Re: biojava3 getting the features from alignedsequence
Hara Dilley <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
That would be very helpful! -----Original Message----- From: Marco Valtas [mailto:[email protected]] Sent: Friday, January 07, 2011 2:03 PM To: Scooter Willis Cc: Hara Dilley; [email protected] Subject: Re: [Biojava-l] biojava3 getting the features from alignedsequence I think in such cases we could throw an exception. what I mean is that having sequences positions counted from 1 and someone tries to fetch a position from 0 a exception could be thrown telling that such index starts at 1. For arrays and lists that not model a sequence will be better keep the computer science convention. Any thoughts? Marco Valtas Developer at ThoughtWorks Sent from my iPhone On 07/01/2011, at 17:51, Scooter Willis <[email protected]> wrote: > 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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l