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