Added source Matlab code for reference

matlab/graph/@phyTree/private/Opttf.m

@@ -0,0 +1,31 @@
+function tf = opttf(pval)
+%OPTTF determines whether input options are true or false
+
+% Copyright 2003-2004 The MathWorks, Inc.
+% $Revision: 1.3.4.2 $   $Date: 2004/12/24 20:42:39 $
+
+
+if islogical(pval)
+    tf = all(pval);
+    return
+end
+if isnumeric(pval)
+    tf = all(pval~=0);
+    return
+end
+if ischar(pval)
+    truevals = {'true','yes','on','t'};
+    k = any(strcmpi(pval,truevals));
+    if k
+        tf = true;
+        return
+    end
+    falsevals = {'false','no','off','f'};
+    k = any(strcmpi(pval,falsevals));
+    if k
+        tf = false;
+        return
+    end
+end
+% return empty if unknown value
+tf = logical([]);

matlab/graph/@phyTree/private/prettyOrder.m

@@ -0,0 +1,39 @@
+function tr = prettyOrder(tr)
+%PRETTYORDER Reorders the leaf nodes to avoid branch crossings.
+%
+%   T2 = PRETTYORDER(T1) Reorders the leaf nodes in the phylogenetic tree
+%   T1 such that the layout of the tree does not contain branch crossings.
+
+% Copyright 2003-2005 The MathWorks, Inc.
+% $Revision: 1.1.8.1 $ $Author: batserve $ $Date: 2005/06/09 21:56:11 $
+
+numBranches = size(tr.tree,1);
+numLeaves = numBranches + 1;
+numLabels = numBranches + numLeaves; 
+
+L = [ones(numLeaves,1); zeros(numBranches,1)];
+for ind = 1 : numBranches
+   L(ind+numLeaves) = sum(L(tr.tree(ind,:)));
+end
+X = zeros(numLabels,1);
+for ind = numBranches:-1:1
+   X(tr.tree(ind,:)) = tr.dist(tr.tree(ind,:))+X(ind+numLeaves);
+end
+Li = zeros(1,numLabels); Ls = Li;
+Ls(numLabels) = numLeaves; 
+for ind = numBranches:-1:1
+    Ls(tr.tree(ind,:)) = Ls(ind+numLeaves);
+    Li(tr.tree(ind,:)) = Li(ind+numLeaves);
+    if diff(X(tr.tree(ind,:)))>=0
+        Ls(tr.tree(ind,1)) = Li(tr.tree(ind,1)) + L(tr.tree(ind,1));
+        Li(tr.tree(ind,2)) = Ls(tr.tree(ind,2)) - L(tr.tree(ind,2));
+    else
+        Ls(tr.tree(ind,2)) = Li(tr.tree(ind,2)) + L(tr.tree(ind,2));
+        Li(tr.tree(ind,1)) = Ls(tr.tree(ind,1)) - L(tr.tree(ind,1));
+    end
+end
+  
+tr.names(Ls(1:numLeaves))=tr.names(1:numLeaves);
+tr.dist(Ls(1:numLeaves))=tr.dist(1:numLeaves);
+Ls(numLeaves+1:numLabels)=numLeaves+1:numLabels;
+tr.tree = Ls(tr.tree);