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jalview.git
2024-05-31 Ben SoaresJAL-4421 Add DS_Store customisation to gradle. Add... commit | commitdiff | tree | snapshot
2024-05-31 Ben SoaresJAL-4421 Python script for customising DS_Store. Separ... commit | commitdiff | tree | snapshot
2024-05-29 Ben SoaresJAL-4409 Allow more URI schemes (e.g. file) to be opene... commit | commitdiff | tree | snapshot
2024-05-29 Ben SoaresJAL-4409 Allow more URI schemes (e.g. file) to filter... commit | commitdiff | tree | snapshot
2024-05-29 Ben SoaresJAL-4414 Add SocketTimeoutException to exceptions that... commit | commitdiff | tree | snapshot
2024-05-29 Ben SoaresJAL-3196 Need more memory for the install4j process... commit | commitdiff | tree | snapshot
2024-05-28 Ben SoaresJAL-4409 JAL-4160 Don't let getdown turn jalviewX:... commit | commitdiff | tree | snapshot
2024-05-28 Ben SoaresJAL-4417 Use a specified props file for consistent... commit | commitdiff | tree | snapshot
2024-05-28 Ben SoaresJAL-4409 TEMPORARY don't clean up image files from... commit | commitdiff | tree | snapshot
2024-05-28 Ben SoaresJAL-4409 Ensure the specific scheme jalviewx is only... commit | commitdiff | tree | snapshot
2024-05-28 Ben SoaresJAL-4409 Don't insist on HttpURLConnection, allows... commit | commitdiff | tree | snapshot
2024-05-27 Ben SoaresMerge branch 'develop' into improvement/JAL-4409_implem... commit | commitdiff | tree | snapshot
2024-05-21 Ben SoaresJAL-1054 Change one more (unused) url.openStream to... commit | commitdiff | tree | snapshot
2024-05-21 Ben SoaresJAL-1054 Change the rest of the url.openConnection... commit | commitdiff | tree | snapshot
2024-05-21 Ben SoaresJAL-4409 Adjust usage of HttpUtils.equivalentJalviewURL... commit | commitdiff | tree | snapshot
2024-05-21 Ben SoaresJAL-4409 Make HttpUtils.equivalentJalviewUrlString... commit | commitdiff | tree | snapshot
2024-05-21 Jim ProcterJAL-4356 release date for 2.11.3.3 is 22nd May 2025 commit | commitdiff | tree | snapshot
2024-05-20 Ben SoaresJAL-4409 Also interpret jalviewX:// URIs in Jalview... commit | commitdiff | tree | snapshot
2024-05-20 Ben SoaresJAL-4397 Another fix on linux commit | commitdiff | tree | snapshot
2024-05-17 Ben SoaresJAL-4420 Add some debugging statements commit | commitdiff | tree | snapshot
2024-05-17 Ben SoaresJAL-4420 Tests for new FileUtils methods commit | commitdiff | tree | snapshot
2024-05-17 Ben SoaresJAL-4420 Allow preprocessing of arguments if they are... commit | commitdiff | tree | snapshot
2024-05-17 Ben SoaresJAL-4409 Checking getdown jars up to date commit | commitdiff | tree | snapshot
2024-05-17 Ben SoaresJAL-3409 Add newline back into Buffered Reader in getdo... commit | commitdiff | tree | snapshot
2024-05-17 Ben SoaresJAL-4409 corrected the umount of dmg to hdiutil detach... commit | commitdiff | tree | snapshot
2024-05-16 Ben SoaresJAL-4409 Added remote JVL files for Linux/Windows commit | commitdiff | tree | snapshot
2024-05-16 Ben SoaresJAL-4409 Added multiple file open to getdown. Added... commit | commitdiff | tree | snapshot
2024-05-16 Jim ProcterJAL-4356 release notes for JAL-3978 patch commit | commitdiff | tree | snapshot
2024-05-16 Jim ProcterMerge branch 'bug/JAL-3978_copy_bin_dir_to_getdownArchi... commit | commitdiff | tree | snapshot
2024-05-16 Ben SoaresJAL-3978 Add the bin dir to be copied from website... bug/JAL-3978_copy_bin_dir_to_getdownArchiveBuild_task commit | commitdiff | tree | snapshot
2024-05-16 Ben SoaresJAL-4409 Easier full install from source for macOS commit | commitdiff | tree | snapshot
2024-05-16 Ben SoaresJAL-4409 more places to check for jalviewd:// commit | commitdiff | tree | snapshot
2024-05-16 Jim ProcterJAL-4418 bump release to 2.11.4.0 commit | commitdiff | tree | snapshot
