d2b68e09da06b	refs/heads/patch/JAL-4333_translatecodonexception
57d5410a932ce5caba3b913c2a27e1a24e012220	refs/heads/patch/JAL-4342_emptyannotationsexport
efee78d45ceeb879d98fedd399a71d84a5ecd5f8	refs/heads/patch/JAL-4345_pae_epas1_doubleclick
9e2fa8ea576657fb12aed3ad639b221c4354b000	refs/heads/patch/JAL-4392_hide_ssconsensus_if_no_data
f32e9d1e19ceda6c3e631012a997f8eed9511314	refs/heads/patch/JAL-4410_multimers_from_3dbeacons
50185f672dd4c8763ab9215fe465fbf8d2be9d21	refs/heads/patch/JAL-4414_for_2114_0_identify_format_or_file_not_found_exception
f59e4dd5ddf41fd74bd463799dcae7d7ff2b2d52	refs/heads/patch/JAL-4422_use_char_arrays_in_redundancy
daf845d1683391b5eddf47298ec37ddf4895ba33	refs/heads/patch/JAL-4428_osx_codesigning_scripts
3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a	refs/heads/patch/Release_2_11_1_Branch_patch_JAL-3490
5faac1104c41690e38e259fae5bb700236021360	refs/heads/patch/Release_2_11_2_6_Branch
573b3bad0aa40ce58c4dae6646523f9133b0564d	refs/heads/patch/VAqua_saveload_update_JAL-2988
d5180397f74424e44495cffe9c822873fc974441	refs/heads/patch/fix_JAL-4470_JAL-4471_for_2_11_4_1
36952139fb50d6ee1d12ecf69f340986ae9bafcc	refs/heads/patch/for2.11.2/JAL-3821_ena_rna_moltype
128ae3671680b3c2bce1eca41919598f5ef56a4a	refs/heads/patch/r2_11_1_branch_JAL-3703_closing_files
46c9ebf10d2411c37988315da6c5df84e36bd893	refs/heads/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency
856afd6d071a489941a42e640b5d40334b0a6f96	refs/heads/portforward/JAL-2675_2102b1to2103
5b799d7fe9409cb9c05368696fae182e25fc7348	refs/heads/release/JAL-1645_r29
37de9310bec3501cbc6381e0c3dcb282fcaad812	refs/heads/releases/Release_2_10_0_Branch
4f02a7cced11020e3fc0c1220c98c3183955ae5c	refs/heads/releases/Release_2_10_1_Branch
ff044a6dc70d85fcef18cac3129386c98d7edda3	refs/heads/releases/Release_2_10_2_Branch
b2a79a3aa3478494eec09258f8031846f6e27fc6	refs/heads/releases/Release_2_10_2b1_Branch
9a92eacef824ed3a5ff0e2ae20ae8d2d88628e3a	refs/heads/releases/Release_2_10_3_Branch
3e1c9452fd504b47a9d982e221a6acb3accce4a5	refs/heads/releases/Release_2_10_4_Branch
5610d0f46a76d4269d25148d42f92d867fa1061a	refs/heads/releases/Release_2_10_5_Branch
f534eb87dd87652bb86db902749fabf4421b4b50	refs/heads/releases/Release_2_10_Branch
4bbd068738ed2e685f580ea1b65a7b11e32d3f3e	refs/heads/releases/Release_2_11_1_4_debianpatches
376327b9f7ecbe5f33164ecfb43c53541272dc97	refs/heads/releases/Release_2_11_1_Branch
c2bb08e5dc01cc9de193f19b625c3f1abd0488c5	refs/heads/releases/Release_2_11_2_Branch
24ed4dabf2f8a9cd26f4b4527d4c3c3e03efc974	refs/heads/releases/Release_2_11_3_Branch
6d1fc3490ca522df0ad2f6f25cadcff87a91eec9	refs/heads/releases/Release_2_11_4_Branch
a148aca2d56223221b45f2ee7fdf82eca83e4c5b	refs/heads/releases/Release_2_11_Branch
d8b9b83f2739ee2c11670af890d2c63b8c1c2b7c	refs/heads/releases/Release_2_9_1_Branch
b4ff9affaf85176402f148c100e24b8546052173	refs/heads/reviews/features/JAL-2136_phyre2_integration_withJims
5ed233c0db216f471a96067281914621f40b342c	refs/heads/reviews/merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
