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

8 files changed, 701 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/GraphViz/Old/CVS/Entries b/sourcecodes/bnt-master/GraphViz/Old/CVS/Entries
new file mode 100644
index 00000000..50af46f1
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/CVS/Entries
@@ -0,0 +1,6 @@
+/dot_to_graph.m/1.1.1.1/Tue Jan 27 21:01:54 2004//
+/draw_dot.m/1.1.1.1/Tue Jan 27 20:42:50 2004//
+/draw_graph.m/1.1.1.1/Tue Jan 27 21:03:56 2004//
+/graphToDot.m/1.1.1.1/Tue Feb  3 17:15:18 2004//
+/pre_pesha_graph_to_dot.m/1.1.1.1/Tue Jan 27 20:47:40 2004//
+D
diff --git a/sourcecodes/bnt-master/GraphViz/Old/CVS/Repository b/sourcecodes/bnt-master/GraphViz/Old/CVS/Repository
new file mode 100644
index 00000000..83ba7005
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/GraphViz/Old
diff --git a/sourcecodes/bnt-master/GraphViz/Old/CVS/Root b/sourcecodes/bnt-master/GraphViz/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/GraphViz/Old/dot_to_graph.m b/sourcecodes/bnt-master/GraphViz/Old/dot_to_graph.m
new file mode 100644
index 00000000..59beb8fc
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/dot_to_graph.m
@@ -0,0 +1,107 @@
+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 
+
+if ~exist(filename)                % Checks whether the specified file exists.
+   error('* * * File does not exist or could not be found. * * *');     return;
+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. * * *');    return;
+end;
+
+Nlns = size(dot_lines,1);             % The number of lines;
+labels = {};
+unread = 1:Nlns;             % 'unread' list of lines which has not been examined yet
+edge_id = 1;
+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, labels, 'exact');
+        Rndx = strmatch(Rnode, labels, 'exact');
+        if isempty(Lndx)         % extend our list of labels 
+            labels{end+1} = Lnode;
+            Lndx = length(labels);
+        end
+        if isempty(Rndx)
+            labels{end+1} = Rnode;
+            Rndx = length(labels);
+        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(labels);    % number of vertices we found  [Do we ever have singleton vertices ???]
+% labels = strvcat(labels); % convert to the searchable array
+x = zeros(1, Nvrt); 
+y = zeros(1, Nvrt);
+lst_node = 0;
+        % Find node's position coordinates if they are contained in 'filename'.
+for line_ndx = unread        % Look for node's coordiantes among the 'unread' lines.
+    line = dot_lines(line_ndx,:);
+    bra_pos  = strfind(line, '[');       % has to have "[" if it has the lable
+    pos_pos = strfind(line, 'pos');     % position of the "pos"
+    for node = 1:Nvrt     % look through the list of labels 
+        %  THE NEXT STATEMENT we assume no label is substring of any other label
+        lbl_pos = strfind(line, labels{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 braket
+                lst_node = node;
+            end
+        end
+    end
+    if (~isempty(pos_pos) & lst_node)   % this line contains SOME position  
+        [node_pos] = sscanf(line(pos_pos:length(line)), ' pos  = "%d,%d"')';
+        x(lst_node) = node_pos(1);
+        y(lst_node) = node_pos(2);
+        lst_node = 0;   %  not to assign position several times 
+    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; 
+
diff --git a/sourcecodes/bnt-master/GraphViz/Old/draw_dot.m b/sourcecodes/bnt-master/GraphViz/Old/draw_dot.m
new file mode 100644
index 00000000..d6f37f81
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/draw_dot.m
@@ -0,0 +1,26 @@
+function draw_dot(adj);
+%
+%  draw_dot(name) 
+%  
+% Sample code illustrating use of dot_to_graph.m function
+% Leon Peshkin  
+if ispc, shell = 'dos'; else, shell = 'unix'; end  %  Which OS ?
