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, 310 insertions, 0 deletions

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');
+