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A patch for graphViz4Matlab toolbox

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A patch for graphViz4Matlab toolbox

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This patch enables automatic change in thickness and also color of the graph edges

graphViz4Matlab
classdef graphViz4Matlab < handle
    % Visualize a graph in a Matlab figure window by specifying an
    % adjacency matrix and optionally node labels, descriptions, colors and the
    % the layout algorithm. The best layout algorithms require that graphViz be
    % installed, available free at <http://www.graphviz.org>.
    %
    % Reza Farrahi Moghaddam
    % Synchromedia Lab, ETS, University of Quebec
	% Montreal (Quebec), Canada
    % Last Patched: January 23, 2013
    % For the copyright and other information, see below.
	%
    % Matthew Dunham
    % University of British Columbia
    % Last Updated: April 24, 2010
    % Requires Matlab version 2008a or newer.
    %
    % Syntax (see more examples below):
    % graphViz4Matlab('-adjMat',adj,'-nodeLabels',labels,'-nodeColors',colors);
    %
    % Self loops are removed and not represented on the graph.
    %
    % Once the graph is displayed, there are several operations you can perform
    % with the mouse.
    % (1) Move a single node around.
    % (2) Draw a mouse box around several nodes and move them all together.
    % (3) Enter a description for a node by double clicking it.
    % (4) Shade the node by right clicking it
    % (5) Display a node's properties on the console by shift clicking it.
    % (6) Increase or decrease the font size
    % (7) Increase or decrease the node size
    % (8) Tighten the axes and relax the square aspect ratio.
    % (9) Ask the current layout algorithm to layout the nodes as though the
    %     arrows were pointing the other way. This only affects some of the
    %     layouts.
    % (10) Change the layout algorithm and refresh the graph
    %
    % Additionally, any operation you could do with a regular Matlab figure can
    % be done here, e.g. annotating or saving as a pdf.
    %
    % Options are specified via name value pairs in any order.
    % [] denote defaults.
    %
    % '-adjMat'           [example matrix] The adjacency matrix
    %
    % '-layout'            [Gvizlayout if graphViz installed, else Gridlayout]
    %                      A layout object, i.e. Gvizlayout | Gridlayout | Circlelayout
    %                     (See knownLayouts Property)
    %
    % '-nodeLabels'        ['1':'n'] A cell array of labels for the nodes
    %
    % '-nodeDescriptions'  [{}] Longer descriptions for the nodes, displayed when
    %                      double clicking on a node.
    %
    % '-nodeColors'        ['c'] A cell array or n-by-3 matrix specifying colors
    %                      for the nodes. If fewer colors than nodes are specified,
    %                      the specified colors are reused and cycled through.
    %
    % '-undirected'        [false] If true, no arrows are displayed.
    %
    % '-edgeColors'        [] An n-by-3 cell array listing
    %                         {fromName,toName,color} for each row. You can
    %                         list only the n < numel(edges) edges you want to
    %                         color. If you do not label the nodes, graphViz4Matlab
    %                         uses '1','2','3', etc, in which case use these.
    %                         You can specify the text 'all' in place of toName,
    %                         to mean all nodes, i.e. {fromName,'all',color}
    %
    %
    % '-splitLabels'       [true] If true, long node labels are split into
    %                       several rows
    %
    % '-doubleClickFn'     (by default, double clicking a node brings up
    %                      an edit box for the node's description, but you
    %                      can pass in a custom function handle. The function
    %                      gets passed the node's label.
    % Examples:
    %
    % adj = rand(5,5) > 0.8;
    % labels = {'First','Second','Third','Fourth','Fifth'};
    % colors = {'g','b'};    % will cycle through
    % s = graphViz4Matlab('-adjMat',adj,'-nodeLabels',labels,'-nodeColors',colors);
    % freeze(s); % convert to an image
    %
    % If you are only specifying an adjacency matrix, you can omit the
    % '-adjMat' name as in graphViz4Matlab(adj).
    %
    % Calling graphViz4Matlab without any parameters displays an example graph.
    %
    
    
    properties(GetAccess = 'public', SetAccess = 'private')
        % read only
        path         = addpath(genpath(fileparts(which(mfilename))));  % automatically adds subdirectories to path
        graphVizPath = setupPath();
        nnodes       = 0;      % The number of nodes
        nedges       = 0;      % The number of edges
        currentLayout= [];     % The current layout object
        layouts      = [];     % List currently added layout objects
        adjMatrix    = [];     % The adjacency matrix
        isvisible    = false;  % True iff the graph is being displayed
        nodeArray    = [];     % The nodes
        edgeArray    = [];     % The edges
        fig          = [];     % The main window
        ax           = [];     % The main axes
        doubleClickFn = [];    % function to execute when a user double clicks on a node, (must be a function handle that takes in the node name
        selectedNode = [];     % The selected node, if any
        minNodeSize  = [];     % A minimum size for the nodes
        maxNodeSize  = [];     % A maximum size for the nodes
        EdgeSize     = [];     %%%%% Reza
        ArrowSize    = [];     %%%%% Reza
        undirected   = false;  % If undirected, arrows are not displayed
        flipped      = false;  % If true, layout is done as though edge directions were reversed.
        % (does not affect the logical layout).
        knownLayouts = {Gvizlayout  ,...   % add your own layout here or use
            Treelayout  ,...   % the addLayout() method
            Radiallayout,...
            Circularlayout,...
            Springlayout,...
            Circlelayout,...
            Gridlayout  ,...
            Randlayout  };
        defaultEdgeColor  = [0,0,0];%[20,43,140]/255;
        edgeColors;
        square      = true;  % amounts to a the call "axis square"
        splitLabels = true;
    end
    