+
+cmdline = strcat(shell,'(''neato -V'')');
+status = eval(cmdline);
+[status, result] = dos('neato -V');  % request version to check NEATO
+if status == 1,  fprintf('Complaining \n'); exit, end
+
+tmpDOTfile = '_GtDout.dot';            % to be platform independant no use of directories
+tmpLAYOUT  = '_LAYout.dot'; 
+directed = 0;                          % assume UN-directed graph
+graph_to_dot(adj > 0, 'directed', directed, 'filename', tmpDOTfile);  % save in file
+
+cmdline = strcat([shell '(''neato -Tdot ' tmpDOTfile ' -o ' tmpLAYOUT ''')']); % preserve trailing spaces 
+status = eval(cmdline);         %  get NEATO todo layout
+
+[adj, labels, x, y] = dot_to_graph(tmpLAYOUT);  %  load layout 
+delete(tmpLAYOUT); delete(tmpDOTfile);     % clean up temporary files
+
+figure(1); clf; axis square      %  now plot 
+[x, y, h] = draw_graph(adj>0, labels, zeros(size(x,2),1), x, y);
\ No newline at end of file
diff --git a/sourcecodes/bnt-master/GraphViz/Old/draw_graph.m b/sourcecodes/bnt-master/GraphViz/Old/draw_graph.m
new file mode 100644
index 00000000..06e3d7a1
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/draw_graph.m
@@ -0,0 +1,310 @@
+function [x, y, h] = draw_graph(adj, labels, node_t, x, y)
+% DRAW_LAYOUT		Draws a layout for a graph 
+%
+%  [<X, Y>] = DRAW_LAYOUT(ADJ, <LABELS, ISBOX, X, Y>)
+%
+% Inputs :
+%	ADJ : Adjacency matrix (source, sink)
+%       LABELS : Cell array containing labels <Default : '1':'N'>
+%       ISBOX : 1 if node is a box, 0 if oval <Default : zeros>
+%       X, Y, : Coordinates of nodes on the unit square <Default : calls make_layout>
+%
+% Outputs :
+%	X, Y : Coordinates of nodes on the unit square
+%       H    : Object handles 
+%
+% Usage Example : [x, y] = draw_layout([0 1;0 0], {'Hidden','Visible'}, [1 0]');
+%
+% h(i,1) is the text handle - color
+% h(i,2) is the circle handle - facecolor
+%
+% Note	:
+% See also MAKE_LAYOUT
+
+% Uses :
+
+% Change History :
+% Date		Time		Prog	Note
+% 13-Apr-2000	 9:06 PM	ATC	Created under MATLAB 5.3.1.29215a (R11.1)
+
+% ATC = Ali Taylan Cemgil,
+% SNN - University of Nijmegen, Department of Medical Physics and Biophysics
+% e-mail : cemgil@mbfys.kun.nl 
+adj = double(adj);
+N = size(adj,1);
+if nargin<2,
+%  labels = cellstr(char(zeros(N,1)+double('+')));
+  labels = cellstr(int2str((1:N)'));
+end;
+
+if nargin<3,
+  node_t = zeros(N,1);
+%  node_t = rand(N,1) > 0.5;
+else
+  node_t = node_t(:);
+end;
+  
+axis([0 1 0 1]);
+set(gca,'XTick',[],'YTick',[],'box','on');
+% axis('square');
+%colormap(flipud(gray));
+
+if nargin<4,
+  [x y] = make_layout(adj);
+end;
+
+idx1 = find(node_t==0); wd1=[];
+if ~isempty(idx1),
+[h1 wd1] = textoval(x(idx1), y(idx1), labels(idx1));
+end;
+
+idx2 = find(node_t~=0); wd2 = [];
+if ~isempty(idx2),
+[h2 wd2] = textbox(x(idx2), y(idx2), labels(idx2));
+end;
+
+wd = zeros(size(wd1,1)+size(wd2,1),2);
+if ~isempty(idx1), wd(idx1, :) = wd1;  end;
+if ~isempty(idx2), wd(idx2, :) = wd2; end;
+
+for i=1:N,
+  j = find(adj(i,:)==1);
+  for k=j,
