function disp_mcomposites2(emesh, panels, m_ref, m_res, varargin)
% disp_mcomposites(emesh, m_ref, m_res, panels, conn, m_res_mesh, m_res_mesh_idx)
% displays composites of reference (m_ref) with others (m_res)
% emesh is standard emesh struct
% m_ref and m_res are indices for emesh
% m_ref must have size of 1, m_res is an array
% m_ref can be also logical, then a synthetic mesh is constructed
% conn is optional, if given will query the gene symbols, can be empty
% m_res_mesh contains the result meshes if emesh should not be used
% m_res_mesh_idx contains the indices of result meshes in case there is no
%               1:1 correspondence between m_res and m_res_mesh

    conn = [];
    % Initialize counter
    counter = 1;
    sym_all = [];
    mesh_src = [];

    if ~isempty(varargin)
        
        i = 1;
        while i <= length(varargin),
            switch(varargin{i}),
                case 'db'
                    i = i+1;
                    conn = varargin{i};
                case 'source'
                    i = i+1;
                    mesh_src = varargin{i};
                case 'symbols'
                    i = i+1;
                    sym_all = varargin{i};
                    if length(sym_all) == 1,
                        sym_name = sym_all;
                        sym_idx = 1:length(sym_all);
                    else
                        sym_name = sym_all{1};
                        sym_idx = sym_all{2};
                    end
                otherwise
                    error('Argument %s not known', varargin{i});
            end
            i = i+1;
        end
    end

    m_resfiles = cell(length(m_res), 1);
    
    % If m_res is a vector, assume it's an index for emesh entries
    if isvector(m_res)
       if isempty(mesh_src),
           for i=1:length(m_res),
               % Test if we query DB for symbols
               if isempty(conn),
                   m_resfiles{i} = emesh.files{m_res(i)};
               elseif isempty(sym_all)
                   fn = emesh.files{m_res(i)};
                   sym = pg_query(conn,0, pg_insitus('symbol'),myinsitu2fn(fn));
                   m_resfiles{i} = sprintf('%s (%s)', sym{1}, fn);
               end
           end
           resmesh = emesh.stain(:, m_res);
       else
           resmesh = mesh_src(:, m_res);
           sym_idx = sym_idx(m_res);
       end
    else
       resmesh = m_res; 
    end
    
    if ~isempty(sym_all),
        if length(sym_idx) ~= size(resmesh, 2),
            error('Symbol idx has different size');
        end
        for i=1:length(m_res),
            if isempty(m_resfiles{i}),
                m_resfiles{i} = sprintf('%s', sym_name{sym_idx(i)});
            else
                m_resfiles{i} = sprintf('%s (%s)', sym_name{sym_idx(i)}, m_resfiles{i});
            end
        end
    end
    
   
   if panels == 1,
       ysize = 0;
   elseif panels == 2,
       ysize = 200;
   elseif panels == 3,
       ysize = 400;
   else
       error('panels=%d but should be 1, 2 or 3', panels);
   end

   if isempty(m_ref),
       refstain = zeros(size(emesh.stain(:,1),1), 1);
       refstain(1:end) = 255;
   elseif islogical(m_ref),
       refstain = zeros(size(emesh.stain(:,1),1), 1);
       refstain(m_ref == 0) = 255;
   else
       refstain = emesh.stain(:, m_ref);
   end
   
   %  Create and then hide the GUI as it is being constructed.
   % minimum [360,500,600,300] w/o list
   f = figure('Visible','off','Position',[360,500,700,260+ysize]);
 