    properties(GetAccess = 'private', SetAccess = 'private')
        % These values store the initial values not the current ones.
        nodeLabels          = {};
        nodeCounters        = {}; %%%%% Reza
        nodeDescriptions    = {};
        nodeColors          = {};
    end
    
    properties(GetAccess = 'protected',SetAccess = 'protected')
        toolbar;                    % The button toolbar
        layoutButtons;              % The layout buttons
        fontSize;                   % last calculated optimal font size
        selectedFontSize;           %
        
        previousMouseLocation;      % last mouse location relative to the axes
        groupSelectionMode = 0;     % current stage in a group selection task
        groupSelectedNodes;         % selected nodes in a group selection
        groupSelectedDims;          % size of enclosing rectangle of selected nodes
        groupSelectedRect;          % a bounding rectangle for the selected nodes
    end
    
    methods
        
        function obj = graphViz4Matlab(varargin)
            % graphViz4Matlab constructor
            if(~exist('processArgs','file')), error('Requires processArgs() function');            end
            obj.addKnownLayouts();
            obj.processInputs(varargin{:})
            obj.addNodes();
            obj.addEdges();
            obj.draw();
        end
        
        function draw(obj)
            % Draw the graph
            if(obj.isvisible)
                obj.erase()
            end
            obj.createWindow();
            obj.calculateMinMaxNodeSize();
            obj.calculateEdgeSize();
            obj.layoutNodes();
            obj.displayGraph();
            obj.isvisible = true;
            obj.paperCrop();
        end
        
        function fig = freeze(obj)
            % Freeze the current image into a regular Matlab figure
            figure(obj.fig);
            print tmp.png -dpng -r300
            fig = figure;
            image(imread('tmp.png'));
            axis off;
            delete tmp.png;
            close(obj.fig);
        end
        
        function redraw(obj)
            % Redraw the graph. (You could also call draw() again but then the
            % window is recreated as well and it doesn't look as nice).
            if(~obj.isvisible)
                obj.draw();
                return;
            end
            cla(obj.ax);
            obj.clearGroupSelection();
            obj.calculateMinMaxNodeSize();
            obj.layoutNodes();
            obj.displayGraph();
        end
        
        function flip(obj,varargin)
            % Have the layout algorithms layout the graph as though the arrows
            % were pointing in the opposite direction. The node connectivity
            % remains the same and if node one pointed to node 2 before, it
            % still does after. This is useful for tree layout, for example to
            % turn the tree on its head. Calling it twice flips it back.
            obj.flipped = ~obj.flipped;
            if(obj.isvisible)
                obj.redraw();
            end
        end
        
        function erase(obj)
            % Erase the graph but maintain the state so that it can be redrawn.
            if(obj.isvisible)
                obj.clearGroupSelection();
                delete(obj.fig);
                obj.isvisible = false;
                
            end
        end
        
        function nodeSelected(obj,node)
            % This function is called by nodes when they are selected by the
            % mouse. It should not be called manually.
            if(obj.groupSelectionMode == 1)
                obj.groupSelectionStage1();
                return;
            end
            if(~isempty(obj.selectedNode))
                node.deselect();
                obj.selectedNode = [];
                return;
            end
            switch get(obj.fig,'SelectionType')
                case 'normal'
                    obj.singleClick(node);
                case 'open'
                    obj.doubleClick(node);
                case 'alt'
                    obj.rightClick(node);
                otherwise
                    obj.shiftClick(node);
            end
        end
        
        function addLayout(obj,layout)
            % Let the graph know about a new layout you have created so that it
            % will be available via a toolbar button. The layout object must be
            % a descendant of the Abstractlayout class. This method does not have
            % to be called for existing layouts, nor does it need to be called
            % if you passed the new layout to the constructor or to the
            % setLayout() method. It will not add two layouts with the same
            % name property.
            if(~ismember(layout.name,fieldnames(obj.layouts)))
                if(layout.isavailable())
                    obj.layouts.(layout.name) = layout;
                    if(obj.isvisible)
                        obj.addButtons();
                    end
                else
                    warning('graphViz4Matlab:layout','This layout is not available');
                end
            end
        end
        
        function setLayout(obj,layout)
            % Set a new layout algorithm and refresh the graph.
            if(layout.isavailable())
                obj.addLayout(layout);
                obj.currentLayout = obj.layouts.(layout.name);
                obj.redraw();
            else
                warning('graphViz4Matlab:layout','Sorry, this layout is not available');
            end
        end
        
        function squareAxes(obj,varargin)
            % Toggle the axes from square to normal and vice versa.
            obj.clearGroupSelection();
            if(obj.square)
                axis(obj.ax,'normal');
                obj.square = false;
            else
                axis(obj.ax,'square');
                obj.square = true;
            end
            
        end
        
        function tightenAxes(obj,varargin)
            % Tighten the axes as much as possible.
            obj.clearGroupSelection();
            xpos = vertcat(obj.nodeArray.xpos);
            ypos = vertcat(obj.nodeArray.ypos);
            r = obj.nodeArray(1).width/2;
            axis(obj.ax,[min(xpos)-r,max(xpos)+r,min(ypos)-r,max(ypos)+r]);
            axis normal;
        end
        