cb7c4a276c52b0bb3e448e6761886fecc0e9d05c	refs/heads/schema/JAL-1764_structureViewAttribute
5eec392de3099482d771ab078f0db57f9c47e81c	refs/heads/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data
9f70ff4b6d193b340031997634c9e3602486bc8e	refs/heads/spike/JAL-1950_hmmer3client
7a5bb267f66d8284f2d190d4c791f39fa773394b	refs/heads/spike/JAL-2778_changelookandfeelOpaqueWindows
9e19bd7c9421b47f1e062a046c589a75c546026b	refs/heads/spike/JAL-3548_exampleRestServer
f876e862532415268bf11b902b27f29dd5baff69	refs/heads/spike/JAL-3622_Scanner_swingjs_J212_merge
b1942c061c52e2d2dcaf044458eac261063cf25d	refs/heads/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin
a0ad835c71ed4b37b0eda5ef45449e7ba8dc7240	refs/heads/spike/JAL-3753_helphtmldupes
5fd892e32ce50ece7c2a626a42c23a0be00ab10a	refs/heads/spike/JAL-3781_2d_scaling
f680b9a507cc1643c9eead990e15026c1eca4e6e	refs/heads/spike/JAL-4047/JAL-4048_columns_in_sequenceID
0725e0e5ff41cf03ad744579921061ccdcce74df	refs/heads/spike/JAL-4055_retire_JDesktop
96502dc1fdbc2b417956583495d6acc8fbb74d62	refs/heads/spike/JAL-4159_pasimap_2113_series
a06feba57df0c199e8ec2513ac1225daf9d1faa8	refs/heads/spike/JAL-4159_pasimap_2114_series
5e8bd075739b756cac8f741a47a7de952c45f879	refs/heads/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure
5e59e8410d369c7ee653f1442c28198d75efbb30	refs/heads/spike/JAL-4386_develop_trial_merge
a92d9ee8c25e41770bf745b793262f9a7937893e	refs/heads/spike/JAL-4386_generate_multiple_leaves_for_ss_sources
e340907f86006b014c2f28b8b2054fa908b594ad	refs/heads/spike/JAL-4386_merge_multiple_leaves
8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52	refs/heads/spike/JAL-4386_merge_with_develop
b03b0404e7e6ff3e6abf0285df7b61fea69319f0	refs/heads/spike/clinvar
2a6bee646361a41a57c7a3868a966635c3d25a27	refs/heads/spike/javier_noseqhack
f39d94943f685a971381d76c2f24323dd2f963c6	refs/heads/spike/jims/Release_2_12_alpha
9bf35f549e0f394ca24385ecf5b2ff4505ac6047	refs/heads/spike/jims_dec_2022_212_merge
0920ff53a47805479a84980bc09886c939c77399	refs/heads/spike/phyre2
e9a1c2c372f4bbf6cf658de3dba73ef326b20c20	refs/heads/spike/try_spotless_JAL-3438
2751f045540a1394839bb889e6036f7853916bc8	refs/heads/spikes/JAL-4113_javafx_with_Jalview_MSA
1a64eb3f07d8d54a605581c7e7338c55bcb3e70c	refs/heads/spikes/JAL-4366_3di_msa_forfoldseeks
c242d1bd498f606f87c5f3c7854b469dd7120730	refs/heads/spikes/geoff
07ec92811fef5090f5c88d1f0460d01a2fb5e951	refs/heads/spikes/jim
e206e623bc46590478da6e52e3c95767fe5f763d	refs/heads/spikes/jims_test
c242d1bd498f606f87c5f3c7854b469dd7120730	refs/heads/spikes/jpred
70f98ab214fefd664892e8c8ec44811d820a802d	refs/heads/spikes/kira
914a9aaf5a2eeb3cdedf136c2e6b4b6e4b5d6174	refs/heads/spikes/koen
2673aff39ac0c0dd997aa1d18daf439d0d509649	refs/heads/spikes/mungo
bc2e488c714f8faa602de0a8966d8248e502e6a2	refs/heads/spikes/phyre
8b2c0525d0a6360b43f8fd5d3433e785996992c6	refs/heads/spikes/thomas
76b8230ef6abfadc38425364af19ea4f47e39b4c	refs/heads/spikes/toch
50721af283710cf622e5c68bd826a87cf223948a	refs/heads/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window
