Default parsing params for AtomCache

I recently got tripped up by the fact that AtomCache's constructor disables alignSeqRes and parseSecStruc specifically.

// we don't need this here
params.setAlignSeqRes(false);
// no secstruc either
params.setParseSecStruc(false);

The current default for FileParsingParams.alignSeqRes is true. I would have expected cache.setFileParsingParams(new FileParsingParams()) to reset a cache to its default state, but this is not true.

Would anyone object if I deleted the above two lines, making alignSeqRes=true the default?

That looks like a bug indeed. Go ahead, it'd be good to have this for 4.2.1

Fix biojava#455. Use parsing params for AtomCache

Could you push the fix to master and bugfixes-4.2?

I think we should be ready for a 4.2.1 release after that. Or are there any other patches coming?

Oh sorry, I now saw the pull request. Let's merge that one then...

Merge pull request #466 from sbliven/fix-455

Fix #455. Use parsing params for AtomCache

I've cherry-picked it to bugfixes-4.2 too. I'll try to produce the 4.2.1 release later.

@josemduarte

Thanks, @josemduarte. I meant to make the pull request directly into bugfixes-4.2 but accidentally used master instead.

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Default parsing params for AtomCache #455

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Default parsing params for AtomCache #455

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josemduarte commented on Apr 21, 2016

josemduarte commented on Apr 27, 2016

josemduarte commented on Apr 27, 2016

josemduarte commented on Apr 27, 2016

sbliven commented on Apr 28, 2016

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