        
        
        
    end % end of public methods
    
    
    methods(Access = 'protected')
        
        function addKnownLayouts(obj)
            % Add all of the known layouts
            obj.layouts = struct;
            for i=1:numel(obj.knownLayouts)
                layout = obj.knownLayouts{i};
                if(layout.isavailable())
                    obj.layouts.(layout.name) = layout;
                end
            end
        end
        
        function processInputs(obj,varargin)
            % Process the inputs and perform error checking
            labels = {'adj', 'adjMatrix', 'adjMat', 'layout', 'nodeLabels', 'nodeDescriptions', 'nodeColors', 'undirected', 'edgeColors', 'splitLabels', 'doubleClickFn'};
            for i=1:numel(varargin)
                arg = varargin{i};
                if ~ischar(arg), continue; end
                for j = 1:numel(labels)
                    if strcmpi(arg, labels{i});
                        varargin{i} = ['-', arg];
                    end
                    if strcmpi(arg, '-adj') || strcmpi(arg, '-adjMatrix')
                        varargin{i} = '-adjMat';
                    end
                end
            end
            
            [adjMatrix, currentLayout, nodeLabels, nodeDescriptions, nodeColors,obj.undirected,obj.edgeColors,obj.splitLabels,obj.doubleClickFn] = processArgs(varargin,...
                '-adjMat'               , []     ,...
                '-layout'               , []     ,...
                '-nodeLabels'           , {}     ,...
                '-nodeDescriptions'     , {}     ,...
                '-nodeColors'           , {}     ,...
                '-undirected'           , false  ,...
                '-edgeColors'           , []     ,...
                '-splitLabels'          , true   ,...
                '-doubleClickFn'        , []     );
            
            
            if(~isempty(currentLayout) && ~isavailable(currentLayout))
                currentLayout = [];
            end
            if(isempty(adjMatrix))
                adjMatrix = [0 0 0 0; 1 0 0 0; 1 1 0 0; 1 1 1 0]; % example graph
            end
            
            if(isempty(currentLayout))
                fields = fieldnames(obj.layouts);
                currentLayout = obj.layouts.(fields{1});
            else
                obj.addLayout(currentLayout);
            end
            obj.nnodes = size(adjMatrix,1);
            obj.adjMatrix = adjMatrix;
            if(isempty(nodeDescriptions))
                nodeDescriptions = repmat({'Enter a description here...'},size(adjMatrix,1),1);
            end
            obj.nodeDescriptions = nodeDescriptions;
            obj.nodeColors = nodeColors;
            
            if(isempty(nodeLabels))
                nodeLabels = cellfun(@(x)num2str(x),mat2cell(1:obj.nnodes,1,ones(1,obj.nnodes)),'UniformOutput',false);
            end
            nodeCounters = cellfun(@(x)num2str(x),mat2cell(1:obj.nnodes,1,ones(1,obj.nnodes)),'UniformOutput',false); %%%%% Reza
            
            obj.nodeLabels = nodeLabels;
            obj.nodeCounters = nodeCounters;
            if(~isequal(numel(obj.nodeLabels),size(adjMatrix,1),size(adjMatrix,2)))
                error('graphViz4Matlab:dimMismatch','The number of labels must match the dimensions of adjmatrix.');
            end
            obj.currentLayout = currentLayout;
        end
        
        function createWindow(obj)
            % Create the main window
            obj.fig = figure(floor(1000*rand) + 1000);
            set(obj.fig,'Name','graphViz4Matlab',...
                'NumberTitle' ,'off',...
                'Color','w'   ,'Toolbar','none');
            obj.createAxes();
            ssize = get(0,'ScreenSize');
            pos = [ssize(3)/2,50,-20+ssize(3)/2,ssize(4)-200];
            set(obj.fig,'Position',pos);
            obj.setCallbacks();
            obj.addButtons();
            
        end
        
        function createAxes(obj)
            % Create the axes upon which the graph will be displayed.
            obj.ax = axes('Parent',obj.fig, 'box', 'off', 'Visible', 'off', 'UserData','main'); %%%%% Reza, box -> off, Visible -> off
            outerpos = get(obj.ax,'OuterPosition');
            axpos = outerpos;
            axpos(4) = 0.90;
            axpos(2) = 0.03;
            axis manual
            if(obj.square)
                axis square
            end
            set(obj.ax,'Position',axpos,'XTick',[],'YTick',[],'LineWidth',0.5);
            set(obj.ax,'ButtonDownFcn',@obj.axPressed);
        end
        
