JAL-4356 release notes for JAL-3978 patch

Merge branch 'bug/JAL-3978_copy_bin_dir_to_getdownArchiveBuild_task' into develop

JAL-3978 Add the bin dir to be copied from website appdir to archive appdir

JAL-4418 bump release to 2.11.4.0

Merge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' into develop

Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation

JAL-4356 bump release date to today, release notes for patching JAL-4407 and known issue report for JAL-3124 and JAL-4415

JAL-4386 Fixed failed test case

Merge branch 'bug/JAL-4416_sview_not_shown_for_local_strucfile' into develop

JAL-4386 Fixed failed test cases

JAL-4416 TODO for fixing JAL-4415 JAL-3124 - need a test for this

JAL-4416 ensure the structure view is shown and any added annotation is displayed

JAL-4416 make sure the structure viewer is actually opened when handling local file view

JAL-4386 Added preferences for secondary structure consensus and it is
set as false by default to skip failed test cases.

Merge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_to_msa' into develop

JAL-4386 - Implementation of retrieving secondary structure
source/provider from matching the annotation description and PDB entry.
Implementation of Show secondary structure menu option. Updated
calculation of secondary structure consensus.

JAL-4217 Upped the main testTask0 timeout to 15 minutes for build server's benefit

JAL-4356 fix release note

JAL-4356 set release date to Weds 15th May and update release notes

JAL-4356 JAL-518 JAL-4413 release notes

Merge branch 'features/JAL-518_justify_seqs_in_region' into develop

JAL-518 better test coverage and support for case preservation

JAL-518 failing test for case preservation on justify

Merge remote-tracking branch 'origin/develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation

Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

JAL-4413 timeouts Merge branch 'improvement/JAL-4217_added_a_timeout_to_tests' into develop

Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

 Conflicts:
src/jalview/api/AlignViewControllerI.java
src/jalview/api/AlignViewportI.java
src/jalview/controller/AlignViewController.java

Merge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' of https://source.jalview.org/git/jalview.git into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation

JAL-4386 - Implementation of substitution matrix and test cases.

JAL-4411 fix typo :(

JAL-4411 store class of provider in PDBEntry

JAL-4217 Sensible timeout for testTask0

JAL-4217 Added a timeout for testTasks. If timeout is exceeded then test execution should be interrupted.

Merge remote-tracking branch 'origin/bug/JAL-4407_no_sec_str_from_draganddrop_to_msa' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation

JAL-4407 don't transfer 'local' settings - leave as default 3d-structure annotation processing

JAL-4407 failing test checking for secondary structure is added when calling the associate pdb file routine

JAL-4392 Merging consensus secondary structure

JAL-4386 Comparing secondary structure similarity directly with a basic
substitution matrix. Some code refactoring.

JAL-4386 Drop down for secondary structure sources in calculate window

JAL-4386 PCA/Tree Calculation for Secondary Structures: Changes related to dropdown in Calculate window.

JAL-4386 Calculate tree using secondary structure annotation - Documentation, Changes to include Secondary structure from JPred.

JAL-4386_Added changes in similarity score calculation for different cases of sequences with undefined secondary structure

JAL-4386 Corrected failed test case.

JAL-4386 Added further checks for sequences that have no secondary structure.

JAL-4386 Calculate tree using secondary structure annotation

JAL-4356 release notes

JAL-4356 update release notes for 2.11.3.3

Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' into develop

Merge branch 'develop' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor

JAL-4367 Limit right and top adjustments

JAL-4290 Fix image comparison between gui and headless output.  Images are now the same

JAL-4290 fixed tests

Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor

Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

JAL-4353 wait for files to be written fully before comparing size with older file

JAL-4353 singleThread all tests

JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is in progress

JAL-4369 uniprotkb - try to avoid another redirect response

JAL-4369 use rest.uniprot.org as fetch domain
t pu# Please enter the commit message for your changes. Lines starting

Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch' into develop

Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into develop

JAL-4373 Setting the jvmmempc and jvmmemmax strings from the Arg.getName() for consistency. Updated some comments.

JAL-4373 Fix Main-Class and other attribute settings in the shadowJar manifest. It requires a 'dummy' Jar task with the correct settings.

JAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file

JAL-4290 Fixed one test

JAL-4290 not quite working tests

JAL-4290 incorrect usage of main()

Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' of https://source.jalview.org/git/jalview into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor

JAL-4290 Add method to allow for specific settings. Revert setting show annotations.

JAL-4290 Set structureSelectionManager settings more generically and when no desktop exists

Merge branch 'bug/JAL-4290_headless_alignment_figure_with_sse' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor

JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations.Worker to run jalview as a separate process to verify headless alignment image export should be same size as when launched with —gui

JAL-4290 Move some annotation visibility settings to after opening a structure. Set synchronously if in headless mode.

JAL-4356 update release notes

Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop

Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

JAL-4353 wait for files to be written fully before comparing size with older file

JAL-4217 singleThread all tests

Merge branch 'bug/JAL-2934proportionalScrolling' into develop

Merge branch 'develop' into bug/JAL-2934proportionalScrolling

JAL-4353 bigger tighter test

JAL-4217 don’t try and export an image when Jmol is also trying to repaint

Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' of https://source.jalview.org/git/jalview into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

JAL-4217 close internal frame on the swing thread to avoid deadlock

JAL-4353 helper method and test for primary/secondary and auxiliary arguments with --structure pdb0 --structureimage png0a --bgcolour col0a --structureimagepng0b --bgcolour col0b --structure pdb1 --...

Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop

JAL-4353 failing test

JAL-4353 fix assert that successive test output files get bigger in structureImageOutputTest and argFilesGlobAndSubstitutionsTest

JAL-4192 more specific info about versions needed

JAL-4353 re-used random color code

JAL-4353 Preserve the user given 'linkedId' with ArgValue, to help with deciding if user deliberately set a wildcard linkedId (or --all), to inform value of sub-args.

JAL-4356 bump RELEASE

JAL-4356 new release notes and whats new for 2.11.3.3 and JAL-840 release notes

Merge branch 'patch/JAL-840_clustalx_docs_fix' into develop

Merge branch 'bug/JAL-2934proportionalScrolling' into develop

JAL-4353 Add a 'random' colour to produce a random colour.

JAL-4353 Add secondary Types for Args, for STRUCTUREIMAGE Type and restrict structureimages between structures on the same open alignment

JAL-4243 Updated bio.tools record and JSON (version number)