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JAL-4366 compute coverage on each side of the pairwise alignment
[jalview.git] / src /
2024-05-24 James ProcterJAL-4366 compute coverage on each side of the pairwise... tree | commitdiff
2024-05-24 Jim ProcterMerge branch 'jims/feature/JAL-4159_pasimap' into featu... tree | commitdiff
2024-05-23 Jim ProcterJAL-4159 fix sense of console/alignment output suppress... tree | commitdiff
2024-05-23 Jim ProcterJAL-4159 disable the score model combo box when pasimap... tree | commitdiff
2024-05-23 MorellThomasFix PaSiMap taking scoreModels input and allow AlignSeq... tree | commitdiff
2024-05-23 MorellThomasFix PaSiMap not having the eigenvalues saved tree | commitdiff
2024-05-22 MorellThomasSave PaSiMap with Jalview Session tree | commitdiff
2024-05-22 MorellThomasRectanuglar selection changed to Mouse Button 3 drag tree | commitdiff
2024-05-21 Jim ProcterJAL-4259 set title using original alignment window... spike/JAL-4159_pasimap_2114_series tree | commitdiff
2024-05-21 Jim ProcterJAL-4159 implement bounds for PASIMAP calculation ... tree | commitdiff
2024-05-21 Jim ProcterJAL-4159 connectivity should be computed for the sequen... tree | commitdiff
2024-05-21 Jim ProcterJAL-4159 PASiMap currently doesn't support different... tree | commitdiff
2024-05-21 Jim ProcterJAL-4159 sometimes the progress bar may not be availabl... tree | commitdiff
2024-05-21 Jim ProcterMerge branch 'feature/JAL-4159_pasimap' into spike... tree | commitdiff
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4159_pasimap tree | commitdiff
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4386_calculate_... tree | 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 tree | commitdiff
2024-05-15 Jim ProcterJAL-4416 ensure the structure view is shown and any... tree | commitdiff
2024-05-15 Jim ProcterJAL-4416 make sure the structure viewer is actually... tree | commitdiff
2024-05-15 Renia CorreyaJAL-4386 Added preferences for secondary structure... tree | commitdiff
2024-05-15 Jim ProcterMerge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_... tree | commitdiff
2024-05-15 Renia CorreyaJAL-4386 - Implementation of retrieving secondary structure tree | commitdiff
2024-05-13 Jim ProcterJAL-518 better test coverage and support for case prese... features/JAL-518_justify_seqs_in_region tree | commitdiff
2024-05-13 Jim ProcterMerge branch 'develop' into features/JAL-518_justify_se... tree | commitdiff
2024-05-13 Renia CorreyaMerge branch 'feature/JAL-4386_calculate_tree_using_sec... tree | commitdiff
2024-05-13 Renia CorreyaJAL-4386 - Implementation of substitution matrix and... tree | commitdiff
2024-05-10 Jim ProcterJAL-4411 fix typo :( tree | commitdiff
2024-05-10 Jim ProcterJAL-4411 store class of provider in PDBEntry tree | commitdiff
2024-05-01 Renia CorreyaMerge remote-tracking branch 'origin/bug/JAL-4407_no_se... tree | commitdiff
2024-05-01 Jim ProcterJAL-4407 don't transfer 'local' settings - leave as... bug/JAL-4407_no_sec_str_from_draganddrop_to_msa tree | commitdiff
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure tree | commitdiff
2024-04-30 Renia CorreyaJAL-4386 Comparing secondary structure similarity direc... tree | commitdiff
2024-04-26 Renia CorreyaJAL-4386 Drop down for secondary structure sources... tree | commitdiff
2024-04-24 Renia CorreyaJAL-4386 PCA/Tree Calculation for Secondary Structures... tree | commitdiff
2024-04-18 MorellThomasMerge branch 'test/progressBar' into feature/JAL-4159_p... tree | commitdiff
2024-04-18 MorellThomasImplemented ProgressBar for PaSiMap tree | commitdiff
2024-04-16 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... tree | commitdiff
2024-04-12 MorellThomasinlcude progress tree | commitdiff
2024-04-09 James ProcterJAL-4390 don't output alignment to text panel and stdou... tree | commitdiff
2024-03-15 MorellThomasFix output of all dimensions tree | commitdiff
2024-03-15 MorellThomasAlogirthm working, but still giving slightly off results tree | commitdiff
2024-03-13 Renia CorreyaJAL-4386_Added changes in similarity score calculation... tree | commitdiff
2024-03-08 Renia CorreyaJAL-4386 Added further checks for sequences that have... tree | commitdiff
2024-03-08 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... tree | commitdiff
2024-03-07 MorellThomasInlcude 8 dimensions tree | commitdiff
2024-03-06 MorellThomasFix PaSiMap on selected sequences tree | commitdiff
2024-03-06 MorellThomasTest version to switch branches tree | commitdiff
2024-01-31 MorellThomasFix output points column labels tree | commitdiff
2024-01-23 James ProcterMerge branch 'develop' into bug/JAL-4290_headless_align... tree | commitdiff
2024-01-23 Ben SoaresJAL-4367 Limit right and top adjustments tree | commitdiff