be5be9d97cdb7248784777fa17face7d345bdd33	refs/heads/task/JAL-1794_jettyExamplesServer
4eb9955fd442f5fa51c1771d00b6c352ff227a4c	refs/heads/task/JAL-2164_mcviewforoldjalviewprojects
f40e44c9db0a689f2df188cf07801b035096c1b1	refs/heads/task/JAL-2196pdbeProperties
ccbd7db9e08c6bda0040a64ec7f4f62790e054f1	refs/heads/task/JAL-2562_SequenceI.findPosition
7bb9eaabdb22172fedefd9d47cdd9543063e9999	refs/heads/task/JAL-2662
692d2b97d40497e462553cdc7269e173d605ec3a	refs/heads/task/JAL-3042_remove_SimpleDocument_dependency
169702be21508ff1d4407eba8aaef1079b8ec9c4	refs/heads/task/JAL-3047_clover2104b1_cherrypick
e2151fb87e2e159ad2dac453b62ddb0ffa195b5c	refs/heads/task/JAL-3047_clovercoverage
2cc0663ace7adaa36478db77ca96daa736993890	refs/heads/task/JAL-3060featureEditor
cee0842270af0aed7091576f3b414fb8a4f96e29	refs/heads/task/JAL-3068lineartDialog
bf484926c15117ef740812a9992698f88a710615	refs/heads/task/JAL-3089annLabelsPopup
cae66e7ef0ed62e152437a0dd3bff62368269971	refs/heads/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS
53c54d0ada46fa839095ace36e18e30ddcf63aa0	refs/heads/task/JAL-3193mergeEnsemblGenomes
67bfdf3d0c42cf38898bd8ce712ce1ab2e924f6c	refs/heads/task/JAL-3210_ben_testing_jalviewJS_building
dbe09b536e34aa19578973d161d7f7a5753de02b	refs/heads/task/JAL-3243_PDB_free_text_error
16561706ec44c7159457dc11b3abee4292e65608	refs/heads/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files
61e1143d502ef80da44657be8486c07a115ee56a	refs/heads/task/JAL-3281_Automatic_installers_download_table_generation
2b1e829c29dd7bd07bb98be1eeb6f34f993c248c	refs/heads/task/JAL-3337-rm-lib-update-sourceDist
5e0bbac5bf413f8ede4844afd67ac08a8ebb679f	refs/heads/task/JAL-3349_Support_cli_JRE_arguments_through_getdown
ef3a7bf0df83ff4fccdcc13dcdd26fc415e3529f	refs/heads/task/JAL-3394_install4j8_option
ca656d98cf6af805074a0e0f50f8b2f67d27fc0a	refs/heads/task/JAL-3510-update-clover-to-4.4.1
3d08653a0dec6b8ce7adb3308cb58faa73c0f466	refs/heads/task/JAL-3521_Slimmed_down_build.gradle_for_debian
5cbf62291e9f90ece7a76cfc9b5c8f3bf23646a2	refs/heads/task/JAL-3577_Jalview_Test_installers
3af9017e1f6c6d045c6c0d41245fcd7bfdae32a6	refs/heads/task/JAL-3763_newDatasetForCds
a82d0d7f4117d6f4d56c307187f3f29e231055a5	refs/heads/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application
0b0c6a6a86ca5a69275771c6569e7b41dcd6f8b9	refs/heads/task/JAL-3805_Remove_Uninstall_Old_Jalview_application_for_develop_branch
6165856bc82c84016c4b5354ab58abe6a6b5fcd7	refs/heads/task/JAL-3911_getdown_improvements
3a39fb5cc1a7483fbf64d0fca8e57f8fc4bc57c2	refs/heads/task/JAL-4001_Plausible_API
b1bc235742d0a5028a561e5c796b0ff7edf943fe	refs/heads/task/JAL-4001_Release_2_11_2_Branch_with_Plausible
a971d440b2079bd1c351a563d9a17e866710ae5a	refs/heads/task/JAL-4001_migrate_googleanalytics_to_GA4
5db8e803feb3d04bf6142d25ded76473ec1cb571	refs/heads/task/JAL-4059_updateJmolandSwingJS
eddc7529cad6e465bce8210665845253a412e89c	refs/heads/task/r2_11_2/JAL-3871_Jmol_dedup
e3aa01ef27f11521dc4ff724055b5ab3d4ad1d25	refs/heads/tasks/JAL-3035_remove_dasobert_dependency
