[Biojava-l] biojava3 getting the features from alignedsequence

[Scooter Willis]

Hara

Figured out the problem. Welcome to the world of biology indexes start at 1
and computer science starts at 0.

If you use 1 as your first index it will work. In the core module we tried
to make that clear by using BioIndex in the method name. I will see what I
can do about getting that added/changed in the alignment module.

Thanks

Scooter

On Fri, Jan 7, 2011 at 12:20 PM, Hara Dilley <hdilley at catbio.com> wrote:

> Thanks Scooter,
>
> Below is the code of how I populate lst. Of course my real sequences are
> different, but for this example it doesn’t matter.
>
>
>
>        List<ProteinSequence> lst = *new* ArrayList<ProteinSequence>();
>
>       ProteinSequence s1 = *new* ProteinSequence(“SHALG”);
>
>       ProteinSequence s2 = *new* ProteinSequence(“SWQVLG”);
>
>       lst.add(s1);
>
>       lst.add(s2);
>
>
>
>
>
>
>
> *From:* willishf at gmail.com [mailto:willishf at gmail.com] *On Behalf Of *Scooter
> Willis
> *Sent:* Thursday, January 06, 2011 6:43 PM
> *To:* Hara Dilley
> *Cc:* biojava-l at lists.open-bio.org
> *Subject:* Re: [Biojava-l] biojava3 getting the features from
> alignedsequence
>
>
>
> Hara
>
>
>
> Can you provide more of the code you are using that shows how you are
> loading the initial sequences.
>
>
>
> Thanks
>
>
> Scooter
>
>
>
> On Thu, Jan 6, 2011 at 7:09 PM, Hara Dilley <hdilley at catbio.com> wrote:
>
> Hi,
>
> I would like to align a set of sequences against a scaffold and get the
> list of the modifications for each aligned sequence.
> I am using biojava3
> I have tried to create a profile  thinking that I can get the
> AlignedSequences from it but that it appears to be null.
> Here is part of my code:
>
> Profile<ProteinSequence, AminoAcidCompound> profile =
> Alignments.getMultipleSequenceAlignment(lst);
> Profile.getAlignedSequence(0);
>
> Can someone please point to an example for this or to the classes I have to
> use.
> Thank you,
> Hara
>
>
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>