+    if x(k)-x(i)==0,
+	sign = 1;
+	if y(i)>y(k), alpha = -pi/2; else alpha = pi/2; end;
+    else
+	alpha = atan((y(k)-y(i))/(x(k)-x(i)));
+	if x(i)<x(k), sign = 1; else sign = -1; end;
+    end;
+    dy1 = sign.*wd(i,2).*sin(alpha);   dx1 = sign.*wd(i,1).*cos(alpha);
+    dy2 = sign.*wd(k,2).*sin(alpha);   dx2 = sign.*wd(k,1).*cos(alpha);    
+    if adj(k,i)==0, % if directed edge
+      arrow([x(i)+dx1 y(i)+dy1],[x(k)-dx2 y(k)-dy2]);
+    else	   
+      line([x(i)+dx1 x(k)-dx2],[y(i)+dy1 y(k)-dy2],'color','k');
+      adj(k,i)=-1; % Prevent drawing lines twice
+    end;
+  end;
+end;
+
+if nargout>2,
+  h = zeros(length(wd),2);
+  if ~isempty(idx1),
+    h(idx1,:) = h1;
+  end;
+  if ~isempty(idx2),
+    h(idx2,:) = h2;
+  end;
+end;
+
+%%%%%
+
+function [t, wd] = textoval(x, y, str)
+% TEXTOVAL		Draws an oval around text objects
+% 
+%  [T, WIDTH] = TEXTOVAL(X, Y, STR)
+%  [..] = TEXTOVAL(STR)  % Interactive
+% 
+% Inputs :
+%    X, Y : Coordinates
+%    TXT  : Strings
+% 
+% Outputs :
+%    T : Object Handles
+%    WIDTH : x and y Width of ovals 
+%
+% Usage Example : [t] = textoval('Visit to Asia?');
+% 
+% 
+% Note     :
+% See also TEXTBOX
+
+% Uses :
+
+% Change History :
+% Date		Time		Prog	Note
+% 15-Jun-1998	10:36 AM	ATC	Created under MATLAB 5.1.0.421
+
+% ATC = Ali Taylan Cemgil,
+% SNN - University of Nijmegen, Department of Medical Physics and Biophysics
+% e-mail : cemgil@mbfys.kun.nl 
+
+temp = [];
+
+switch nargin,
+  case 1,
+    str = x;
+    if ~isa(str,'cell') str=cellstr(str); end;
+    N = length(str);
+    wd = zeros(N,2);
+    for i=1:N,
+      [x, y] = ginput(1);
+      tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle');
+      [ptc wx wy] = draw_oval(tx, x, y);
+      wd(i,:) = [wx wy];
+      delete(tx);      
+      tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle');
+      temp = [temp ; tx ptc];
+    end;
+  case 3,
+    if ~isa(str,'cell') str=cellstr(str); end;
+    N = length(str);    
+    wd = zeros(N,2);
+    for i=1:N,
+      tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle');
+     [ptc wx wy] = draw_oval(tx, x(i), y(i));
+      wd(i,:) = [wx wy];
+      delete(tx);
+      tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle');      
+      temp = [temp;  tx ptc];
+    end;
+  otherwise,
+end;  
+
+if nargout>0, t = temp; end;
+
+%%%%%%%%%
+
+
+function [ptc, wx, wy] = draw_oval(tx, x, y)
+% Draws an oval box around a tex object
+sz = get(tx,'Extent');
+wy = sz(4);
+wx = max(2/3*sz(3), wy); 
+wx = 0.5*wx; % KPM
+wy = 0.5*wy;
+ptc = ellipse(x, y, wx, wy);
+set(ptc, 'FaceColor','w');
+
+
+%%%%%%%%%%%%%
+
+function [p] = ellipse(x, y, rx, ry, c)
+% ELLIPSE		Draws Ellipse shaped patch objects
+% 
+%  [<P>] = ELLIPSE(X, Y, Rx, Ry, C)
+% 
+% Inputs :
+%    X : N x 1 vector of x coordinates
+%    Y : N x 1 vector of y coordinates
+%    Rx, Ry : Radii
+%    C : Color index
+%
+% 
+% Outputs :
+%    P = Handles of Ellipse shaped path objects
+% 
+% Usage Example : [] = ellipse();
+% 
+% 
+% Note     :