        
        
        function setCallbacks(obj)
            % Set the callback functions for the figure, i.e. functions that
            % will be called when the user performs various actions.
            set(obj.fig,'ResizeFcn'             ,@obj.windowResized);
            set(obj.fig,'WindowButtonMotionFcn' ,@obj.mouseMoved);
            set(obj.fig,'WindowButtonUpFcn'     ,@obj.buttonUp);
            set(obj.fig,'DeleteFcn'             ,@obj.deleted);
        end
        
        function addNodes(obj)
            % Add all of the nodes to the graph structure, but don't display
            % them yet.
            obj.nodeArray = [];
            for i=1:obj.nnodes
                newnode = graphViz4MatlabNode(obj.nodeLabels{i});
                newnode.counter = obj.nodeCounters{i}; %%%%% Reza
                newnode.containingGraph = obj;
                newnode.showFullLabel = ~obj.splitLabels;
                obj.nodeArray = [obj.nodeArray newnode];
            end
            obj.addNodeDescriptions(obj.nodeDescriptions);
            obj.addNodeColors(obj.nodeColors);
        end
        
        function addNodeDescriptions(obj,nodeDescriptions)
            % Add any descriptions to the newly created nodes.
            if(~isempty(nodeDescriptions))
                if(numel(nodeDescriptions) == 1)
                    nodeDescriptions = repmat(nodeDescriptions,obj.nnodes,1);
                end
                for i=1:obj.nnodes
                    obj.nodeArray(i).description = nodeDescriptions{i};
                end
            end
        end
        
        function addNodeColors(obj,nodeColors)
            % Shade the nodes according to the specified colors. If too few
            % colors are specified, they are cycled through.
            if(~isempty(nodeColors))
                if(~iscell(nodeColors))
                    nodeColors = mat2cell(nodeColors,ones(1,size(nodeColors,1)),size(nodeColors,2));
                end
                if(size(nodeColors,2) > size(nodeColors,1))
                    nodeColors = nodeColors';
                end
                if(numel(nodeColors) < obj.nnodes)
                    nodeColors = repmat(nodeColors,ceil(obj.nnodes/numel(nodeColors)),1);
                    nodeColors = nodeColors(1:obj.nnodes);
                end
                for i=1:obj.nnodes
                    obj.nodeArray(i).shade(nodeColors{i});
                end
                obj.nodeColors = nodeColors;
            end
        end
        
        function addEdges(obj)
            % Add all of the edges to the graph structure, but don't display
            % them yet.
            if(any(diag(obj.adjMatrix)))
                fprintf('\nRemoving Self Loops\n');
                obj.adjMatrix = obj.adjMatrix - diag(diag(obj.adjMatrix));
            end
            obj.edgeArray = struct('from',[],'to',[],'arrow',[], 'adjWeight', []); %%%%% Reza
            counter = 1;
            for i=1:obj.nnodes
                for j=1:obj.nnodes
                    if(obj.adjMatrix(i,j))
                        obj.edgeArray(counter) = struct('from',obj.nodeArray(i),'to',obj.nodeArray(j),'arrow',-1, 'adjWeight', []); %%%%% Reza
                        obj.nodeArray(i).outedges = [obj.nodeArray(i).outedges,counter];
                        obj.nodeArray(j).inedges =  [obj.nodeArray(j).inedges,counter];
                        counter = counter + 1;
                    end
                end
            end
            obj.nedges = counter -1;
        end
        
        function calculateMinMaxNodeSize(obj)
            % calculates the maximum and minimum node sizes in data units
            SCREEN_PROPORTION_MAX = 1/10 * 2 / sqrt(obj.nnodes); %%%%% Reza
            SCREEN_PROPORTION_MIN = 1/35 * 2 / sqrt(obj.nnodes); %%%%% Reza
            units = get(0,'Units');
            set(0,'Units','pixels');
            screensize = get(0,'ScreenSize');
            set(0,'Units',units);
            axunits = get(obj.ax,'Units');
            set(obj.ax,'Units','pixels');
            axsize = get(obj.ax,'Position');
            set(obj.ax,'Units',axunits);
            if(screensize(3) < screensize(4))
                dataUnitsPerPixel = abs(diff(xlim))/axsize(3);
                obj.minNodeSize = (SCREEN_PROPORTION_MIN*screensize(3))*dataUnitsPerPixel;
                obj.maxNodeSize = (SCREEN_PROPORTION_MAX*screensize(3))*dataUnitsPerPixel;
                obj.ArrowSize = obj.maxNodeSize / 1.5; %%%%% Reza
            else
                dataUnitsPerPixel = abs(diff(ylim))/axsize(4);
                obj.minNodeSize = (SCREEN_PROPORTION_MIN*screensize(4))*dataUnitsPerPixel;
                obj.maxNodeSize = (SCREEN_PROPORTION_MAX*screensize(4))*dataUnitsPerPixel;
                obj.ArrowSize = obj.maxNodeSize / 1.5; %%%%% Reza
            end
        end
        
        function calculateEdgeSize(obj)
            %%%%% Reza calculates the maximum and minimum node sizes in data units
            obj.EdgeSize =  max([1.75, 100 / obj.nnodes]);
        end        
        
        
        function layoutNodes(obj)
            % Layout the nodes and edges according to the current layout
            % algorithm.
            if(obj.flipped)
                adj = obj.adjMatrix';
            else
                adj = obj.adjMatrix;
            end
            obj.currentLayout.dolayout(adj,obj.ax,obj.maxNodeSize);
            nodesize = obj.currentLayout.nodeSize();
            locs = obj.currentLayout.centers();
            for i=1:obj.nnodes
                node = obj.nodeArray(i);
                node.resize(nodesize);
                node.move(locs(i,1),locs(i,2));
            end
        end
        
        function displayGraph(obj)
            % Display all of the nodes and edges.
            cla(obj.ax);
            obj.setFontSize();
            displayEdges(obj); %%%%% Reza: moved above nodes to keep nodes visible.            
            for i=1:obj.nnodes
                node = obj.nodeArray(i);
                node.fontSize = obj.fontSize;
                node.draw(obj.ax);
            end

        end
        
        function displayEdges(obj,indices)
            % Display or refresh the specified edges. If none specified, all
            % are refreshed. Currently only works with round nodes.
            figure(obj.fig);
            if(nargin < 2)
                indices = 1:obj.nedges;
            else
                indices = unique(indices);
            end
            for i=1:numel(indices)
                edge = obj.edgeArray(indices(i));
                edge.adjWeight = 0.5 * (obj.adjMatrix(str2num(edge.from.counter), str2num(edge.to.counter)) + obj.adjMatrix(str2num(edge.to.counter), str2num(edge.from.counter))); %%%%% Reza
                [X,Y,Xarrow,Yarrow] = obj.calcPositions(edge);
                if(ishandle(edge.arrow))
                    delete(edge.arrow)
                end
                hold on;
                edgeColor = 1 - ((1 - obj.defaultEdgeColor) * (edge.adjWeight) ^ 5);
                if ~isempty(obj.edgeColors)
                    candidates = obj.edgeColors(findString(edge.from.label,obj.edgeColors(:,1)),:);
                    if size(candidates,1)==1 && strcmpi(candidates(1,2),'all')
                        edgeColor = candidates{1,3};
                    else
                        edgeCol = candidates(findString(edge.to.label,candidates(:,2)),3);
                        if ~isempty(edgeCol); edgeColor = edgeCol{1}; end
                    end
                end
                edge.arrow = plot(X,Y,'LineWidth', obj.EdgeSize * edge.adjWeight,'HitTest','off','Color',edgeColor); %%%%% Reza
                if(~obj.undirected)
                    arrowHead = obj.displayArrowHead(X,Y,Xarrow,Yarrow,edgeColor);
                    edge.arrow = [edge.arrow arrowHead];
                end
                hold off;
                obj.edgeArray(indices(i)) = edge;
            end
        end
        
        function arrowHead = displayArrowHead(obj,X,Y,Xarrow,Yarrow,arrowColor)   %#ok
            % Displays the arrow head given the appropriate coordinates
            % calculated via the calcPositions() function.
            
            arrowHead = patch('Faces'      ,[1,2,3]                                             ,...
                'Vertices'  ,[Xarrow(1) Yarrow(1); Xarrow(2) Yarrow(2) ;X(2) Y(2)],...
                'FaceColor' ,arrowColor);
        end
        
        function [X,Y,Xarrow,Yarrow] = calcPositions(obj,edge)
            % Helper function for displayEdges() - calculates edge and arrow
            % start and end positions in data units.
            X = [edge.from.xpos edge.to.xpos];
            Y = [edge.from.ypos edge.to.ypos];
            ratio = (Y(2) - Y(1))/(X(2)-X(1));
            if(isinf(ratio))
                ratio = realmax;
            end
            % dx:  x-distance from node1 center to perimeter in direction of node2
            % dy:  y-distance from node1 center to perimeter in direction of node2
            % ddx: x-distance from node1 perimeter to base of arrow head
            % ddy: y-distance from node1 perimeter to base of arrow head
            % dpx: x-offset away from edge in perpendicular direction, for arrow head
            % dpy: y-offset away from edge in perpendicular direction, for arrow head
            
            arrowSize = obj.ArrowSize; %%%%% Reza, obj.maxNodeSize/10;
            [dx,dy] = pol2cart(atan(ratio),edge.from.width/2);
            [ddx,ddy] = pol2cart(atan(ratio),arrowSize);
            ratio = 1/ratio; % now work out perpendicular directions.
            if(isinf(ratio))
                ratio = realmax;
            end
            [dpx dpy] = pol2cart(atan(ratio),arrowSize/2);
            ddx = abs(ddx); ddy = abs(ddy); dpx = abs(dpx); dpy = abs(dpy);
            dx = abs(dx); dy = abs(dy);
            if(X(1) < X(2))
                X(1) = X(1) + dx; X(2) = X(2) - dx;
            else
                X(1) = X(1) - dx; X(2) = X(2) + dx;
            end
            if(Y(1) < Y(2))
                Y(1) = Y(1) + dy; Y(2) = Y(2) - dy;
            else
                Y(1) = Y(1) - dy; Y(2) = Y(2) + dy;
            end
            if(X(1) <= X(2) && Y(1) <= Y(2))
                Xarrow(1) = X(2) - ddx - dpx; Xarrow(2) = X(2) - ddx + dpx;
                Yarrow(1) = Y(2) - ddy + dpy; Yarrow(2) = Y(2) - ddy - dpy;
            elseif(X(1) <= X(2) && Y(1) >= Y(2))
                Xarrow(1) = X(2) - ddx - dpx; Xarrow(2) = X(2) - ddx + dpx;
                Yarrow(1) = Y(2) + ddy - dpy; Yarrow(2) = Y(2) + ddy + dpy;
            elseif(X(1) >= X(2) && Y(1) <= Y(2))
                Xarrow(1) = X(2) + ddx - dpx; Xarrow(2) = X(2) + ddx + dpx;
                Yarrow(1) = Y(2) - ddy - dpy; Yarrow(2) = Y(2) - ddy + dpy;
            else % (X(1) >= (X(2) && Y(1) >= Y(2))
                Xarrow(1) = X(2) + ddx - dpx; Xarrow(2) = X(2) + ddx + dpx;
                Yarrow(1) = Y(2) + ddy + dpy; Yarrow(2) = Y(2) + ddy - dpy;
            end
        end
        