2024-01-23 Ben SoaresJAL-4290 Fix image comparison between gui and headless... tree | commitdiff
2024-01-23 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... tree | commitdiff
2024-01-23 James ProcterJAL-4369 invokeAndWait to avoid hang whilst calling... tree | commitdiff
2024-01-23 James ProcterJAL-4369 uniprotkb - try to avoid another redirect... tree | commitdiff
2024-01-23 James ProcterJAL-4369 use rest.uniprot.org as fetch domain tree | commitdiff
2024-01-23 James ProcterMerge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignor... tree | 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 tree | commitdiff
2024-01-10 MorellThomasFixed PaSiMap output columns tree | 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 tree | commitdiff
2023-12-19 Ben SoaresJAL-4290 Fixed one test tree | commitdiff
2023-12-18 Ben SoaresJAL-4290 incorrect usage of main() tree | commitdiff
2023-12-15 Ben SoaresJAL-4290 Add method to allow for specific settings... tree | commitdiff
2023-12-15 Ben SoaresJAL-4290 Set structureSelectionManager settings more... tree | commitdiff
2023-12-15 Ben SoaresJAL-4290 Move some annotation visibility settings to... tree | commitdiff
2023-12-14 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... tree | commitdiff
2023-12-14 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... tree | commitdiff
2023-12-14 James ProcterMerge branch 'develop' into bug/JAL-2934proportionalScr... bug/JAL-2934proportionalScrolling tree | commitdiff
2023-12-12 James ProcterJAL-4217 don’t try and export an image when Jmol is... tree | commitdiff
2023-12-12 Ben SoaresMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... tree | commitdiff
2023-12-12 James ProcterMerge branch 'develop' into bug/JAL-4353_cannot_output_... tree | commitdiff
2023-12-12 James ProcterJAL-4217 close internal frame on the swing thread to... tree | commitdiff
2023-12-12 Ben SoaresJAL-4353 helper method and test for primary/secondary... tree | commitdiff
2023-12-12 James ProcterMerge branch 'bug/JAL-4353_cannot_output_multiple_diffe... tree | commitdiff
2023-12-06 Ben SoaresJAL-4353 re-used random color code tree | commitdiff
2023-12-06 Ben SoaresJAL-4353 Preserve the user given 'linkedId' with ArgVal... tree | commitdiff
2023-12-06 James ProcterMerge branch 'patch/JAL-840_clustalx_docs_fix' into... tree | commitdiff
2023-12-06 James ProcterMerge branch 'bug/JAL-2934proportionalScrolling' into... tree | commitdiff
2023-12-06 Ben SoaresJAL-4353 Add a 'random' colour to produce a random... tree | commitdiff
2023-12-05 Ben SoaresJAL-4353 Add secondary Types for Args, for STRUCTUREIMA... tree | commitdiff
2023-12-05 MorellThomasCleanup, note: rectangular selection works by holding... tree | commitdiff
2023-12-05 MorellThomasAdapts PCA points to support rectangular selection tree | commitdiff
2023-12-05 MorellThomasEnable rectangular selection for PaSiMap tree | commitdiff
2023-12-04 MorellThomasNew independent jbgui Panel for PaSiMap. Revert the... tree | commitdiff
2023-12-04 MorellThomasNew GPCAPanel button : output pairwise alignments ... tree | commitdiff
2023-12-01 MorellThomasApplying adjustablenw_params.patch (JAL-4159) tree | commitdiff
2023-11-30 James ProcterJAL-4342 test and patch checking annotation csv export... patch/JAL-4342_emptyannotationsexport tree | commitdiff
2023-11-30 James ProcterPatch fixes JAL-4165 - added to release notes JAL-4351 tree | commitdiff
2023-11-30 Ben SoaresJAL-4344 careful application of -Djava.awt.headless... tree | commitdiff
2023-11-22 James ProcterMerge branch 'patch/JAL-4345_pae_epas1_doubleclick... tree | commitdiff
2023-11-21 James ProcterJAL-4345 patch and release notes patch/JAL-4345_pae_epas1_doubleclick tree | commitdiff
2023-11-20 Ben SoaresJAL-4348 Add newer versions of Chimera and ChimeraX... tree | commitdiff
2023-11-20 James ProcterJAL-4343 patch for JAL-4347 uniprot non-pos feature... tree | commitdiff
2023-11-15 James ProcterMerge branch 'bug/JAL-4334_unknownstartenduniprotfeatur... tree | commitdiff
2023-11-15 James ProcterMerge branch 'patch/JAL-4222_100s_timeout_on_imagexport... tree | commitdiff
2023-11-15 James ProcterJAL-4273 actually pass startSeq etc on to rendering... tree | commitdiff
2023-11-15 James ProcterJAL-4222 bail if we wait too long for Jmol to save... patch/JAL-4222_100s_timeout_on_imagexport tree | commitdiff
2023-11-15 James ProcterJAL-4090 blocker patch JAL-3772 tidy up groovy console... tree | commitdiff
2023-11-15 James ProcterJAL-4090 JAL-4334 position status when start, end or... bug/JAL-4334_unknownstartenduniprotfeatures tree | commitdiff
2023-11-13 James ProcterJAL-4090 JAL-1551 source license tree | commitdiff
2023-11-13 James ProcterJAL-4236 don’t look for headers in JalviewJS tree | commitdiff
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