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jim procter <j.procter@dundee.ac.uk> in jalview

JAL-3871 replaced Jmol with zip -F version fo Jmol and added excludeDuplicates flags to build.gradle

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Merge branch 'develop' into doc/JAL-3746_Release_2_11_2

Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg' into develop

JAL-3746 fix bad merge from 2.11.1.4/5 branch cherrypick

JAL-3842 fix automatic what's new link for custom version builds

JAL-3842 2.11.1.5 what’s new, release notes, and version bump Conflicts: RELEASE

JAL-3816 bump version number and cut release notes

Conflicts:

RELEASE

doc/building.html

JAL-3766 cut new patch release Conflicts: RELEASE

JAL-3758 2.11.1.2 patch release notes and version bump Conflicts: RELEASE

JAL-3741 http to https (and jar to jvp for exampleFile defaults!) Conflicts: src/jalview/bin/Jalview.java src/jalview/gui/Desktop.java

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    /help/help/html/features/commandline.html
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    /help/help/html/features/search.html
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    /help/help/html/logging.html
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    /help/help/html/webServices/newsreader.html
  1. … 6 more files in changeset.
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

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    /help/help/html/features/clarguments.html
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    /help/help/html/features/commandline.html
JAL-3675 version update and documentation for JAL-3493 JAL-3680 JAL-3638 Conflicts: RELEASE

JAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in cursor mode. help/help/html/keys.html

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3829 parallel not welcome here

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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 test flakiness and human flakiness

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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 more info on test fail - seems to be flaky

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    /test/jalview/gui/StructureChooserTest.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3551 - doc tweak

JAL-3855 JAL-3829 better checks on PDB or mmCIF file based on URL path (though should really determine when processing via jmolData now we have mechanism) - ChimeraX in particular cares about file endings

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    /src/jalview/gui/StructureViewerBase.java
JAL-3829 JAL-3855 moved routing for retrieving structures prior to opening a Jmol view to AppJmolBinding - this could be refactored further

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    /src/jalview/gui/AppJmolBinding.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-3829 JAL-3855 ignore case when detecting alphafold ID

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    /src/jalview/ws/dbsources/EBIAlfaFold.java
JAL-3855 detect an alphafold model and import its temperature factor as reliability

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    /src/jalview/ext/jmol/JmolParser.java
JAL-3829 move mock query and responses to files

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    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
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    /test/jalview/gui/StructureChooserTest.java
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Merge branch 'feature/JAL-2422ChimeraX' into develop

JAL-3829 3d-beacons doesn’t work as a sequence source just now