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: [email protected] [mailto:[email protected]] On Behalf Of Scooter Willis
Sent: Thursday, January 06, 2011 6:43 PM
To: Hara Dilley
Cc: [email protected]
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
<[email protected]<mailto:[email protected]>> 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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