Added source Matlab code for reference

matlab/spatial/private/preprocAln.m

@@ -0,0 +1,97 @@
+function c = preprocAln(alnMat)
+% This function preprocess the alignment matrix to cliques and separators
+% Lu Cheng, 24.05.2011
+
+[nSeq nLoci] = size(alnMat);
+
+alnCell = mat2cell(alnMat,nSeq,ones(1,nLoci));
+
+arrUniqBase = cellfun(@unique,alnCell,'UniformOutput',false);  % unique base at each loci
+arrUniqBaseNum = cellfun(@length,arrUniqBase);
+
+arrCqNum = arrUniqBaseNum(1:end-2).*arrUniqBaseNum(2:end-1).*arrUniqBaseNum(3:end);
+arrSpNum = arrUniqBaseNum(2:end-2).*arrUniqBaseNum(3:end-1);
+
+nMaxCqCodes = max(arrCqNum);
+nMaxSpCodes = max(arrSpNum);
+
+cqCodes = cellfun(@myProd,arrUniqBase(1:end-2),arrUniqBase(2:end-1),arrUniqBase(3:end), ...
+    'UniformOutput',false);
+spCodes = cellfun(@myProd,arrUniqBase(2:end-2),arrUniqBase(3:end-1), ...
+    'UniformOutput',false);
+
+cqData = zeros(nSeq,length(cqCodes));
+spData = zeros(nSeq,length(spCodes));
+
+cqCounts = zeros(nMaxCqCodes,length(cqCodes));
+spCounts = zeros(nMaxSpCodes,length(spCodes));
+
+cqPrior = ones(nMaxCqCodes,length(cqCodes));
+spPrior = ones(nMaxSpCodes,length(spCodes));
+
+for i=1:nLoci-2
+    
+    nCodeTmp =  size(cqCodes{i},1);
+    for j=1:nCodeTmp
+        tmpInds = ismember(alnMat(:,i:i+2),cqCodes{i}(j,:),'rows');
+        cqData(tmpInds,i) = j;
+        cqCounts(j,i) = sum(tmpInds);
+    end
+    
+    cqPrior(1:nCodeTmp,i) = 1/nCodeTmp;
+    
+    if i==1
+        continue;
+    end
+    
+    k=i-1;
+    nCodeTmp = size(spCodes{k},1);
+    for j=1:nCodeTmp
+        tmpInds = ismember(alnMat(:,i:i+1),spCodes{k}(j,:),'rows');
+        spData(tmpInds,k) = j;
+        spCounts(j,k) = sum(tmpInds);
+    end
+    
+    spPrior(1:nCodeTmp,k) = 1/nCodeTmp;
+end
+
+c.nSeq = nSeq;
+% c.alnMat = alnMat;
+
+c.arrUniqBase = arrUniqBase;
+c.arrUniqBaseNum = arrUniqBaseNum;
+
+c.nMaxCqCodes = nMaxCqCodes;
+c.nMaxSpCodes = nMaxSpCodes;
+
+c.cqCodes = cqCodes;
+c.spCodes = spCodes;
+
+c.cqData = cqData;
+c.spData = spData;
+
+c.cqCounts = cqCounts;
+c.spCounts = spCounts;
+
+c.cqPrior = cqPrior;
+c.spPrior = spPrior;
+
+
+function y = myProd(varargin)
+% calculate the cartesian product for the input
+% Lu Cheng, 24.05.2011
+
+if nargin==2
+    set1 = varargin{1};
+    set2 = varargin{2};
+    [t1 t2] = meshgrid(set1,set2);
+    y = [t1(:) t2(:)];
+elseif nargin==3
+    set1 = varargin{1};
+    set2 = varargin{2};
+    set3 = varargin{3};
+    [t1 t2 t3] = meshgrid(set1,set2,set3);
+    y = [t1(:) t2(:) t3(:)];
+else
+    y = [];
+end