968305a24f7a2d9b89dd419f3a327961ff85dba8	refs/heads/tasks/JAL-3067_slivkaprep
6749a5b122dd78b4abbf0940dbe854dc0298ae65	refs/heads/tasks/JAL-3070_wsinterfaces
88153d5bb04acd2b8e7fbc3e6789622b77b6cf58	refs/heads/tasks/JAL-3311_removeVamsasMenu
4468c1e39c57fbb67192207b4c8750dab1b1dedd	refs/heads/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame
c05539a51cc57a9fabb10e01bb7b2e4123da628c	refs/heads/testbuild/JAL-3412_getIdWidth_test
34a1ef54cc5d13727129e9b57137356d6d9c1d86	refs/heads/testing/JAL-3577_jalviewversion_autoset_fixed
e6f25fadd43d5865b62c5ef749ad12f6c9a3a583	refs/heads/testpaches/JAL-2719_JAL-1264_testfails
610c3b982af35c03ca23cb8592a5519f478157cc	refs/heads/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker
1a98afcef550946aec217833bb7e0cf467f00c49	refs/heads/update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more
af958407a40e7d7045f7191f4fa213f4384e6f56	refs/heads/update/JAL-4108_212_testng_jar_update
966e2e639242c252f4ed9e5f0e3e91b0389bd2de	refs/heads/vamsasDemo
90ae01c1c1504e0ae42817f78116f1d35b317c47	refs/remotes/origin/spikes/koen
2d348a0c5220b0f108d8c029a6503dd8f751b0ff	refs/tags/Archived_Release_2_7
5d501d5230ad1c42f1e17a485cb86a04ba8b538a	refs/tags/Develop-2_11_2_0-d20201215
5ee9c5f4c92a8dcebe6c31697181983efb116e8a	refs/tags/Develop-2_11_2_0-d20210205
aa3f623a1ff44113f3fcea09f28ab89ffc54768d	refs/tags/Jalview_2_4_0b2
5b799d7fe9409cb9c05368696fae182e25fc7348	refs/tags/Jalview_2_9
fffa7168c3a0104a3cfa773a2a3b1d0723d6c7b9	refs/tags/Release_2_0
5e1ff455191eccb49a15dcaab8b0ebe1626563f7	refs/tags/Release_2_01
a938578363db9452d4fee93666c8bfe343b7710f	refs/tags/Release_2_02
503ebba0021fa583fa7af58f9406f9234274fd7c	refs/tags/Release_2_03
50101c6da4cd0c6cd3d0438fa66905aae30b58b7	refs/tags/Release_2_04
5e34f249e1565c22cad33fb37037047236ba8eca	refs/tags/Release_2_05
d783fbae7be6592377a870e21b45012dbd7bbe08	refs/tags/Release_2_05b
41aa357b0c6071062fbee339e598fc7fbffef02f	refs/tags/Release_2_06
7bbb724c84401ce9456a427593c6ae34f94d1c03	refs/tags/Release_2_07
61704c27d12b651a766594552da77857a5d8ab4c	refs/tags/Release_2_08
3626ea082cc69ff0609eb68b206c85d80e2b1c36	refs/tags/Release_2_08_1
d157b5d6c9aa88a3eb70afb0cccee08d8ec86afd	refs/tags/Release_2_1
4e1d9a661070768f2b74a8ef7925c38372ee83d6	refs/tags/Release_2_10_0
4dc7619bed1c475c35f328601b5d7d46116327a6	refs/tags/Release_2_10_0b1
5f16fae89ea1f8e43fc847521d702ef78a4185c2	refs/tags/Release_2_10_0b1_final
d9c7868a610eff29a8eddb160b6dc78a94a72470	refs/tags/Release_2_10_0b1_sourcepub
260f6abfaaafac067d5bda703e5b21be480bcc8f	refs/tags/Release_2_10_1
7750a4b02d54025e18a216183957fa70a91e3682	refs/tags/Release_2_10_2
272e577b577ff9bd3db547d527aaeff08de26ab9	refs/tags/Release_2_10_2b1
488e8b4ff975fbb83eac40f9e9f16d40c5a33d34	refs/tags/Release_2_10_2b2
7757b97abcc080b0e0d7a6bdbf5b7fcd04571bd8	refs/tags/Release_2_10_3
9a92eacef824ed3a5ff0e2ae20ae8d2d88628e3a	refs/tags/Release_2_10_3b1
c0a005cd8531b018cd5eee375ec51581bb2e4105	refs/tags/Release_2_10_4
5d0c7db11ef8e4ce6deffc3dbf976b63554b2141	refs/tags/Release_2_10_4b1
5610d0f46a76d4269d25148d42f92d867fa1061a	refs/tags/Release_2_10_5