2024-05-16 Jim ProcterMerge branch 'feature/JAL-4386_calculate_tree_using_sec... commit | commitdiff | tree | snapshot
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4386_calculate_... commit | commitdiff | tree | snapshot
2024-05-16 Jim ProcterJAL-4356 bump release date to today, release notes... commit | commitdiff | tree | snapshot
2024-05-15 Ben SoaresJAL-4397 IdWidth tests slightly less restrictive for... commit | commitdiff | tree | snapshot
2024-05-15 Ben SoaresJAL-4409 extra schemes now opening correctly in macos commit | commitdiff | tree | snapshot
2024-05-15 Renia CorreyaJAL-4386 Fixed failed test case commit | commitdiff | tree | snapshot
2024-05-15 Jim ProcterMerge branch 'bug/JAL-4416_sview_not_shown_for_local_st... commit | commitdiff | tree | snapshot
2024-05-15 Renia CorreyaJAL-4386 Fixed failed test cases commit | commitdiff | tree | snapshot
2024-05-15 Jim ProcterJAL-4416 TODO for fixing JAL-4415 JAL-3124 - need a... bug/JAL-4416_sview_not_shown_for_local_strucfile commit | commitdiff | tree | snapshot
2024-05-15 Jim ProcterJAL-4416 ensure the structure view is shown and any... commit | commitdiff | tree | snapshot
2024-05-15 Jim ProcterJAL-4416 make sure the structure viewer is actually... commit | commitdiff | tree | snapshot
2024-05-15 Renia CorreyaJAL-4386 Added preferences for secondary structure... commit | commitdiff | tree | snapshot
2024-05-15 Ben SoaresJAL-4409 minor change for mac testing commit | commitdiff | tree | snapshot
2024-05-15 Ben SoaresJAL-4409 Updated getdown classes commit | commitdiff | tree | snapshot
2024-05-15 Ben SoaresJAL-4409 Refactoring to allow easier reuse of classes... commit | commitdiff | tree | snapshot
2024-05-15 Jim ProcterMerge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_... commit | commitdiff | tree | snapshot
2024-05-15 Renia CorreyaJAL-4386 - Implementation of retrieving secondary structure commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresJAL-1054 JAL-4414 Tests for the HttpUtils redirect... commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresJAL-1054 Also recognise UnknownHostException as a file... commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresMerge branch 'develop' into improvement/JAL-4409_implem... commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresJAL-4217 Upped the main testTask0 timeout to 15 minutes... improvement/JAL-4217_added_a_timeout_to_tests commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresJAL-1054 Tests for the HttpUtils redirection wrappers commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresMerge branch 'bug/JAL-4397_failing_idWidth_tests' into... commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresMerge branch 'develop' into bug/JAL-4397_failing_idWidt... bug/JAL-4397_failing_idWidth_tests commit | commitdiff | tree | snapshot
2024-05-14 Ben SoaresJAL-4414 Add a FileNotFoundException when identifying... commit | commitdiff | tree | snapshot
2024-05-14 Jim ProcterJAL-4356 fix release note commit | commitdiff | tree | snapshot
2024-05-14 Jim ProcterJAL-4356 set release date to Weds 15th May and update... commit | commitdiff | tree | snapshot
2024-05-13 Jim ProcterJAL-4356 JAL-518 JAL-4413 release notes commit | commitdiff | tree | snapshot
2024-05-13 Jim ProcterMerge branch 'features/JAL-518_justify_seqs_in_region... commit | commitdiff | tree | snapshot
2024-05-13 Ben SoaresJAL-1054 Fix wrappers for following http->https redirects commit | commitdiff | tree | snapshot
2024-05-13 Jim ProcterJAL-518 better test coverage and support for case prese... features/JAL-518_justify_seqs_in_region commit | commitdiff | tree | snapshot
2024-05-13 Jim ProcterJAL-518 failing test for case preservation on justify commit | commitdiff | tree | snapshot
2024-05-13 Ben SoaresMerge branch 'develop' into improvement/JAL-4409_implem... commit | commitdiff | tree | snapshot
