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Fix #917: Symmetry doesn't display with non-US locales #918

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merged 4 commits into from
Mar 2, 2021

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@sbliven sbliven commented Mar 1, 2021

The core of this is the locale fix, which is necessary for CESymm/QuatSymm to function properly on non-US systems.

I've also included some commits for general cleanup and tests. If any of these are controversial I can revert them or move them to separate PRs.

- Always use the US locale when printing jmol scripts
- Update Jmol to 14.31.10 while we're at it.
This runs QuatSymmetryDetector. It would be better to mock the results,
but this is nontrivial with the current implementation.
These seem to be regularly deleted by IDEs running on different JDKs.
If you see a warning, please find the correct syntax to silence it 
rather than deleting the cast.
@sbliven sbliven requested a review from lafita March 1, 2021 16:56
@sbliven sbliven added the bug Bugs and bugfixes label Mar 1, 2021
@sbliven sbliven added this to the BioJava 6.0.0 milestone Mar 1, 2021
@sbliven sbliven linked an issue Mar 1, 2021 that may be closed by this pull request
@sbliven sbliven self-assigned this Mar 1, 2021
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LGTM, thanks!

@sbliven sbliven merged commit c600773 into biojava:master Mar 2, 2021
sbliven added a commit to sbliven/biojava-sbliven that referenced this pull request Jul 31, 2021
biojava#918 showed that locales which use commas for floating-point numbers
can cause problems with output formats. This commit fixes a number
of other cases.

- Force Locale.US when outputting floats to files/streams
- Usually don't force Locale.US when outputting floats to standard out &
  logging (would lead to more consistent logs but breaks localization)
- Replace some `println(String.format(` calls with Java 5 `printf`
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Symmetry doesn't display with non-US locales
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