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, 121 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/GraphViz/dot_to_graph.m b/sourcecodes/bnt-master/GraphViz/dot_to_graph.m
new file mode 100644
index 00000000..05b47480
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/dot_to_graph.m
@@ -0,0 +1,121 @@
+function [Adj, labels, x, y] = dot_to_graph(filename)
+% [Adj, labels, x, y] = dot_to_graph(filename)
+% Extract a matrix representation, node labels, and node position coordinates
+% from a file in GraphViz format http://www.research.att.com/sw/tools/graphviz
+%
+% INPUTS:
+%    'filename' - the file in DOT format containing the graph layout.
+% OUTPUT:
+%  'Adj'    - an adjacency matrix representation of the graph in 'filename';
+% 'labels'  - a character array with the names of the nodes of the graph;
+%    'x'    - a row vector with the x-coordinates of the nodes in 'filename';
+%    'y'    - a row vector with the y-coordinates of the nodes in 'filename'.
+%
+% WARNINGS: not guaranted to parse ANY GraphViz file. Debugged on undirected 
+%       sample graphs from GraphViz(Heawood, Petersen, ER, ngk10_4, process). 
+%       Complaines about RecursionLimit set only to 500 on huge graphs.
+%       Ignores singletons (disjoint nodes).         
+% Sample DOT code "ABC.dot", read by [Adj, labels, x, y] = dot_to_graph('ABC.dot')
+% digraph G {
+%       A [pos="28,31"];
+%       B [pos="74,87"];
+%       A -- B [pos="e,61,71 41,47 46,53 50,58 55,64"];
+% }
+%                                                     last modified: Jan 2004
+% by Alexi Savov:  asavov @wustl.edu  |  http://artsci.wustl.edu/~azsavov
+%    Leon Peshkin: pesha @ai.mit.edu  |  http://www.ai.mit.edu/~pesha 
+%    Tom Minka
+
+if ~exist(filename)                % Checks whether the specified file exists.
+  error('* * * File does not exist or could not be found. * * *');
+end;
+
+lines = textread(filename,'%s','delimiter','\n','commentstyle','c');  % Read file into cell array
+dot_lines = strvcat(lines);                                % of lines, ignoring C-style comments
+
+if findstr(dot_lines(1,:), 'graph ') == []           % Is this a DOT file ?
+  error('* * * File does not appear to be in valid DOT format. * * *');
+end;
+
+Nlns = size(dot_lines,1);             % The number of lines;
+nodes = {};
+unread = 1:Nlns;             % 'unread' list of lines which has not been examined yet
+edge_id = 1;
+Adj = [];
+for line_ndx = 1:Nlns   % This section sets the adjacency matrix A(Lnode,Rnode) = edge_id.
+  line = dot_lines(line_ndx,:);
+  Ddash_pos = strfind(line, ' -- ') + 1;    % double dash positions
+  arrow_pos = strfind(line, ' -> ') + 1;    % arrow  dash positions
+  tokens = strread(line,'%s','delimiter',' "');
+  left_bound = 1;
+  for dash_pos = [Ddash_pos arrow_pos];  % if empty - not a POS line
+    Lnode = sscanf(line(left_bound:dash_pos -2), '%s');
+    Rnode = sscanf(line(dash_pos +3 : length(line)-1),'%s',1);
+    Lndx = strmatch(Lnode, nodes, 'exact');
+    Rndx = strmatch(Rnode, nodes, 'exact');
+    if isempty(Lndx)         % extend our list of nodes 
+      nodes{end+1} = Lnode;
+      Lndx = length(nodes);
+    end
+    if isempty(Rndx)
+      nodes{end+1} = Rnode;
+      Rndx = length(nodes);
+    end
+    Adj(Lndx, Rndx) = edge_id;
+    if  ismember(dash_pos, Ddash_pos)   % The edge is undirected, A(Rndx,LndxL) is also set to 1;
+      Adj(Rndx, Lndx) = edge_id;
+    end
+    edge_id = edge_id + 1; 
+    left_bound = dash_pos + 3;
+    unread = setdiff(unread, line_ndx); 
+  end
+end
+Nvrt = length(nodes);    % number of vertices we found  [Do we ever have singleton vertices ???]
+% nodes = strvcat(nodes); % convert to the searchable array
+x = zeros(1, Nvrt); 
+y = zeros(1, Nvrt);
+labels = nodes;
+% Find node's position coordinates if they are contained in 'filename'.
+for line_ndx = unread        % Look for node's coordinates among the 'unread' lines.
+  line = dot_lines(line_ndx,:);
+  bra_pos = strfind(line, '[');       % has to have "[" if it has the label
+  lst_node = 0;
+  for node = 1:Nvrt     % look through the list of nodes 
+    %  THE NEXT STATEMENT we assume no node is substring of any other node
+    lbl_pos = strfind(line, nodes{node});
+    if (~isempty(lbl_pos) & ~isempty(bra_pos) & (x(node) == 0))  % make sure we have not seen it 
+      if (lbl_pos(1) < bra_pos(1))  % label has to be to the left of bracket
+	lst_node = node;
+      end
+    end
+  end
+  if lst_node
+    pos_pos = strfind(line, 'pos');     % position of the "pos"
+    if ~isempty(pos_pos)   % this line contains SOME position  
+      [node_pos] = sscanf(line(pos_pos:end), ' pos  = "%d,%d"')';
+      x(lst_node) = node_pos(1);
+      y(lst_node) = node_pos(2);
+    end
+    % minka
+    label_pos = strfind(line, 'label'); % position of the "label"
+    if ~isempty(label_pos)
+      label_end = strfind(line(label_pos:end),',');
+      labels{lst_node} = unquote(line(label_pos+(6:label_end(1)-2)));
+    end
+  end
+end
+
+if (isempty(find(x)) & (nargout > 2))   % If coordinates were requested, but not found in 'filename'.
+  warning('File does not contain node coordinates.');
+end;
+if ~(size(Adj,1)==size(Adj,2))           % Make sure Adj is a square matrix. ? 
+  Adj = eye(max(size(Adj)),size(Adj,1))*Adj*eye(size(Adj,2),max(size(Adj)));
+end;
+x = .9*(x-min(x))/range(x)+.05;  % normalise and push off margins 
+y = .9*(y-min(y))/range(y)+.05; 
+
+
+
+function s = unquote(s)
+
+s = strrep(s,'"','');