jalview

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JAL-3393 updated Jalview Test DMG background image

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    /doc/README-DMG_background_image_creation.md
JAL-3878 Create web service menu manager.

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    /src/jalview/ws2/gui/WebServicesMenuManager.java
JAL-3878 Add hasPresets and hasParameters utility methods to ParamDatastoreI

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    /src/jalview/ws/params/ParamDatastoreI.java
JAL-3393 improved flexibility of script and updated doc

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    /utils/install4j/mk_ds_store.sh
JAL-3973 This fixes the gradle build when not in a git repo. (Part 1 of the issue)

JAL-3393 Made an all-in-one script to create the DS_Store from scratch (has to be run on a mac desktop, it incorporates the AppleScript Finder adjustments). Updated docs. Updated the release DMG background image with the script. Changed install4j9 to put the background image as .background/background.png.

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    /utils/install4j/mk_ds_store.sh
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    /utils/install4j/set_relative_dmg_background_image.applescript
Merge branch 'master' into releases/Release_2_11_2_Branch

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    /j11digestonly/intervalstore-v1.0.jar
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    /j8digestonly/intervalstore-v1.0.jar
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    /test/jalview/gui/SplitFrameTest.java
Merge branch 'develop' into improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store

JAL-3393 Added version number to DMG Volume name. New jalview_dmg_DS_Store and documentation about it

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    /utils/install4j/set_relative_dmg_background_image.applescript
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 bump release date to 10th March - after UoD network maintenance

JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

JAL-3878 Add WebServiceProviderI - a view of services.

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    /src/jalview/ws2/client/api/WebServiceProviderI.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert

JAL-3878 Improve performance of gap sequence construction.

JAL-3972 replace the VAqua 5 patched library with latest VAqua 10

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 JAL-3841 fix README typo

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 more docs tweaking and release notes

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    /help/help/html/features/preferences.html
Merge branch 'spike/try_spotless_JAL-3438' into develop

JAL-3746 apply copyright to tests

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    /test/jalview/bin/HiDPISettingTest1.java
  1. … 59 more files in changeset.
JAL-3746 apply copyright to source

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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
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    /src/jalview/fts/api/StructureFTSRestClientI.java
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    /src/jalview/fts/service/threedbeacons/.gitignore
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    /src/jalview/gui/ChimeraXViewFrame.java
  1. … 31 more files in changeset.
JAL-3438 spotless for 2.11.2.0

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    /src/com/stevesoft/pat/ChangeRule.java
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    /src/com/stevesoft/pat/Ctrl.java
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    /src/com/stevesoft/pat/FastBracket.java
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    /src/com/stevesoft/pat/Regex.java
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    /src/com/stevesoft/pat/RegexWriter.java
  1. … 647 more files in changeset.
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes

JAL-3108 updated Ensembl client and model species names

JAL-3746 new release date for 2.11.2

JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes