<div dir="ltr">Hi John,<div><br></div><div>It would help if you would explain a bit more detailed, what you are tyring to do. Have you seen the new BioJava tutorial on github? For example there is a page that explains how to translate various sequence types</div><div><br></div><div><a href="https://github.com/biojava/biojava-tutorial/blob/master/core/translating.md">https://github.com/biojava/biojava-tutorial/blob/master/core/translating.md</a><br></div><div><br></div><div>Does that help? If not, perhaps provide some more info, what you want to do?</div><div><br></div><div>Thanks,</div><div><br></div><div>Andreas</div><div><br></div><div><br></div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Aug 7, 2015 at 6:29 AM, John Stalker <span dir="ltr"><<a href="mailto:jstalker@coreinformatics.com" target="_blank">jstalker@coreinformatics.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hi there,</div>
<div> I’m working on some code multi-frame translation code and I think I’m missing a fundamental property here.</div>
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<div> I want to be using DNASequence, RNASequence, and ProteinSequence classes, but operations I’m using end up returning Sequence<C> or SequenceView<C>. What is the conversion / wrapper path from the latter to the former?</div>
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<div> So for example, if I get a subSequence from DNASequence, I have a SequenceView<NucleotideCompound>. How do I wrap that in a new DNASequence? Similarly, when I have instances of Sequence<AminoAcidCompound> (the result of TranscriptionEngine.multipleFrameTranslation),
how do I wrap that with ProteinSequence?</div>
<div> Looking a the constructors for the main *Sequence classes, there’s nothing (save String) that stands out. The implementations of SequenceReader (for DNASequence) and ProxySequenceReader (for RNASequence and ProteinSequence…why are these not all the
same interface is another question) don’t stand out as being appropriate.</div>
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<div> I’m might just be dense here, but any help would be appreciated! Thanks!</div><span class="HOEnZb"><font color="#888888">
<div>John</div>
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