2024-05-13 Renia CorreyaMerge remote-tracking branch 'origin/develop' into... commit | commitdiff | tree | snapshot
2024-05-13 Jim ProcterMerge branch 'develop' into features/JAL-518_justify_se... commit | commitdiff | tree | snapshot
2024-05-13 Jim ProcterJAL-4413 timeouts Merge branch 'improvement/JAL-4217_ad... commit | commitdiff | tree | snapshot
2024-05-13 Ben SoaresJAL-4409 Fix some file extensions (including remove... commit | commitdiff | tree | snapshot
2024-05-13 Ben SoaresJAL-1054 Add wrappers for URL.openConnection(), URL... commit | commitdiff | tree | snapshot
2024-05-13 Jim ProcterMerge branch 'develop' into features/JAL-518_justify_se... commit | commitdiff | tree | snapshot
2024-05-13 Renia CorreyaMerge branch 'feature/JAL-4386_calculate_tree_using_sec... commit | commitdiff | tree | snapshot
2024-05-13 Renia CorreyaJAL-4386 - Implementation of substitution matrix and... commit | commitdiff | tree | snapshot
2024-05-10 Jim ProcterJAL-4411 fix typo :( commit | commitdiff | tree | snapshot
2024-05-10 Jim ProcterJAL-4411 store class of provider in PDBEntry commit | commitdiff | tree | snapshot
2024-05-10 Ben SoaresJAL-4409 Add jalviewhttp and jalviewhttps schemes to... commit | commitdiff | tree | snapshot
2024-05-02 Ben SoaresJAL-4217 Sensible timeout for testTask0 commit | commitdiff | tree | snapshot
2024-05-02 Ben SoaresJAL-4217 Added a timeout for testTasks. If timeout... commit | commitdiff | tree | snapshot
2024-05-01 Renia CorreyaMerge remote-tracking branch 'origin/bug/JAL-4407_no_se... commit | commitdiff | tree | snapshot
2024-05-01 Jim ProcterJAL-4407 don't transfer 'local' settings - leave as... bug/JAL-4407_no_sec_str_from_draganddrop_to_msa commit | commitdiff | tree | snapshot
2024-05-01 Jim ProcterJAL-4407 failing test checking for secondary structure... commit | commitdiff | tree | snapshot
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure commit | commitdiff | tree | snapshot
2024-04-30 Renia CorreyaJAL-4386 Comparing secondary structure similarity direc... commit | commitdiff | tree | snapshot
2024-04-27 Ben SoaresJAL-4397 Removed debugging statement commit | commitdiff | tree | snapshot
2024-04-26 Ben SoaresJAL-4397 Adjustments for macOS HiDPI commit | commitdiff | tree | snapshot
2024-04-26 Ben SoaresJAL-4397 Test all fixed on linux. Given leeway to... commit | commitdiff | tree | snapshot
2024-04-26 Renia CorreyaJAL-4386 Drop down for secondary structure sources... commit | commitdiff | tree | snapshot
2024-04-24 Renia CorreyaJAL-4386 PCA/Tree Calculation for Secondary Structures... commit | commitdiff | tree | snapshot
2024-04-22 Ben SoaresJAL-4397 Allow some leeway in automatically calculated... commit | commitdiff | tree | snapshot
2024-04-18 Ben SoaresJAL-4397 fixed testresetIdWidth() test on macos commit | commitdiff | tree | snapshot
2024-04-16 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... commit | commitdiff | tree | snapshot
2024-03-13 Renia CorreyaJAL-4386_Added changes in similarity score calculation... commit | commitdiff | tree | snapshot
2024-03-08 Renia CorreyaJAL-4386 Corrected failed test case. commit | commitdiff | tree | snapshot
2024-03-08 Renia CorreyaJAL-4386 Added further checks for sequences that have... commit | commitdiff | tree | snapshot
2024-03-08 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4356 release notes commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4356 update release notes for 2.11.3.3 commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'bug/JAL-4290_headless_alignment_export_wi... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'develop' into bug/JAL-4290_headless_align... commit | commitdiff | tree | snapshot
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