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BasicValidator.ValidateIsotopeExistence(IIsotope isotope) when isotope.mass is null #477

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k-ujihara opened this issue Jul 28, 2018 · 2 comments
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BasicValidator.ValidateIsotopeExistence(IIsotope isotope) when isotope.mass is null #477

k-ujihara opened this issue Jul 28, 2018 · 2 comments
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@egonw

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@k-ujihara
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This post is transferred from the post on k-ujihara/NCDK#10.
I don't know what is the proper behavior of org.openscience.cdk.validate.BasicValidator.ValidateIsotopeExistence(IIsotope isotope) method when isotope.getMassNumber() is null or 0.
I guess report.addWarning(isotopeExists) is better than addError.

Do you have any idea?
@johnmay
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johnmay commented Jul 28, 2018

null = natural abundance, a lot of other toolkits will use 0 (I actually prefer that to avoid the NPE). Therefore I believe It should treat null the same as it currently treats 0. Also it could check this before fetching the list of possible of isotopes.

@egonw egonw self-assigned this Oct 11, 2018
@johnmay johnmay mentioned this issue Oct 16, 2018
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johnmay commented Oct 16, 2018

Closed via #489

@johnmay johnmay closed this as completed Oct 16, 2018
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