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jalview.git
2024-05-23 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2024-05-23 Jim ProcterJAL-4159 first stab at injecting blosum62 similarity... commit | commitdiff | tree | snapshot
2024-05-23 Jim ProcterJAL-4423 provide option in calc dialog to re-use the... commit | commitdiff | tree | snapshot
2024-05-23 Jim ProcterJAL-4159 fix sense of console/alignment output suppress... commit | commitdiff | tree | snapshot
2024-05-23 Jim ProcterJAL-4159 disable the score model combo box when pasimap... commit | commitdiff | tree | snapshot
2024-05-23 MorellThomasFix PaSiMap not having the eigenvalues saved commit | commitdiff | tree | snapshot
2024-05-22 MorellThomasrevert build.gradle changes commit | commitdiff | tree | snapshot
2024-05-22 MorellThomasSave PaSiMap with Jalview Session commit | commitdiff | tree | snapshot
2024-05-22 MorellThomasRectanuglar selection changed to Mouse Button 3 drag commit | commitdiff | tree | snapshot
2024-05-21 Jim ProcterJAL-4259 set title using original alignment window... spike/JAL-4159_pasimap_2114_series commit | commitdiff | tree | snapshot
2024-05-21 Jim ProcterJAL-4159 implement bounds for PASIMAP calculation ... commit | commitdiff | tree | snapshot
2024-05-21 Jim ProcterJAL-4159 connectivity should be computed for the sequen... commit | commitdiff | tree | snapshot
2024-05-21 Jim ProcterJAL-4159 PASiMap currently doesn't support different... commit | commitdiff | tree | snapshot
2024-05-21 Jim ProcterJAL-4159 sometimes the progress bar may not be availabl... commit | commitdiff | tree | snapshot
2024-05-21 Jim ProcterMerge branch 'feature/JAL-4159_pasimap' into spike... commit | commitdiff | tree | snapshot
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4159_pasimap 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 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 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-4217 Upped the main testTask0 timeout to 15 minutes... improvement/JAL-4217_added_a_timeout_to_tests 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 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 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 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
2024-05-02 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
2024-04-26 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
2024-04-18 MorellThomasMerge branch 'test/progressBar' into feature/JAL-4159_p... commit | commitdiff | tree | snapshot
2024-04-18 MorellThomasImplemented ProgressBar for PaSiMap commit | commitdiff | tree | snapshot
2024-04-16 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... commit | commitdiff | tree | snapshot
2024-04-12 MorellThomasinlcude progress commit | commitdiff | tree | snapshot
2024-04-09 James ProcterJAL-4159 recover 2.11.3 series gradle/build.properties... spike/JAL-4159_pasimap_2113_series commit | commitdiff | tree | snapshot
2024-04-09 James ProcterJAL-4390 don't output alignment to text panel and stdou... commit | commitdiff | tree | snapshot
2024-03-15 MorellThomasFix output of all dimensions commit | commitdiff | tree | snapshot
2024-03-15 MorellThomasAlogirthm working, but still giving slightly off results 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
2024-03-07 MorellThomasInlcude 8 dimensions commit | commitdiff | tree | snapshot
2024-03-06 MorellThomasFix PaSiMap on selected sequences commit | commitdiff | tree | snapshot
2024-03-06 MorellThomasTest version to switch branches commit | commitdiff | tree | snapshot
2024-01-31 MorellThomasFix output points column labels 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
2024-01-23 Ben SoaresJAL-4367 Limit right and top adjustments commit | commitdiff | tree | snapshot
2024-01-23 Ben SoaresJAL-4290 Fix image comparison between gui and headless... commit | commitdiff | tree | snapshot
2024-01-23 Ben SoaresJAL-4290 fixed tests commit | commitdiff | tree | snapshot
2024-01-23 Ben SoaresMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff | tree | snapshot
2024-01-23 Ben SoaresMerge branch 'develop' into bug/JAL-4353_cannot_output_... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4353 wait for files to be written fully before... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4353 singleThread all tests commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4369 invokeAndWait to avoid hang whilst calling... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4369 uniprotkb - try to avoid another redirect... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterJAL-4369 use rest.uniprot.org as fetch domain commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignor... commit | commitdiff | tree | snapshot
2024-01-23 James ProcterMerge branch 'bug/JAL-4368_default_colourscheme_applied... commit | commitdiff | tree | snapshot
2024-01-19 Ben SoaresJAL-4373 Setting the jvmmempc and jvmmemmax strings... bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch commit | commitdiff | tree | snapshot
2024-01-19 Ben SoaresJAL-4373 Fix Main-Class and other attribute settings... commit | commitdiff | tree | snapshot
2024-01-10 MorellThomasFixed PaSiMap output columns commit | commitdiff | tree | snapshot
2024-01-05 Ben SoaresJAL-4368 Only set a colour scheme if --colour is given... bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately commit | commitdiff | tree | snapshot
2023-12-19 Ben SoaresJAL-4290 Fixed one test commit | commitdiff | tree | snapshot
2023-12-18 Ben SoaresJAL-4290 not quite working tests commit | commitdiff | tree | snapshot
2023-12-18 Ben SoaresJAL-4290 incorrect usage of main() commit | commitdiff | tree | snapshot
2023-12-15 Ben SoaresMerge branch 'bug/JAL-4290_headless_alignment_export_wi... commit | commitdiff | tree | snapshot
2023-12-15 Ben SoaresJAL-4290 Add method to allow for specific settings... commit | commitdiff | tree | snapshot
2023-12-15 Ben SoaresJAL-4290 Set structureSelectionManager settings more... commit | commitdiff | tree | snapshot
2023-12-15 James ProcterMerge branch 'bug/JAL-4290_headless_alignment_figure_wi... commit | commitdiff | tree | snapshot
2023-12-15 James ProcterJAL-4290 new CommandsTest.headlessOrGuiImageOutputTest... bug/JAL-4290_headless_alignment_figure_with_sse commit | commitdiff | tree | snapshot
2023-12-15 Ben SoaresJAL-4290 Move some annotation visibility settings to... commit | commitdiff | tree | snapshot
2023-12-14 James ProcterJAL-4356 update release notes commit | commitdiff | tree | snapshot
2023-12-14 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff | tree | snapshot
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