+% See also 
+
+% Uses :
+
+% Change History :
+% Date		Time		Prog	Note
+% 27-May-1998	 9:55 AM	ATC	Created under MATLAB 5.1.0.421
+
+% ATC = Ali Taylan Cemgil,
+% SNN - University of Nijmegen, Department of Medical Physics and Biophysics
+% e-mail : cemgil@mbfys.kun.nl 
+
+if (nargin < 2) error('Usage Example : e = ellipse([0 1],[0 -1],[1 0.5],[2 0.5]); '); end;
+if (nargin < 3) rx = 0.1; end;
+if (nargin < 4) ry = rx; end;
+if (nargin < 5) c = 1; end;
+
+if length(c)==1, c = ones(size(x)).*c; end;
+if length(rx)==1, rx = ones(size(x)).*rx; end;
+if length(ry)==1, ry = ones(size(x)).*ry; end;
+  
+n = length(x);
+p = zeros(size(x));
+t = 0:pi/30:2*pi;
+for i=1:n,
+	px = rx(i)*cos(t)+x(i);
+	py = ry(i)*sin(t)+y(i);
+	p(i) = patch(px,py,c(i));
+end;
+
+if nargout>0, pp = p; end;
+
+%%%%%
+
+function [t, wd] = textbox(x,y,str)
+% TEXTBOX	Draws A Box around the text 
+% 
+%  [T, WIDTH] = TEXTBOX(X, Y, STR)
+%  [..] = TEXTBOX(STR)
+% 
+% Inputs :
+%    X, Y : Coordinates
+%    TXT  : Strings
+% 
+% Outputs :
+%    T : Object Handles
+%    WIDTH : x and y Width of boxes 
+%% 
+% Usage Example : t = textbox({'Ali','Veli','49','50'});
+% 
+% 
+% Note     :
+% See also TEXTOVAL
+
+% Uses :
+
+% Change History :
+% Date		Time		Prog	Note
+% 09-Jun-1998	11:43 AM	ATC	Created under MATLAB 5.1.0.421
+
+% ATC = Ali Taylan Cemgil,
+% SNN - University of Nijmegen, Department of Medical Physics and Biophysics
+% e-mail : cemgil@mbfys.kun.nl 
+
+% See
+temp = [];
+
+switch nargin,
+  case 1,
+    str = x;
+    if ~isa(str,'cell') str=cellstr(str); end;
+    N = length(str);  
+    wd = zeros(N,2);
+    for i=1:N,
+      [x, y] = ginput(1);
+      tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle');
+      [ptc wx wy] = draw_box(tx, x, y); 
+      wd(i,:) = [wx wy];
+      delete(tx);
+      tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle');      
+      temp = [temp; tx ptc];
+    end;
+  case 3,
+    if ~isa(str,'cell') str=cellstr(str); end;    
+    N = length(str);
+    for i=1:N,
+      tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle');
+      [ptc wx wy] = draw_box(tx, x(i), y(i));
+      wd(i,:) = [wx wy];
+      delete(tx);
+      tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle');      
+      temp = [temp; tx ptc];
+    end;
+     
+  otherwise,
+
+end;  
+
+if nargout>0, t = temp; end;
+
+
+function [ptc, wx, wy] = draw_box(tx, x, y)
+% Draws a box around a tex object
+      sz = get(tx,'Extent');
+      wy = 2/3*sz(4);
+      wx = max(2/3*sz(3), wy);
+      ptc = patch([x-wx x+wx x+wx x-wx], [y+wy y+wy y-wy y-wy],'w');
+      set(ptc, 'FaceColor','w');
+
diff --git a/sourcecodes/bnt-master/GraphViz/Old/graphToDot.m b/sourcecodes/bnt-master/GraphViz/Old/graphToDot.m
new file mode 100644
index 00000000..1f3d232e
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/graphToDot.m
@@ -0,0 +1,84 @@
+function graphToDot(adj, varargin)
+% GRAPHTODOT Makes a GraphViz (AT&T) ile representing  an adjacency matrix
+% function graphToDot(adj, ...)
