31 lines
785 B
Mathematica
31 lines
785 B
Mathematica
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function [aln2] = encodealn(aln)
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%ENCODEALN - Convert nucleotide in alignment to integer.
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%
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% Syntax: [aln2] = encodealn(aln)
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%
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% Inputs:
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% aln - Alignment structure letter representation
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%
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% Outputs:
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% aln2 - Alignment structure integer representation
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%
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%
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% See also: CODONISESEQ, ENCODESEQ
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% Molecular Biology & Evolution Toolbox, (C) 2005
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% Author: James J. Cai
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% Email: jamescai@hkusua.hku.hk
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% Website: http://web.hku.hk/~jamescai/
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% Last revision: 5/28/2005
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if ~(aln.seqtype) error('Do not know the type of sequence! ... BAPS'); end
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aln2=aln;
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switch (aln2.seqtype)
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case (1)
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aln2.seq = i_encode_n(aln2.seq);
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case (2)
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aln2.seq = i_encode_n(aln2.seq);
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case (3)
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aln2.seq = i_encode_a(aln2.seq);
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end
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