[Biojava-l] Row order from multiple sequence alignment

[Spencer Bliven]

The original sequences are also in a permuted order. I took your suggestion
to store the order in the accessions. That worked fine.

Thanks,

Spencer

On Tue, Mar 1, 2016 at 7:43 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Spencer,
>
> You might have to compare the accession codes of the sequences...
>
> // 1 is the first sequence in the alignment, not 0...
>  AlignedSequence<ProteinSequence, AminoAcidCompound> as =
> profile.getAlignedSequence(1);
>       System.out.println(as.getAccession());
>
> Alternatively, what is the order of sequences that comes out of profile.getOriginalSequences()
> ?
>
>
> A
>
>
>
> On Mon, Feb 29, 2016 at 9:15 AM, Spencer Bliven <spencer.bliven at gmail.com>
> wrote:
>
>> I'm creating a multiple sequence alignment using
>> Alignments.getMultipleSequenceAlignment, as described in the cookbook
>> <http://biojava.org/wiki/BioJava:CookBook3:MSA>. The problem is that the
>> returned profile has rows in a different order than the input array of
>> sequenced. How can I map from an index in the inputs to the rows of the
>> profile?
>>
>> Thanks,
>> Spencer
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> RCSB PDB Protein Data Bank
> Technical & Scientific Team Lead
> University of California, San Diego
>
> Editor Software Section
> PLOS Computational Biology
>
> BioJava Project Lead
> -----------------------------------------------------------------------
>
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