JAL-4392 Bug fixing and code refactoring.

JAL-4386 Fixed some identified bugs in recent changes

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

JAL-4386 Added secondary structure providers check boxes in show
secondary structure menu. Implemented displaying of secondary structure
and consensus based on user selection. Added secondary structure
providers option in calculate window. Added provider label in pca panel
and tree panel for secondary structure similarity.

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)

JAL-4351 update release notes for JAL-4342