[Biojava-l] Constructing (wrapping) DNASequence from a SequenceView<NucleotideCompound>

Andreas Prlic andreas at sdsc.edu
Tue Aug 11 23:09:37 UTC 2015

Did you see the getSequenceAsString method?

ProteinSequence ps = new

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.


On Tue, Aug 11, 2015 at 4:43 AM, John Stalker <jstalker at coreinformatics.com>

> 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: <andreas.prlic at gmail.com> on behalf of Andreas Prlic
> Date: Tuesday, August 11, 2015 at 12:58 AM
> To: John Stalker
> Cc: "biojava-l at mailman.open-bio.org"
> 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 <jstalker at coreinformatics.com
> > 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
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