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Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure...
[jalview.git] / src /
38 hours ago Jim ProcterMerge branch 'develop' into feature/JAL-4386_calculate_... feature/JAL-4386_calculate_tree_using_secondary_structure_annotation tree | commitdiff
2 days ago Jim ProcterJAL-4416 TODO for fixing JAL-4415 JAL-3124 - need a... bug/JAL-4416_sview_not_shown_for_local_strucfile tree | commitdiff
2 days ago Jim ProcterJAL-4416 ensure the structure view is shown and any... tree | commitdiff
2 days ago Jim ProcterJAL-4416 make sure the structure viewer is actually... tree | commitdiff
2 days ago Renia CorreyaJAL-4386 Added preferences for secondary structure... tree | commitdiff
2 days ago Jim ProcterMerge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_... tree | commitdiff
2 days ago Renia CorreyaJAL-4386 - Implementation of retrieving secondary structure tree | commitdiff
4 days ago Jim ProcterJAL-518 better test coverage and support for case prese... features/JAL-518_justify_seqs_in_region tree | commitdiff
4 days ago Jim ProcterMerge branch 'develop' into features/JAL-518_justify_se... tree | commitdiff
4 days ago Renia CorreyaMerge branch 'feature/JAL-4386_calculate_tree_using_sec... tree | commitdiff
4 days ago Renia CorreyaJAL-4386 - Implementation of substitution matrix and... tree | commitdiff
7 days ago Jim ProcterJAL-4411 fix typo :( tree | commitdiff
7 days ago 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
2024-04-16 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... 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
2024-01-23 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
2024-01-05 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
2023-11-30 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
2023-11-13 James ProcterJAL-4336 set preferred dimensions for JTextBox workarou... tree | commitdiff
2023-11-13 James ProcterJAL-4090 fix JAL-4236 - just put the name of the class... tree | commitdiff
2023-11-13 James ProcterJAL-4331 construct and pass on overview title before... tree | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-11-02 James ProcterJAL-4169 fix up urls to faq and documentation tree | commitdiff
2023-11-02 James ProcterMerge branch 'develop' into patch/JAL-3921_jmol_session... tree | commitdiff
2023-11-02 James ProcterJAL-4217 wrap progress bar creation in an invokeLater... tree | commitdiff
2023-11-02 James ProcterJAL-1551 formatting tree | commitdiff
2023-11-02 James ProcterMerge branch 'develop' into patch/JAL-3088_finalbraceno... tree | commitdiff
2023-11-02 James ProcterJAL-4289 JAL-4253 lower end of group boundary vertical... tree | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4281_idwidthandannotHeight_in_p... tree | commitdiff
2023-11-01 James ProcterMerge branch 'feature/JAL-4315_fc_draganddrop' into... tree | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4317_enablefeaturewhenadjusting... tree | commitdiff
2023-11-01 James ProcterMerge branch 'develop' into patch/JAL-4281_idwidthandan... tree | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4260_fix_up_select_via_ruler_in... tree | commitdiff
2023-11-01 James ProcterJAL-4260 encapsulate logic for resolving nearest column... patch/JAL-4260_fix_up_select_via_ruler_in_wrapped tree | commitdiff
2023-11-01 James ProcterJAL-4260 reinstate annotation auto-id-width for wrapped... tree | commitdiff
2023-10-31 James ProcterJAL-4260 fix up click/drags on ruler area in wrapped... tree | commitdiff
2023-10-31 James ProcterJAL-4260 right align the annotation labels regardless... tree | commitdiff
2023-10-31 James ProcterJAL-244 noticed NPE exception was possible when visibil... tree | commitdiff
2023-10-31 James ProcterJAL-244 knock on - make sure alignPanel is laid out... tree | commitdiff
2023-10-30 James ProcterJAL-4317 enable display of feature when showing its... patch/JAL-4317_enablefeaturewhenadjustingstyle tree | commitdiff
2023-10-30 James ProcterHandle feature settings files loaded via drag and drop... feature/JAL-4315_fc_draganddrop tree | commitdiff
2023-10-30 James ProcterJAL-4315 allow feature settings to be loaded from a... tree | commitdiff
2023-10-30 James ProcterJAL-4315 identify feature settings file from its xml... tree | commitdiff
2023-10-26 James ProcterMerge branch 'bug/JAL-4313_cme_in_tests' into patch... tree | commitdiff
2023-10-25 Ben SoaresMerge branch 'develop' into bug/JAL-4289_group_boundary... bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpaint_or_paint tree | commitdiff
2023-10-25 James ProcterJAL-4312 defend against ConcurrentModificationException bug/JAL-4313_cme_in_tests tree | commitdiff
2023-10-25 James ProcterJAL-4312 call AlignFrame.setAnnotationsVisibility on... tree | commitdiff
2023-10-23 James ProcterJAL-4311 fix ranking so models with like scores are... improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews tree | commitdiff
2023-10-23 James ProcterJAL-4311 failing test case for 3d-beacons epas1_human... tree | commitdiff
2023-10-23 James ProcterJAL-4310 let the user know when model pages are not... tree | commitdiff
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