Did you see the getSequenceAsString method? ProteinSequence ps = new ProteinSequence(results.get(frame).getSequenceAsString());
The difference is that you go from a view of a sequence, (which, if I remember correctly, does not take much memory), to an newly allocated sequence instance. Andreas On Tue, Aug 11, 2015 at 4:43 AM, John Stalker <[email protected]> wrote: > Hi Andreas, > Thanks for the reply! In fact, the example page you provided is exactly > what I was attempting to do, but I moved away from it. > This example is so very nearly complete, but it’s missing one line in > the for loop which prints the 6 frame results — I want to end up with > ProteinSequence objects, wrapped from the individual Sequence<AminoAcid> > objects. I can take the naïve approach and create ProteinSequence objects > from the String form of the Sequence object, but that doesn’t scale well. > > In my code, I abandoned the .multipleFrameTranslation call and simply > did this: > for (Frame frame : Frame.getAllFrames()) { > ProteinSequence seq = dna.getRNASequence(frame).getProteinSequence(te); > //etc > } > > Ultimately, it’s not obvious what the is ‘right’ way to go from > Sequence<C> to the proper wrapper class (i.e. Sequence<AminoAcidCompound> > -> ProteinSequence) > Thanks! > John > > From: <[email protected]> on behalf of Andreas Prlic > Date: Tuesday, August 11, 2015 at 12:58 AM > To: John Stalker > Cc: "[email protected]" > Subject: Re: [Biojava-l] Constructing (wrapping) DNASequence from a > SequenceView<NucleotideCompound> > > Hi John, > > 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 > > https://github.com/biojava/biojava-tutorial/blob/master/core/translating.md > > Does that help? If not, perhaps provide some more info, what you want to > do? > > Thanks, > > Andreas > > > > > > On Fri, Aug 7, 2015 at 6:29 AM, John Stalker <[email protected] > > wrote: > >> Hi there, >> I’m working on some code multi-frame translation code and I think I’m >> missing a fundamental property here. >> >> 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? >> >> 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? >> 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. >> >> I’m might just be dense here, but any help would be appreciated! >> Thanks! >> John >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://mailman.open-bio.org/mailman/listinfo/biojava-l >> > > > > >
_______________________________________________ Biojava-l mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biojava-l