+% Optional arguments should be passed as name/value pairs [default]
+%
+% 'filename' - if omitted, writes to 'tmp.dot'
+% 'arc_label' - arc_label{i,j} is a string attached to the i-j arc [""]
+% 'node_label' - node_label{i} is a string attached to the node i ["i"]
+% 'width'     - width in inches [10]
+% 'height'    - height in inches [10]
+% 'leftright' - 1 means layout left-to-right, 0 means top-to-bottom [0]
+% 'directed'  - 1 means use directed arcs, 0 means undirected [1]
+%
+% For details on graphviz, See http://www.research.att.com/sw/tools/graphviz
+%
+% See also dot_to_graph and draw_dot
+%
+% First version written by Kevin Murphy 2002.
+% Modified by Leon Peshkin, Jan 2004.
+                   
+node_label = [];   arc_label = [];   % set default args
+width = 10;        height = 10;
+leftright = 0;     directed = 1;     filename = 'tmp.dot';
+           
+for i = 1:2:nargin-1                    % get optional args
+    switch varargin{i}
+        case 'filename', filename = varargin{i+1};
+        case 'node_label', node_label = varargin{i+1};
+        case 'arc_label', arc_label = varargin{i+1};
+        case 'width', width = varargin{i+1};
+        case 'height', height = varargin{i+1};
+        case 'leftright', leftright = varargin{i+1};
+        case 'directed', directed = varargin{i+1};
+    end
+end
+
+fid = fopen(filename, 'w');
+if directed
+    fprintf(fid, 'digraph G {\n');
+    arctxt = '->'; 
+    if isempty(arc_label)
+        labeltxt = '';
+    else
+        labeltxt = '[label="%s"]';
+    end
+else
+    fprintf(fid, 'graph G {\n');
+    arctxt = '--'; 
+    if isempty(arc_label)
+        labeltxt = '[dir=none]';
+    else
+        labeltext = '[label="%s",dir=none]';
+    end
+end
+edgeformat = strcat(['%d ',arctxt,' %d ',labeltxt,';\n']);
+fprintf(fid, 'center = 1;\n');
+fprintf(fid, 'size=\"%d,%d\";\n', width, height);
+if leftright
+    fprintf(fid, 'rankdir=LR;\n');
+end
+Nnds = length(adj);
+for node = 1:Nnds               %  process nodes 
+    if isempty(node_label)
+        fprintf(fid, '%d;\n', node);
+    else
+        fprintf(fid, '%d [ label = "%s" ];\n', node,
+node_label{node});
+    end
+end
+for node1 = 1:Nnds   % process edges
+    if directed
+        arcs = find(adj(node1,:));         % children(adj, node);
+    else
+        arcs = find(adj(node1,node1+1:Nnds)); % remove duplicate arcs
+    end
+    for node2 = arcs
+        fprintf(fid, edgeformat, node1, node2);
+    end
+end
+fprintf(fid, '}');
+fclose(fid); 
+
+
+
diff --git a/sourcecodes/bnt-master/GraphViz/Old/pre_pesha_graph_to_dot.m b/sourcecodes/bnt-master/GraphViz/Old/pre_pesha_graph_to_dot.m
new file mode 100644
index 00000000..49f226f6
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/Old/pre_pesha_graph_to_dot.m
@@ -0,0 +1,166 @@
+function graph_to_dot(G, varargin)
+% DAG_TO_DOT Make a file representing the directed graph in dotty format.
+% dag_to_dot(G, ...)
