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Attempt to fix issue #659 - Error parsing FASTA in multiple passes - #687
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The tests are not working because of travis problems that are now fixed in master. Could you merge |
josemduarte
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Jul 9, 2017
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This looks good to me, thanks a lot @arojnuckarin !
It would be helpful if people that are more familiar with this could comment, @aalhossary, @psoares others?
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Thanks for the PR, @arojnuckarin! The tests are particularly good to see. |
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Take out what look to be remnant of fixes Endless loop when using FastaReader #282 (reverted by reverting #282 to never return null, managed blank lines anywhere #292) in org.biojava.nbio.core.sequence.io.FastaReader.java
Add a bunch of JUnit test cases to make sure stuffs still work as best I understand them
Some comments on issue Endless loop when using FastaReader #282 and reverting #282 to never return null, managed blank lines anywhere #292 by original author @aalhossary seem to say that process(int) should never return null, but a number of existing test cases (e.g. org.biojava.nbio.core.sequence.io.FastReaderTest.java) still rely on this method returning null to stop processing. This pull request keeps the same behavior.