        function addButtons(obj)
            % Add user interface buttons.
            if(~isempty(obj.toolbar))
                if(ishandle(obj.toolbar))
                    delete(obj.toolbar);
                    obj.toolbar = [];
                end
            end
            obj.toolbar = uitoolbar(obj.fig);
            
            % button icons
            load glicons;
            
            uipushtool(obj.toolbar,...
                'ClickedCallback'   ,@obj.decreaseFontSize,...
                'TooltipString'     ,'Decrease Font Size',...
                'CData'             ,icons.downblue);
            
            uipushtool(obj.toolbar,...
                'ClickedCallback'   ,@obj.increaseFontSize,...
                'TooltipString'     ,'Increase Font Size',...
                'CData'             ,icons.upblue);
            
            uipushtool(obj.toolbar,...
                'ClickedCallback'   ,@obj.tightenAxes,...
                'TooltipString'     ,'Tighten Axes',...
                'CData'             ,icons.expand);
            
            uipushtool(obj.toolbar,...
                'ClickedCallback' ,@obj.flip,...
                'TooltipString'   ,'Flip/Reset Layout',...
                'CData'           , icons.flip);
            
            uipushtool(obj.toolbar,...
                'ClickedCallback' ,@obj.shrinkNodes,...
                'TooltipString'   ,'Decrease Node Size',...
                'CData'           , icons.downdarkblue);
            
            uipushtool(obj.toolbar,...
                'ClickedCallback' ,@obj.growNodes,...
                'TooltipString'   ,'Increase Node Size',...
                'CData'           , icons.updarkblue);
            
            if(~isempty(obj.layoutButtons))
                for i=1:numel(obj.layoutButtons)
                    if(ishandle(obj.layoutButtons(i)))
                        delete(obj.layoutButtons(i));
                    end
                end
                obj.layoutButtons = [];
            end
            
            layoutNames = fieldnames(obj.layouts);
            for i=1:numel(layoutNames)
                layout = obj.layouts.(layoutNames{i});
                layoutButton = uipushtool(obj.toolbar,...
                    'ClickedCallback', @obj.layoutButtonPushed,...
                    'TooltipString', layout.shortDescription,...
                    'UserData'     , layoutNames{i},...
                    'Separator'    , 'on',...
                    'CData'        , layout.image);
                obj.layoutButtons = [obj.layoutButtons,layoutButton];
            end
        end
        
        function setFontSize(obj)
            % fontsize = obj.maxFontSize;
            fontSize = 20;
            maxchars = size(char(obj.nodeLabels),2);
            width = obj.nodeArray(1).width;
            height = obj.nodeArray(1).height;
            xpos = -10; ypos = -10;
            t = text(xpos,ypos,repmat('g',1,maxchars),...
                'FontUnits'           , 'points'    ,...
                'Units'               , 'data'      ,...
                'HorizontalAlignment' , 'center'    ,...
                'VerticalAlignment'   , 'middle'    ,...
                'FontWeight'          , 'demi'      ,...
                'LineStyle'           , 'none'      ,...
                'Margin'              , 0.01        ,...
                'FontSize'            , fontSize    ,...
                'Color'               , 'w'         );
            
            extent = get(t,'Extent');
            
            while(extent(3) > width || extent(4) > height)
                fontSize = fontSize - 1;
                if(fontSize < 2), break,end
                set(t,'FontSize',fontSize);
                extent = get(t,'Extent');
            end
            obj.fontSize = fontSize;
            
        end
        
        function asp = aspectRatio(obj)
            % Return the current aspect ratio of the figure, width/height
            
            units = get(obj.ax,'Units');
            set(obj.ax,'Units','pixels');
            pos = get(obj.ax,'Position');
            set(obj.ax,'Units',units);
            asp = (pos(3)/pos(4));
            
        end
        
        function paperCrop(obj)
            % Make the papersize the same as the the figure size. This is
            % useful when saving as pdf.
            units = get(obj.fig,'Units');
            set(obj.fig,'Units','inches');
            pos = get(obj.fig,'Position');
            set(obj.fig,'Units',units);
            set(obj.fig,'PaperPositionMode','auto','PaperSize',pos(3:4));
        end
        %%
        % Callbacks
        
