Re: biojava3 getting the features from alignedsequence

The javadoc on the interface indicates the intent to throw an
IndexOutOfBoundsException with javadoc that indicates start with 1. Just
needs to be better defined as a general rule in the method name
 getAlignedSequenceBioIndex(int index) as an example.  BioIndex should be
used in all methods where the desire is to use 1 instead of 0. We should
also provide the equivalent getAlignedSequence(int index) with index = 0; If
not this mistake will be made often.

Thanks

Scooter



On Fri, Jan 7, 2011 at 5:04 PM, Hara Dilley <[email protected]> wrote:

> 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