97 lines
2.3 KiB
Mathematica
97 lines
2.3 KiB
Mathematica
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function c = preprocAln(alnMat)
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% This function preprocess the alignment matrix to cliques and separators
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% Lu Cheng, 24.05.2011
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[nSeq nLoci] = size(alnMat);
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alnCell = mat2cell(alnMat,nSeq,ones(1,nLoci));
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arrUniqBase = cellfun(@unique,alnCell,'UniformOutput',false); % unique base at each loci
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arrUniqBaseNum = cellfun(@length,arrUniqBase);
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arrCqNum = arrUniqBaseNum(1:end-2).*arrUniqBaseNum(2:end-1).*arrUniqBaseNum(3:end);
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arrSpNum = arrUniqBaseNum(2:end-2).*arrUniqBaseNum(3:end-1);
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nMaxCqCodes = max(arrCqNum);
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nMaxSpCodes = max(arrSpNum);
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cqCodes = cellfun(@myProd,arrUniqBase(1:end-2),arrUniqBase(2:end-1),arrUniqBase(3:end), ...
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'UniformOutput',false);
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spCodes = cellfun(@myProd,arrUniqBase(2:end-2),arrUniqBase(3:end-1), ...
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'UniformOutput',false);
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cqData = zeros(nSeq,length(cqCodes));
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spData = zeros(nSeq,length(spCodes));
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cqCounts = zeros(nMaxCqCodes,length(cqCodes));
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spCounts = zeros(nMaxSpCodes,length(spCodes));
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cqPrior = ones(nMaxCqCodes,length(cqCodes));
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spPrior = ones(nMaxSpCodes,length(spCodes));
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for i=1:nLoci-2
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nCodeTmp = size(cqCodes{i},1);
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for j=1:nCodeTmp
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tmpInds = ismember(alnMat(:,i:i+2),cqCodes{i}(j,:),'rows');
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cqData(tmpInds,i) = j;
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cqCounts(j,i) = sum(tmpInds);
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end
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cqPrior(1:nCodeTmp,i) = 1/nCodeTmp;
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if i==1
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continue;
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end
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k=i-1;
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nCodeTmp = size(spCodes{k},1);
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for j=1:nCodeTmp
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tmpInds = ismember(alnMat(:,i:i+1),spCodes{k}(j,:),'rows');
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spData(tmpInds,k) = j;
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spCounts(j,k) = sum(tmpInds);
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end
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spPrior(1:nCodeTmp,k) = 1/nCodeTmp;
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end
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c.nSeq = nSeq;
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% c.alnMat = alnMat;
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c.arrUniqBase = arrUniqBase;
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c.arrUniqBaseNum = arrUniqBaseNum;
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c.nMaxCqCodes = nMaxCqCodes;
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c.nMaxSpCodes = nMaxSpCodes;
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c.cqCodes = cqCodes;
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c.spCodes = spCodes;
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c.cqData = cqData;
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c.spData = spData;
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c.cqCounts = cqCounts;
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c.spCounts = spCounts;
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c.cqPrior = cqPrior;
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c.spPrior = spPrior;
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function y = myProd(varargin)
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% calculate the cartesian product for the input
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% Lu Cheng, 24.05.2011
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if nargin==2
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set1 = varargin{1};
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set2 = varargin{2};
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[t1 t2] = meshgrid(set1,set2);
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y = [t1(:) t2(:)];
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elseif nargin==3
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set1 = varargin{1};
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set2 = varargin{2};
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set3 = varargin{3};
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[t1 t2 t3] = meshgrid(set1,set2,set3);
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y = [t1(:) t2(:) t3(:)];
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else
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y = [];
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end
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