        function layoutButtonPushed(obj,buttonPushed,varargin)
            % Called when a layout button is pushed.
            name = get(buttonPushed,'UserData');
            obj.currentLayout = obj.layouts.(name);
            axis square;
            obj.redraw;
        end
        
        function windowResized(obj,varargin)
            % This function is called whenever the window is resized. It
            % redraws the whole graph.
            if(obj.isvisible)
                obj.redraw;
                obj.paperCrop();
            end
            
        end
        
        function mouseMoved(obj,varargin)
            % This function is called whenever the mouse moves within the
            % figure.
            if(obj.groupSelectionMode == 2)
                % Move all of the nodes & rectangle
                currentPoint = get(obj.ax,'CurrentPoint');
                xlimits = get(obj.ax,'XLim');
                ylimits = get(obj.ax,'YLim');
                sdims = obj.groupSelectedDims;
                xdiff = currentPoint(1,1) - obj.previousMouseLocation(1,1);
                ydiff = currentPoint(1,2) - obj.previousMouseLocation(1,2);
                
                if(xdiff <=0)
                    xdiff = max(xdiff,(xlimits(1)-sdims(1)));
                else
                    xdiff = min(xdiff,xlimits(2)-sdims(2));
                end
                if(ydiff <=0)
                    ydiff = max(ydiff,(ylimits(1)-sdims(3)));
                else
                    ydiff = min(ydiff,ylimits(2)-sdims(4));
                end
                xnodepos = vertcat(obj.groupSelectedNodes.xpos) + xdiff;
                ynodepos = vertcat(obj.groupSelectedNodes.ypos) + ydiff;
                for i=1:numel(obj.groupSelectedNodes)
                    obj.groupSelectedNodes(i).move(xnodepos(i),ynodepos(i));
                end
                recpos = get(obj.groupSelectedRect,'Position');
                recpos(1) = recpos(1) + xdiff;
                recpos(2) = recpos(2) + ydiff;
                obj.groupSelectedDims = [recpos(1),recpos(1)+recpos(3),recpos(2),recpos(2)+recpos(4)];
                set(obj.groupSelectedRect,'Position',recpos);
                edges = [obj.groupSelectedNodes.inedges,obj.groupSelectedNodes.outedges];
                obj.displayEdges(edges);
                obj.previousMouseLocation = currentPoint;
            else
                if(isempty(obj.selectedNode)), return,end
                currentPoint = get(obj.ax,'CurrentPoint');
                x = currentPoint(1,1); y = currentPoint(1,2);
                xl = xlim + [obj.selectedNode.width,-obj.selectedNode.width]/2;
                yl = ylim + [obj.selectedNode.height,-obj.selectedNode.height]/2;
                x = min(max(xl(1),x),xl(2));
                y = min(max(yl(1),y),yl(2));
                obj.selectedNode.move(x,y);
                obj.displayEdges([obj.selectedNode.inedges,obj.selectedNode.outedges]);
            end
        end
        
        function buttonUp(obj,varargin)
            % This function executes when the mouse button is released.
            if(obj.groupSelectionMode == 2)
                obj.clearGroupSelection();
                return;
            end
            if(isempty(obj.selectedNode)),return,end
            obj.selectedNode.deselect();
            
            obj.selectedNode.useFullLabel = false;
            obj.selectedNode.fontSize = obj.selectedFontSize;
            obj.selectedNode.redraw();
            obj.selectedNode = [];
            set(gcf,'Pointer','arrow');
        end
        
        function axPressed(obj,varargin)
            % Called when the user selects the axes but not a node
            switch obj.groupSelectionMode
                case 0         % hasn't been selected yet
                    xpos = vertcat(obj.nodeArray.xpos);
                    ypos = vertcat(obj.nodeArray.ypos);
                    p1 = get(obj.ax,'CurrentPoint');
                    rbbox;               % returns after box drawn
                    p2 = get(obj.ax,'CurrentPoint');
                    xleft  = min(p1(1,1),p2(1,1));
                    xright = max(p1(1,1),p2(1,1));
                    ylower = min(p1(1,2),p2(1,2));
                    yupper = max(p1(1,2),p2(1,2));
                    selectedX = (xpos <= xright) & (xpos >= xleft);
                    selectedY = (ypos <= yupper) & (ypos >= ylower);
                    selected = selectedX & selectedY;
                    if(~any(selected)),return,end
                    obj.groupSelectionMode = 1;
                    obj.groupSelectedNodes = obj.nodeArray(selected);
                    for i=1:numel(obj.groupSelectedNodes)
                        node = obj.groupSelectedNodes(i);
                        node.select();
                        node.redraw();
                    end
                    
                    w = obj.groupSelectedNodes(1).width/2;
                    h = obj.groupSelectedNodes(1).height/2;
                    x = vertcat(obj.groupSelectedNodes.xpos);
                    y = vertcat(obj.groupSelectedNodes.ypos);
                    minx = min(x)-w; maxx = max(x)+w; miny = min(y)-h; maxy = max(y)+h;
                    obj.groupSelectedDims = [minx,maxx,miny,maxy];
                    obj.groupSelectedRect = rectangle('Position',[minx,miny,maxx-minx,maxy-miny],'LineStyle','--','EdgeColor','r');
                case 1         % nodes selected
                    obj.groupSelectionStage1();
                case 2         %not ever reached in this function
                    obj.clearGroupSelection();
            end
        end
        
