[Biojava-l] biojava3 getting the features from alignedsequence

[Scooter Willis]

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 <hdilley at catbio.com> wrote:

> That would be very helpful!
>
> -----Original Message-----
> From: Marco Valtas [mailto:mavcunha at gmail.com]
> Sent: Friday, January 07, 2011 2:03 PM
> To: Scooter Willis
> Cc: Hara Dilley; biojava-l at lists.open-bio.org
> 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 <willishf at ufl.edu> 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 <hdilley at catbio.com> 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:* 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> 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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> >>
> >>
> >>
> >
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