[Biojava-l] biojava3 getting the features from alignedsequence

[Hara Dilley]

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<mailto: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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