+%
+% Optional arguments should be passed as name/value pairs [default]
+%
+% 'filename' - if omitted, we write to 'tmp.dot', convert this to 'tmp.ps',
+%              and then call ghostview automatically 
+% 'arc_label' - arc_label{i,j} is a string attached to the i->j arc. [""]
+% 'node_label' - node_label{i} is a string attached to node i. ["i"]
+% 'width'      - width in inches [10]
+% 'height'     - height in inches [10]
+% 'leftright'  - 1 means layout left-to-right, 0 means top-to-bottom [0]
+% 'directed'  - 1 means use directed arcs, 0 means undirected [1]
+%
+% For details on dotty, See http://www.research.att.com/sw/tools/graphviz
+%
+% Example:
+% G = rand(5,5);
+% names = cell(5,5);
+% names{1,2} = 'arc 1-2';
+% graph_to_dot(G, 'arc_label', names)
+% or graph_to_dot(G, 'arc_label', 'numbers') % prints value of G(i,j) on i->j arc 
+
+% Kevin Murphy, 1998
+
+% set default args
+filename = [];
+node_label = [];
+arc_label = [];
+width = 10;
+height = 10;
+leftright = 0;
+directed = 1;
+% get optional args
+args = varargin;
+for i=1:2:length(args)
+  switch args{i}
+   case 'filename', filename = args{i+1};
+   case 'node_label', node_label = args{i+1};
+   case 'arc_label', arc_label = args{i+1};
+   case 'width', width = args{i+1};
+   case 'height', height = args{i+1};
+   case 'leftright', leftright = args{i+1};
+   case 'directed', directed = args{i+1};
+  end
+end
+
+if isstr(arc_label) & strcmp(arc_label, 'numbers')
+  N = length(G);
+  arc_label = cell(N,N);
+  for i=1:N
+    for j=1:N
+      arc_label{i,j} = sprintf('%4.2f', G(i,j));
+    end
+  end
+end
+
+if isempty(filename)
+  make_file(G, 'tmp.dot', node_label, arc_label, width, height, leftright, directed);
+  if isunix
+    !dot -Tps tmp.dot -o tmp.ps
+
+    !gs tmp.ps &
+  else
+    dos('dot -Tps tmp.dot -o tmp.ps');
+    dos('gsview32 tmp.ps &');
+  end
+else
+  
+  
+  make_file(G, filename, node_label, arc_label, width, height, leftright, directed);
+end
+
+
+%%%%%%
+
+function make_file(G, filename, node_label, arc_label, width, height, leftright, directed)
+
+n = length(G);
+fid = fopen(filename, 'w');
+if directed
+  fprintf(fid, 'digraph G {\n');
+else
+  fprintf(fid, 'graph G {\n');
+end
+fprintf(fid, 'center = 1;\n');
+fprintf(fid, 'size=\"%d,%d\";\n', width, height);
+if leftright
+  fprintf(fid, 'rankdir=LR;\n');
+end
+for i=1:n
+  if isempty(node_label)
+    fprintf(fid, '%d;\n', i);
+  else
+    fprintf(fid, '%d [ label = "%s" ];\n', i, node_label{i});
+  end
+end
+if directed
+  for i=1:n
+    cs = children(G,i);
+    for j=1:length(cs)
+      c = cs(j);
+      if isempty(arc_label)
+	fprintf(fid, '%d -> %d;\n', i, c);
+      else
+	fprintf(fid, '%d -> %d [label="%s"];\n', i, c, arc_label{i,c});
+      end
+    end
+  end
+else
+  for i=1:n
+    ns = intersect(neighbors(G,i), i+1:n); % remove duplicate arcs
+    for j=1:length(ns)
+      c = ns(j);
+      if isempty(arc_label)
+	fprintf(fid, '%d -- %d [dir=none];\n', i, c);
+      else
+	fprintf(fid, '%d -- %d [label="%s",dir=none];\n', i, c, arc_label{i,c});
+      end
+    end
+  end
+end
+fprintf(fid, '\n}');
+fclose(fid);
+
+
+
+%%%%%%%%%%%%%%%
+
+function cs = children(adj_mat, i, t)
+% CHILDREN Return the indices of a node's children in sorted order
+% c = children(adj_mat, i, t)
+%
+% t is an optional argument: if present, dag is assumed to be a 2-slice DBN
+
+if nargin < 3 
+  cs = find(adj_mat(i,:));
+else
+  if t==1
+    cs = find(adj_mat(i,:));
+  else
+    ss = length(adj_mat)/2;
+    j = i+ss;
+    cs = find(adj_mat(j,:)) + (t-2)*ss;
+  end
+end
+
+%%%%%%%%%%%%
+
+function ps = parents(adj_mat, i)
+% PARENTS Return the list of parents of node i
+% ps = parents(adj_mat, i)
+
+ps = find(adj_mat(:,i))';
+
+%%%%%%%%%%%%%
+
+function ns = neighbors(adj_mat, i)
+% NEIGHBORS Find the parents and children of a node in a graph.
+% ns = neighbors(adj_mat, i)
+
+ns = union(children(adj_mat, i), parents(adj_mat, i));
+
+
+