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 <[email protected]> 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:* [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]> 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 > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
