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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview
2024-05-24 Jim ProcterJAL-4159 peek in a Jalview project's PCA viewer's title... commit | commitdiff
2024-05-24 Jim ProcterJAL-4257 JAL-4159 JAL-789 tidy up passing of score... commit | commitdiff
2024-05-24 James ProcterJAL-789 pairwise alignment via calculations dialog... commit | commitdiff
2024-05-24 James ProcterJAL-4366 compute coverage on each side of the pairwise... commit | commitdiff
2024-05-24 Jim ProcterMerge branch 'jims/feature/JAL-4159_pasimap' into featu... commit | commitdiff
2024-05-23 Jim ProcterJAL-4159 fix sense of console/alignment output suppress... commit | commitdiff
2024-05-23 Jim ProcterJAL-4159 disable the score model combo box when pasimap... commit | commitdiff
2024-05-23 MorellThomasFix PaSiMap taking scoreModels input and allow AlignSeq... commit | commitdiff
2024-05-23 MorellThomasFix PaSiMap not having the eigenvalues saved commit | commitdiff
2024-05-22 MorellThomasSave PaSiMap with Jalview Session commit | commitdiff
2024-05-22 MorellThomasRectanuglar selection changed to Mouse Button 3 drag commit | commitdiff
2024-05-21 Jim ProcterJAL-4259 set title using original alignment window... spike/JAL-4159_pasimap_2114_series commit | commitdiff
2024-05-21 Jim ProcterJAL-4159 implement bounds for PASIMAP calculation ... commit | commitdiff
2024-05-21 Jim ProcterJAL-4159 connectivity should be computed for the sequen... commit | commitdiff
2024-05-21 Jim ProcterJAL-4159 PASiMap currently doesn't support different... commit | commitdiff
2024-05-21 Jim ProcterJAL-4159 sometimes the progress bar may not be availabl... commit | commitdiff
2024-05-21 Ben SoaresJAL-1054 Change one more (unused) url.openStream to... commit | commitdiff
2024-05-21 Ben SoaresJAL-1054 Change the rest of the url.openConnection... commit | commitdiff
2024-05-21 Ben SoaresJAL-4409 Make HttpUtils.equivalentJalviewUrlString... commit | commitdiff
2024-05-21 Jim ProcterMerge branch 'feature/JAL-4159_pasimap' into spike... commit | commitdiff
2024-05-20 Ben SoaresJAL-4409 Also interpret jalviewX:// URIs in Jalview... commit | commitdiff
2024-05-17 Ben SoaresJAL-4420 Add some debugging statements commit | commitdiff
2024-05-17 Ben SoaresJAL-4420 Allow preprocessing of arguments if they are... commit | commitdiff
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4159_pasimap commit | commitdiff
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4386_calculate_... commit | commitdiff
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
2024-05-15 Jim ProcterJAL-4416 ensure the structure view is shown and any... commit | commitdiff
2024-05-15 Jim ProcterJAL-4416 make sure the structure viewer is actually... commit | commitdiff
2024-05-15 Renia CorreyaJAL-4386 Added preferences for secondary structure... commit | commitdiff
2024-05-15 Ben SoaresJAL-4409 Refactoring to allow easier reuse of classes... commit | commitdiff
2024-05-15 Jim ProcterMerge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_... commit | commitdiff
2024-05-15 Renia CorreyaJAL-4386 - Implementation of retrieving secondary structure commit | commitdiff
2024-05-14 Ben SoaresJAL-1054 Also recognise UnknownHostException as a file... commit | commitdiff
2024-05-14 Ben SoaresMerge branch 'bug/JAL-4397_failing_idWidth_tests' into... commit | commitdiff
2024-05-14 Ben SoaresMerge branch 'develop' into bug/JAL-4397_failing_idWidt... bug/JAL-4397_failing_idWidth_tests commit | commitdiff
2024-05-14 Ben SoaresJAL-4414 Add a FileNotFoundException when identifying... commit | commitdiff
2024-05-13 Ben SoaresJAL-1054 Fix wrappers for following http->https redirects commit | commitdiff
2024-05-13 Jim ProcterJAL-518 better test coverage and support for case prese... features/JAL-518_justify_seqs_in_region commit | commitdiff
2024-05-13 Ben SoaresJAL-1054 Add wrappers for URL.openConnection(), URL... commit | commitdiff
2024-05-13 Jim ProcterMerge branch 'develop' into features/JAL-518_justify_se... commit | commitdiff
2024-05-13 Renia CorreyaMerge branch 'feature/JAL-4386_calculate_tree_using_sec... commit | commitdiff
2024-05-13 Renia CorreyaJAL-4386 - Implementation of substitution matrix and... commit | commitdiff
2024-05-10 Jim ProcterJAL-4411 fix typo :( commit | commitdiff
2024-05-10 Jim ProcterJAL-4411 store class of provider in PDBEntry commit | commitdiff
2024-05-01 Renia CorreyaMerge remote-tracking branch 'origin/bug/JAL-4407_no_se... commit | commitdiff
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
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure commit | commitdiff
2024-04-30 Renia CorreyaJAL-4386 Comparing secondary structure similarity direc... commit | commitdiff
