jalview

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Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3990 gradle spotlessApply

JAL-3990 release notes for 2.11.2.1 patch release

Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop

JAL-3878 Introduce IProgressIndicator#addProgressBar

addProgressBar adds a bar to the panel if it doesn't exist

ensuring that the bar is present after the call contrary

to setProgressBar which toggles the progress bar on and off.

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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/ProgressBar.java
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    /src/jalview/gui/StructureChooser.java
JAL-3878 Fix method name to fireTaskRestarted

JAL-3878 Add char[] constructor to Sequence

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    /src/jalview/datamodel/Sequence.java
JAL-3878 Make BaseJob setters public so they can be accessed by other tasks.

JAL-3878 Add fullName to BaseAction class which combines service and action name

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    /src/jalview/ws2/actions/BaseAction.java
JAL-3878 Move status precedence list to JobStatus class

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    /src/jalview/ws2/api/JobStatus.java
JAL-3878 Add uid to WS Tasks

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    /src/jalview/ws2/actions/api/TaskI.java
JAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some commented out path changes to gradle.properties for future gathering of built files into more sensible places

JAL-3989 fix a build date once in build.gradle, not each time getDate() is called.

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3983 release note for JAL-3985

Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop

Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop

Merge branch 'develop' into improvement/JAL-3978_add_gradle_task_to_make_getdown_archive_dir

JAL-3085 update tests and mock responses, new P0dtd1 testcase

JAL-3985 formatting

JAL-3985 split PDB id queries into multiple queries so server doesn’t 414

Merge branch 'feature/JAL-3982_mouseover_highlighting_viaJAL-3860' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3847 Add some dependencies that gradle 7 mildly complains about

Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop

JAL-3976 fix mock PDBFTS query & responses

JAL-3983 known issue note for JAL-3984

JAL-3851 comment out some debugging

JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984

Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop

JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..

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    /src/jalview/gui/TextColourChooser.java