biojava/biojava — pull request #141 by sroughley (2014-08-04 15:51:33+00:00)
Title: Wait for start

Added an additional 'waitForStartCodon' option to the RNAToAminoAcidTranslator class. This is similar to the previously added stopAtStopCodons option, allowing the user to optionally specify that translation will not start until a valid start codon in the current codon table and reading frame is encountered. The start codon will be translated as the first residue in the resulting ProteinSequence object.

The TranscriptionEngine#Builder class has been updated to allow setting the new option.

A test case has been added to TranslationTest.

Default is set to 'false', in order to maintain backwards compatability with existing code.

If accepted, would suggest removing the intermediate constructor from the RNAToAminoAcidTranslator class in the released version, as would not be needed.