2024-04-29 Ben SoaresJAL-4398 Instantiate (static) JMenu windowMenu at the... commit | commitdiff
2024-04-26 Renia CorreyaJAL-4386 Drop down for secondary structure sources... commit | commitdiff
2024-04-24 Renia CorreyaJAL-4386 PCA/Tree Calculation for Secondary Structures... commit | commitdiff
2024-04-18 Ben SoaresJAL-4397 fixed testresetIdWidth() test on macos commit | commitdiff
2024-04-18 MorellThomasMerge branch 'test/progressBar' into feature/JAL-4159_p... commit | commitdiff
2024-04-18 MorellThomasImplemented ProgressBar for PaSiMap commit | commitdiff
2024-04-16 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... commit | commitdiff
2024-04-12 MorellThomasinlcude progress commit | commitdiff
2024-04-09 James ProcterJAL-4390 don't output alignment to text panel and stdou... commit | commitdiff
2024-03-15 MorellThomasFix output of all dimensions commit | commitdiff
2024-03-15 MorellThomasAlogirthm working, but still giving slightly off results commit | commitdiff
2024-03-13 Renia CorreyaJAL-4386_Added changes in similarity score calculation... commit | commitdiff
2024-03-08 Renia CorreyaJAL-4386 Added further checks for sequences that have... commit | commitdiff
2024-03-08 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... commit | commitdiff
2024-03-07 MorellThomasInlcude 8 dimensions commit | commitdiff
2024-03-06 MorellThomasFix PaSiMap on selected sequences commit | commitdiff
2024-03-06 MorellThomasTest version to switch branches commit | commitdiff
2024-01-31 MorellThomasFix output points column labels commit | commitdiff
2024-01-23 James ProcterMerge branch 'develop' into bug/JAL-4290_headless_align... commit | commitdiff
2024-01-23 Ben SoaresJAL-4367 Limit right and top adjustments commit | commitdiff
2024-01-23 Ben SoaresJAL-4290 Fix image comparison between gui and headless... commit | commitdiff
2024-01-23 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff
2024-01-23 James ProcterJAL-4369 invokeAndWait to avoid hang whilst calling... commit | commitdiff
2024-01-23 James ProcterJAL-4369 uniprotkb - try to avoid another redirect... commit | commitdiff
2024-01-23 James ProcterJAL-4369 use rest.uniprot.org as fetch domain commit | commitdiff
2024-01-23 James ProcterMerge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignor... commit | commitdiff
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
2024-01-10 MorellThomasFixed PaSiMap output columns commit | commitdiff
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
2023-12-19 Ben SoaresJAL-4290 Fixed one test commit | commitdiff
2023-12-18 Ben SoaresJAL-4290 incorrect usage of main() commit | commitdiff
2023-12-15 Ben SoaresJAL-4290 Add method to allow for specific settings... commit | commitdiff
2023-12-15 Ben SoaresJAL-4290 Set structureSelectionManager settings more... commit | commitdiff
2023-12-15 Ben SoaresJAL-4290 Move some annotation visibility settings to... commit | commitdiff
2023-12-14 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff
2023-12-14 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff
2023-12-14 James ProcterMerge branch 'develop' into bug/JAL-2934proportionalScr... bug/JAL-2934proportionalScrolling commit | commitdiff
2023-12-12 James ProcterJAL-4217 don’t try and export an image when Jmol is... commit | commitdiff
2023-12-12 Ben SoaresMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff
2023-12-12 James ProcterMerge branch 'develop' into bug/JAL-4353_cannot_output_... commit | commitdiff
2023-12-12 James ProcterJAL-4217 close internal frame on the swing thread to... commit | commitdiff
2023-12-12 Ben SoaresJAL-4353 helper method and test for primary/secondary... commit | commitdiff
2023-12-12 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... commit | commitdiff
2023-12-06 Ben SoaresJAL-4353 re-used random color code commit | commitdiff
2023-12-06 Ben SoaresJAL-4353 Preserve the user given 'linkedId' with ArgVal... commit | commitdiff
2023-12-06 James ProcterMerge branch 'patch/JAL-840_clustalx_docs_fix' into... commit | commitdiff
2023-12-06 James ProcterMerge branch 'bug/JAL-2934proportionalScrolling' into... commit | commitdiff
2023-12-06 Ben SoaresJAL-4353 Add a 'random' colour to produce a random... commit | commitdiff
2023-12-05 Ben SoaresJAL-4353 Add secondary Types for Args, for STRUCTUREIMA... commit | commitdiff
2023-12-05 MorellThomasCleanup, note: rectangular selection works by holding... commit | commitdiff
2023-12-05 MorellThomasAdapts PCA points to support rectangular selection commit | commitdiff
2023-12-05 MorellThomasEnable rectangular selection for PaSiMap commit | commitdiff
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