   %  Construct the components
   hforw = uicontrol('Style','pushbutton','String','Forward >',...
          'Position',[380,15,70,25],...
          'Callback',{@forwardbutton_Callback});
   hback = uicontrol('Style','pushbutton','String','<    Back',...
          'Position',[50,15,70,25],...
          'Callback',{@backbutton_Callback});
   htext = uicontrol('Style','text','String', m_resfiles{counter},...
          'Position',[500,15,120,15]);
   hlist = uicontrol('Style', 'listbox', 'String', m_resfiles,...
          'Min', 1, 'Max', 1, 'Position',[500, 50, 150, 200+ysize],...
          'Callback',{@listbox_Callback});
   hp = uipanel('Units','Pixels','Position',[50,50,400,200+ysize]); 
   ha = axes('Parent', hp, 'Units','Pixels','Position',[0,0,400,200+ysize]);
%   align([hforw,hback,htext],'Center','None');
      
   % Initialize the GUI.
   %Change units to normalized so components resize automatically.
   set([f,ha,hp,hforw, hback, htext, hlist],...
   'Units','normalized');
   %Create a plot in the axes.
   displaypanels(panels, refstain, resmesh(:, counter), emesh.p_scale, emesh.t);
   % Assign the GUI a name to appear in the window title.
   set(f,'Name','Composite insitus')
   % Move the GUI to the center of the screen.
   movegui(f,'center')
   % Make the GUI visible.
   set(f,'Visible','on');
 
   %  Callbacks for simple_gui. These callbacks automatically have 
   %  access to component handles and initialized data because
   %  they are nested at a lower level.
   
   function listbox_Callback(source, eventdata)
         % Determine the selected data set.
         str = get(source, 'String');
         val = get(source,'Value');
         % Set current data to the selected data set.
        counter = val;
        set(htext, 'String', m_resfiles{counter});
        displaypanels(panels, refstain, resmesh(:, counter), emesh.p_scale, emesh.t);
   end
   
   % Push button callbacks. Each callback plots current_data in the
   % specified plot type.
 
   function forwardbutton_Callback(source,eventdata) 
   % Display surf plot of the currently selected data.
      if counter < length(m_res),
        counter = counter + 1;
        set(htext, 'String', m_resfiles{counter});
        set(hlist, 'Value', counter);
        displaypanels(panels, refstain, resmesh(:, counter), emesh.p_scale, emesh.t);
      end
   end
 
   function backbutton_Callback(source,eventdata) 
   % Display mesh plot of the currently selected data.
      if counter > 1,
        counter = counter - 1;
        set(htext, 'String', m_resfiles{counter});
        set(hlist, 'Value', counter);
        displaypanels(panels, refstain, resmesh(:, counter), emesh.p_scale, emesh.t);
      end
   end
  
end


function displaypanels(panels, refmesh, compmesh, p_scale,t)
    
    subplot(panels,1,panels); displaydmesh(refmesh, compmesh, p_scale, t);
    if panels > 1,
        subplot(panels,1,panels-1); displaycmesh(compmesh, p_scale, t, 1);
        if panels > 2,
            subplot(panels,1,panels-2); displaycmesh(refmesh, p_scale, t, 0);
        end
    end

end

function displaydmesh(refmesh, compmesh, p_scale,t)

    axis ij; axis off;
    hold on;
    
    cmesh = zeros(length(refmesh), 3);
    cmesh(:,1) = (255 - refmesh) ./ 255;
    cmesh(:,2) = (255 - compmesh) ./ 255;
    
    for i = 1:size(t,1)

        roic = fix(p_scale(t(i,:),1)');
        roir = fix(p_scale(t(i,:),2)');
        fill(roic,roir,cmesh(i,:), 'EdgeColor', cmesh(i,:));
    end;

end


function displaycmesh(stain, p_scale, t, green)

    axis ij; axis off;
    hold on;

    cmesh = zeros(length(stain), 3);
    if green == 0,
        cmesh(:,1) = (255 - stain) ./ 255;
    else
        cmesh(:,2) = (255 - stain) ./ 255;
    end
    
    for i = 1:size(t,1)
        roic = fix(p_scale(t(i,:),1)');
        roir = fix(p_scale(t(i,:),2)');
        fill(roic,roir,cmesh(i,:),'EdgeColor', cmesh(i,:));
    end;
    hold off;
end