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JAL-4020 class reformatting

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
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JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places starting with default install dir. Added a new version (1.3) to ChimeraX

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
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JAL-3438 spotless for 2.11.2.0

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    ./edu/ucsf/rbvi/strucviz2/ChimUtils.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraChain.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
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    ./vamsas/JpredSoapBindingStub.java
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    ./vamsas/MuscleWSSoapBindingStub.java
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    ./vamsas/RegistryServiceSoapBindingStub.java
  1. … 647 more files in changeset.
Looks good. I've bumped the version to 1.8.3-1.2.12 and recompiled jars.

Looks good. I've bumped the version to 1.8.3-1.2.12 and recompiled jars.

JAL-3438 - all src and test run through spotless..

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    ./edu/ucsf/rbvi/strucviz2/ChimUtils.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraChain.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
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    ./edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
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    ./vamsas/JpredSoapBindingStub.java
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    ./vamsas/MuscleWSSoapBindingStub.java
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    ./vamsas/RegistryServiceSoapBindingStub.java
  1. … 654 more files in changeset.
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src

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    ./edu/ucsf/rbvi/strucviz2/ChimUtils.java
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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
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JAL-2422 Also look in ~/Applications for ChimeraX on macOS

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon). Better UTF-8 Name call.

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon)

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.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

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
JAL-2422 this is for testing only. do not merge.

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Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
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JAL-3390: Option to hide unmapped residues in structure viewer
JAL-3390: Option to hide unmapped residues in structure viewer
JAL-3674 more finessed asynchronous structure commands
JAL-3674 more finessed asynchronous structure commands
JAL-3674 more finessed asynchronous structure commands

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

src/jalview/ext/jmol/JmolCommands.java

src/jalview/ext/pymol/PymolCommands.java

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

src/jalview/ext/rbvi/chimera/ChimeraXCommands.java

src/jalview/gui/JalviewChimeraBindingModel.java

src/jalview/structure/StructureCommandsBase.java

src/jalview/structure/StructureCommandsI.java

src/jalview/structures/models/AAStructureBindingModel.java

test/jalview/ext/pymol/PymolCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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JAL-3672 debug=false means no debug output

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
JAL-3518 separation of ChimeraXManager, pull up of closeViewer etc

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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JAL-3664 support for user.home, user.dir, user

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
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I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

JAL-2422 highlight ChimeraX selection (ChimeraX-1.0-rc-2020.05.21 +)

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
JAL-2422 ChimeraX paths (versions up to 1.0) added for Windows

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
JAL-1333 additional Chimera versions for Windows installation paths

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    ./edu/ucsf/rbvi/strucviz2/StructureManager.java
JAL-3518 more extraction of ChimeraX commands as overrides

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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JAL-2422 remove temporary debug code

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
JAL-2422 fixed stopProgressBar (broken in pull up refactoring)

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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JAL-2422 temporary hacks removed; use hex colours for Chimera[X]

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    ./edu/ucsf/rbvi/strucviz2/ChimeraManager.java
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