        function groupSelectionStage1(obj)
            % Called after a group of nodes has been selected and the mouse
            % button has been pressed somewhere on the axes, (or on a node).
            p = get(obj.ax,'CurrentPoint');
            obj.previousMouseLocation = p;
            dims = obj.groupSelectedDims;
            if(p(1,1) >= dims(1) && p(1,1) <= dims(2) && p(1,2) >= dims(3) && p(1,2) <=dims(4))
                set(gcf,'Pointer','hand');
                obj.groupSelectionMode = 2;
            else
                obj.clearGroupSelection();
            end
        end
        
        function clearGroupSelection(obj)
            % Clear a group selection
            if(ishandle(obj.groupSelectedRect))
                delete(obj.groupSelectedRect);
            end
            obj.groupSelectedRect = [];
            for i=1:numel(obj.groupSelectedNodes)
                obj.groupSelectedNodes(i).deselect();
            end
            obj.groupSelectedNodes = [];
            obj.groupSelectedDims = [];
            obj.groupSelectionMode = 0;
            set(gcf,'Pointer','arrow');
        end
        
        function deleted(obj,varargin)
            % Called when the figure is deleted by the user.
            obj.isvisible = false;
            obj.clearGroupSelection();
        end
        
        function singleClick(obj,node)
            % Called when a user single clicks on a node.
            obj.selectedNode = node;
            node.select();
            set(gcf,'Pointer','hand');
            obj.selectedFontSize = node.fontSize;
            node.useFullLabel = true;
            node.fontSize = max(15,node.fontSize*1.5);
            node.redraw();
        end
        
        function doubleClick(obj,node)
            % Called when a user double clicks on a node
            if isempty(obj.doubleClickFn)
                description = node.description;
                if(~iscell(description))
                    description = {description};
                end
                answer = inputdlg('',node.label,4,description);
                if(~isempty(answer))
                    node.description = answer;
                end
            else
                obj.doubleClickFn(node.label);
            end
        end
        
        function rightClick(obj,node)                 %#ok
            % Called when a user right clicks on a node
            if(node.isshaded)
                node.unshade();
            else
                node.shade();
            end
        end
        
        function shiftClick(obj,node)                 %#ok
            % Called when a user shift clicks on a node
            display(node);
        end
        
        
    end
    
    methods
        % Callbacks that can be called by the user programmatically.
        function shrinkNodes(obj,varargin)
            % Shrink the nodes to 95% of their original size, (but not smaller
            % than a calculated minimum.
            obj.clearGroupSelection();
            s = max(0.8*obj.nodeArray(1).width,obj.minNodeSize);
            obj.nodeArray(1).resize(s);
            obj.setFontSize();
            for i=1:obj.nnodes
                node = obj.nodeArray(i);
                node.fontSize = obj.fontSize;
                node.resize(s);
            end
            obj.displayEdges();
        end
        
        function growNodes(obj,varargin)
            % Grow the nodes to 1/0.95 times their original size, (but not
            % larger than a calculated maximum.
            obj.clearGroupSelection();
            s = min(obj.nodeArray(1).width/0.8,1.5*obj.maxNodeSize);
            obj.nodeArray(1).resize(s);
            obj.setFontSize();
            for i=1:obj.nnodes
                node = obj.nodeArray(i);
                node.fontSize = obj.fontSize;
                node.resize(s);
            end
            obj.displayEdges();
        end
        
        function increaseFontSize(obj,varargin)
            % Increase the fontsize of all the nodes by 0.5 points.
            current = get(obj.nodeArray(1).labelhandle,'FontSize');
            newsize = current + 1;
            for i=1:numel(obj.nodeArray)
                node = obj.nodeArray(i);
                node.fontSize = newsize;
                node.redraw();
            end
        end
        
        function decreaseFontSize(obj,varargin)
            % Decrease the fontsize of all the nodes by 0.5 points.
            current = get(obj.nodeArray(1).labelhandle,'FontSize');
            newsize = max(current - 1,1);
            for i=1:numel(obj.nodeArray)
                node = obj.nodeArray(i);
                node.fontSize = newsize;
                node.redraw();
            end
        end
        
        function XY = getNodePositions(obj)
            % Return the current positions of the nodes. The bottom left
            % corner is [0 0] and the top right is [1 1]. Node positions
            % refer to the centre of a node.
            XY = zeros(obj.nnodes, 2);
            for i=1:obj.nnodes
                XY(i, 1) = obj.nodeArray(i).xpos;
                XY(i, 2) = obj.nodeArray(i).ypos;
            end
        end
        
        function setNodePositions(obj, XY)
            % Programmatically set the node positions
            % XY(i, 1) is the xposition of node i, XY(i, 2) is the yposition.
            for i=1:obj.nnodes
                obj.nodeArray(i).move(XY(i, 1), XY(i, 2));
            end
            obj.displayGraph();
        end
        
        function moveNode(obj, nodeIndex, xpos, ypos)
            % Programmatically set a node position.
            obj.nodeArray(nodeIndex).move(xpos, ypos);
            obj.displayGraph();
        end
        
    end
end

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