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 <[email protected]> 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 <[email protected]> > 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 - [email protected] >> 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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