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, 86 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/docs/adj2pajek2.m b/sourcecodes/bnt-master/docs/adj2pajek2.m
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+% ADJ2PAJEK2 Converts an adjacency matrix representation to a Pajek .net read format
+% adj2pajek2(adj, filename-stem, 'argname1', argval1, ...)
+%
+% Set A(i,j)=-1 to get a dotted line
+%
+% Optional arguments
+%
+%  nodeNames - cell array, defaults to {'v1','v2,...}
+%  shapes - cell array, defaults to {'ellipse','ellipse',...}
+%     Choices are 'ellipse', 'box', 'diamond', 'triangle', 'cross', 'empty'
+%  partition - vector of integers, defaults to [1 1 ... 1]
+%    This will automatically color-code the vertices by their partition
+%
+% Run pajek (available from http://vlado.fmf.uni-lj.si/pub/networks/pajek/)
+% Choose File->Network->Read from the menu
+% Then press ctrl-G (Draw->Draw)
+% Optional: additionally load the partition file then press ctrl-P (Draw->partition)
+%
+% Examples
+% A=zeros(5,5);A(1,2)=-1;A(2,1)=-1;A(1,[3 4])=1;A(2,5)=1;
+% adj2pajek2(A,'foo') % makes foo.net
+%
+% adj2pajek2(A,'foo','partition',[1 1 2 2 2]) % makes foo.net and foo.clu
+% 
+% adj2pajek2(A,'foo',...
+%            'nodeNames',{'TF1','TF2','G1','G2','G3'},...
+%            'shapes',{'box','box','ellipse','ellipse','ellipse'});
+%
+%
+% The file format is documented on p68 of the pajek manual
+% and good examples are on p58, p72
+%
+% Written by Kevin Murphy, 30 May 2007
+% Based on adj2pajek by Gergana Bounova
+% http://stuff.mit.edu/people/gerganaa/www/matlab/routines.html
+% Fixes a small bug (opens files as 'wt' instead of 'w' so it works in windows)
+% Also, simplified her code and added some features.
+
+function []=adj2pajek2(adj,filename, varargin)
+
+N = length(adj);
+for i=1:N
+  nodeNames{i} = strcat('"v',num2str(i),'"');
+  shapes{i} = 'ellipse';
+end
+
+[nodeNames, shapes, partition] = process_options(varargin, ...
+    'nodeNames', nodeNames, 'shapes', shapes, 'partition', []);
+
+if ~isempty(partition)
+  fid = fopen(sprintf('%s.clu', filename),'wt','native'); 
+  fprintf(fid,'*Vertices  %6i\n',N);
+  for i=1:N
+    fprintf(fid, '%d\n', partition(i));
+  end
+  fclose(fid);
+end
+
+fid = fopen(sprintf('%s.net', filename),'wt','native'); 
+
+fprintf(fid,'*Vertices  %6i\n',N);
+for i=1:N
+  fprintf(fid,'%3i %s %s\n', i, nodeNames{i}, shapes{i});
+end
+
+%fprintf(fid,'*Edges\n');
+fprintf(fid,'*Arcs\n'); % directed
+for i=1:N
+  for j=1:N
+    if adj(i,j) ~= 0
+      fprintf(fid,' %4i   %4i   %2i\n',i,j,adj(i,j));
+    end
+  end
+end
+fclose(fid)
+
+
+if 0
+adj2pajek2(A,'foo',...
+            'nodeNames',{'TF1','TF2','G1','G2','G3'},...
+            'shapes',{'box','box','ellipse','ellipse','ellipse'});
+
+N = 100; part = ones(1,N); part(intersect(reg.tfidxTest,1:N))=2;
+G = reg.Atest(1:N, 1:N)';
+adj2pajek2(G, 'Ecoli100', 'partition', part)
+end