a148aca2d56223221b45f2ee7fdf82eca83e4c5b	refs/tags/Release_2_11_0
30119dce1634085c41372d55b528a7a878b03b23	refs/tags/Release_2_11_1_0
4d959452a9c486b6d94291d8e819036ec19b09ef	refs/tags/Release_2_11_1_1
433635c8784cfa421da35e45aa24dd6f16a8bf6b	refs/tags/Release_2_11_1_2
6875edc608179e9710388439099542296f263c15	refs/tags/Release_2_11_1_3
930bcaf01651a15d371c961b1276d9b139f586e2	refs/tags/Release_2_11_1_4
2c0496537b3ea1fb76dca30c7c3b5d87c0333260	refs/tags/Release_2_11_1_5
a7e71732f248a74c0fe30b5ff400584b91960791	refs/tags/Release_2_11_1_6
376327b9f7ecbe5f33164ecfb43c53541272dc97	refs/tags/Release_2_11_1_7
2040e7e728e666d0135f31c65f3eaccc0bfe40ae	refs/tags/Release_2_11_2_0
56955fc6a526b35bff79df13613bc88390824fec	refs/tags/Release_2_11_2_1
11c0c1e2426619039052264ce0f2b06a78cd9194	refs/tags/Release_2_11_2_2
bc93afe8b03eeafdba761dac61cd212434e3de7b	refs/tags/Release_2_11_2_3
92a19874dd2397604d4c7284a15eb54f8a3cba58	refs/tags/Release_2_11_2_4
519295fc0459e0a76e5be32292c085d9bde51484	refs/tags/Release_2_11_2_5
d5bd34eb49f43735e240058f8875ab0bfcae4441	refs/tags/Release_2_11_2_6
bd990168d0b3c7772c961b56144c3dee94a09054	refs/tags/Release_2_11_2_7
6544c5e45b8151892de506391662111afcae1052	refs/tags/Release_2_11_3_0
bec7c06338ee402f6cde54173ddff2295ca702df	refs/tags/Release_2_11_3_1
63363f5d656679c0eb0276c95be65b3b7b2c5ae2	refs/tags/Release_2_11_3_2
24ed4dabf2f8a9cd26f4b4527d4c3c3e03efc974	refs/tags/Release_2_11_3_3
7edd0787457cf0a01f95f26e3c89b49175b48de0	refs/tags/Release_2_11_4_0
6d1fc3490ca522df0ad2f6f25cadcff87a91eec9	refs/tags/Release_2_11_4_1
e059f46e77f5106185c5ebd6be7c5c31c2fbd230	refs/tags/Release_2_1_1
56d4c1b68866f75613556f7f93da4eb8ce463f42	refs/tags/Release_2_2
9c1a0325b6cd763f212f838f4a2998c38b052490	refs/tags/Release_2_3
9c1a0325b6cd763f212f838f4a2998c38b052490	refs/tags/Release_2_3_buildfix
affd42b5ca69723c9d0d114404d1700e5757806b	refs/tags/Release_2_4
fa80736070da3ccf2dbd28ef31ad9dcfe3231e22	refs/tags/Release_2_4_0
b917c7905a12b147c6f99b62e92c3fca6f9bf719	refs/tags/Release_2_5
a10a465359de7b8c0baff4925d4b267a28eb0071	refs/tags/Release_2_5_1
b917c7905a12b147c6f99b62e92c3fca6f9bf719	refs/tags/Release_2_5_branch
069f21298ab1fe4460067f6158745ba3c6726e81	refs/tags/Release_2_6
4230b657b444c3667e9c8cc7974730681130ebae	refs/tags/Release_2_6_1
f335ea905223c014fb305051b45960ec7e28cfc4	refs/tags/Release_2_7
159f36a8d3aa393ee0931dd13ac9e8cc38a36e8d	refs/tags/Release_2_8
a90ca46aae39b99ea2fbfc1aefc9cc197d590689	refs/tags/Release_2_8_0b1
2928ced13b8509bd769fa02e75132ddd8a00430e	refs/tags/Release_2_8_1
2525e88afc4d572c6d232719362f57cb9a84d609	refs/tags/Release_2_8_1^{}
4cf475567facc11b4be0f6e0849c73cbfc98508d	refs/tags/Release_2_8_2
ec669c13867d001e07c9cef157c268afe03be9f3	refs/tags/Release_2_8_2b1
eb9c652416a69e6db0531e956dd2011012eac898	refs/tags/Release_2_9_0b1
c19d2a91ca05e052e3408bf5852d88eb5d0608f1	refs/tags/Release_2_9_0b2
8549afc7ca45e84e3425631475ac703b2f7506a8	refs/tags/Root_Release_2_5_Branch
c5ae36527ac4366160ba09b88e5e74568f71b836	refs/tags/Root_VamJalview_2_07b+
1ecf6419aba86993b3c223bf5ec0fa79427baf85	refs/tags/start