jalview

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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 feature/JAL-2422ChimeraX

JAL-2422 Also look in ~/Applications for ChimeraX on macOS

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

JAL-3829 avoid sending rubbish to PDBe search api

JAL-3829 some providers don’t provide model quality, some experimental methods don’t provide a resolution - try to leave these in their natural order

JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks

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    /src/jalview/fts/core/FTSRestClient.java
JAL-2422 More helpful highlighting/user guidance of missing structure viewer path

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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon). Better UTF-8 Name call.

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon)

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

Merge branch 'releases/Release_2_11_2_Branch' into develop

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

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into releases/Release_2_11_2_Branch

JAL-3829 ensure unmock the FTS PDB and TDB clients after mocking for a test

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    /test/jalview/gui/StructureChooserTest.java
JAL-2422 Added linux rpm and deb install locations. Changed macOS to also look for version numbers in Chimera/X (e.g. '/Applications/ChimeraX-1.2.5.app') as this is default macOS installation. Changed macOS preferences to check endswith '.app' and look for '....app/Contents/MacOS/ChimeraX' so user can select the .app folder

JAL-3829 minimal test of additional TDB filters - not at all robust

JAL-3829 select single best TDB structure and select structures from particular provider (this code is horrific !)

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/FilterOption.java
JAL-3829 JalviewJS workarounds/patches

JAL-3829 upgrade Jmol to 14.31.53, SwingJS-JSMol to 14.31.54 and SwingJS to 3.3.1

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    /j11lib/Jmol-14.31.53.jar
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    /j8lib/Jmol-14.31.53.jar
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    /swingjs/ver/3.3.1-j11/DEV_NOTES.txt
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    /swingjs/ver/3.3.1-j11/SwingJS-site.zip
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    /swingjs/ver/3.3.1-j11/_j2sclasslist.txt
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    /swingjs/ver/3.3.1-j11/differences.txt
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    /swingjs/ver/3.3.1-j11/net.sf.j2s.core-j11.jar
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