BNW using Octave instead of Matlab.

This version of BNW should perform the same as the original version. The only difference is that it uses Octave instead of Matlab when running BayesNet Toolbox during parameter learning.

I am calling this BNW_1.02. It can be accessed at:
compbio.uthsc.edu/BNW_1.02

1 files changed, 66 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/KPMtools/subv2indKPM.m b/sourcecodes/bnt-master/KPMtools/subv2indKPM.m
new file mode 100644
index 00000000..d0a16618
--- /dev/null
+++ b/sourcecodes/bnt-master/KPMtools/subv2indKPM.m
@@ -0,0 +1,66 @@
+function ndx = subv2indKPM(siz, subv)
+% SUBV2IND Like the built-in sub2ind, but the subscripts are given as row vectors.
+% ind = subv2ind(siz,subv)
+%
+% siz can be a row or column vector of size d.
+% subv should be a collection of N row vectors of size d.
+% ind will be of size N * 1.
+%
+% Example:
+% subv = [1 1 1;
+%         2 1 1;
+%         ...
+%         2 2 2];
+% subv2ind([2 2 2], subv) returns [1 2 ... 8]'
+% i.e., the leftmost digit toggles fastest.
+%
+% See also IND2SUBV.
+
+
+if isempty(subv)
+  ndx = [];
+  return;
+end
+
+if isempty(siz)
+  ndx = 1;
+  return;
+end
+
+[ncases ndims] = size(subv);
+
+%if length(siz) ~= ndims
+%  error('length of subscript vector and sizes must be equal');
+%end
+
+if all(siz==2)
+  %rbits = subv(:,end:-1:1)-1; % read from right to left, convert to 0s/1s
+  %ndx = bitv2dec(rbits)+1; 
+  twos = pow2(0:ndims-1);
+  ndx = ((subv-1) * twos(:)) + 1;
+  %ndx = sum((subv-1) .* twos(ones(ncases,1), :), 2) + 1; % equivalent to matrix * vector
+  %ndx = sum((subv-1) .* repmat(twos, ncases, 1), 2) + 1; % much slower than ones
+  %ndx = ndx(:)';
+else
+  %siz = siz(:)';
+  cp = [1 cumprod(siz(1:end-1))]';
+  %ndx = ones(ncases, 1);
+  %for i = 1:ndims
+  %  ndx = ndx + (subv(:,i)-1)*cp(i);
+  %end
+  ndx = (subv-1)*cp + 1;
+end
+
+%%%%%%%%%%%
+
+function d = bitv2dec(bits)
+% BITV2DEC Convert a bit vector to a decimal integer
+% d = butv2dec(bits)
+%
+% This is just like the built-in bin2dec, except the argument is a vector, not a string.
+% If bits is an array, each row will be converted.
+
+[m n] = size(bits);
+twos = pow2(n-1:-1:0);
+d = sum(bits .* twos(ones(m,1),:),2);
+