function locke_05b_network(mode)
global LIGHT_COLS;
global TEMPERATURE;
global modelname;
global spaces;
global listOfPFiles;
global listOfEFiles;
global paramFile;
global envFile;
global title;
global legend1;
global aspect;
if nargin == 0 %initialisation
% colormap('default');
feature ('javafigures',0); %must re-anable dwhen closing!!!!!!!!!!!!
LoadingTime('init');
modelname = 'locke_05b';
LIGHT_COLS = [];
TEMPERATURE = [];
spaces = {' '};
my_Dir = pwd;
%get settings required for analysis
[Settings, SettingVals] = textread('Settings.set','%[^=]%*c%[^\n]');
for j = 1:size(Settings, 1); %search names for a match with state name
%when found, get corresponding value
if strcmp(Settings(j), 'LD') ~= 0
%wavelengths expected in vals file
LIGHT_COLS = SplitString(SettingVals(j));%separates names delimited by spaces
elseif strcmp(Settings(j), 'TEMP') ~= 0
TEMPERATURE = str2double(SettingVals(j));
elseif strcmp(Settings(j), 'exePath') ~= 0
exePath = char(SettingVals(j));
elseif strcmp(Settings(j), 'paramFile') ~= 0
paramFile = char(SettingVals(j));
elseif strcmp(Settings(j), 'envFile') ~= 0
envFile = char(SettingVals(j));
end
end
% delete('Settings.set');
LoadingTime;
paramFile = strcat(exePath,paramFile);
%find all params files
if ~isempty(exePath)
chdir(exePath);
end
l = dir(strcat(paramFile, '*.pv'));
listOfPFiles = cell(0);
for i = 1:size(l,1)
fn = l(i).name;
%remove ext
fn = fn(1:size(fn,2)-3);
listOfPFiles = [listOfPFiles; {fn}];
end
if isempty(l)
ShowError('No parameters files can be found! Unable to launch the program.');
return;
end
LoadingTime;
if ~isempty(LIGHT_COLS) | TEMPERATURE > 0
envFile = strcat(exePath,envFile);
l = dir(strcat(envFile, '*.env'));
listOfEFiles = cell(0);
for i = 1:size(l,1)
fn = l(i).name;
%remove ext
fn = fn(1:size(fn,2)-4);
listOfEFiles = [listOfEFiles; {fn}];
end
if isempty(l)
ShowError('No environment files can be found! Unable to launch the program.');
return;
end
else
listOfEFiles = {'NA'};
end
LoadingTime;
SetParamsFile(paramFile, listOfPFiles{1});
SetEnvFile(envFile, listOfEFiles{1});
chdir(my_Dir);
title = modelname;
modelname = strcat(exePath, modelname);
LoadingTime;
vc;
else
vc(mode);
end
%=============================================
function vc(action)
global speedHndl;
global valHndl;
global pValUpHndl;
global pValDownHndl;
global ApplyPHndl;
global defHndl;
global eValUpHndl;
global eValDownHndl;
global ApplyEHndl;
global edefHndl;
global envValHndl;
global envHndl;
global pHndl;
global envparamsHndl
global pulseHndl;
global pValues;
global pDefValues;
global envDefValues;
global envValues;
global tfinal;
global y0;
global pnames;
global lastDay;
global pulseOn;
global t;
global spaces;
global CP;
global pauseHndl;
global envParams;
global modelEnvs;
global listOfPFiles;
global listOfEFiles;
global pFilesHndl;
global eFilesHndl;
global paramFile;
global envFile;
global LIGHT_COLS;
global TEMPERATURE;
global title;
global btncol;
global colours;
global envCols;
global btnLen;
global pmode;
global Blocks;
global BlockIndexes;
global SubBlocks;
global SubBlockIndexes;
global BlockPosition;
global light;
global lightidx;
global temperature;
global maxSize;
global maxHeadSize;
global timeHndl;
global Arrows;
global ArrowSizes;
global LightSizes
global linewidth;
global rates;
global effectOfLight;
global xRange;
global yRange;
global axHndl;
global xmin;
global xmax;
global ymin;
global ymax;
global x_op;
global y_ops;
global time_to_plot;
global colours;
global lcolours;
global dcolours;
global envCols;
global head;
global tail;
global envLine;
global PlotEnv;
global showLegendSubMenu;
global showMarkersSubMenu;
global ShowMarkers;
global ShowLegend;
global pmode;
global eplotHndl;
global axSelectHndl;
global axHndl;
global naxHndl;
global t_toplot;
global y_toplot;
global env_toplot;
global resolution;
global maxres;
global ArrowHeads;
global LightArrowHeads;
global recording;
global recHndl;
global opfile;
maxres = 20; %every 20th point plotted
MyName = 'vc';
if nargin == 0,
action='initialize';
end;
play= 1;
stop=-1;
if strcmp(action,'initialize'),
btncol = [0.8 0.8 0.8];
innerframecol = [0.2 0.2 0.2];
tfinal=10000;
resolution = maxres/2;
numCycles = 5; %num periods to showon time axis
envCols = [[1 1 1];[0 0 1];[0 1 0];[1 0 0];[1 0 0];[1 0 1];[1 1 0]]; %light colours
pmode = 'stopped';
recording = 0;
oldFigNumber=watchon;
figNumber=figure('Name',char(strcat({'Visualise Model Network - '}, title)),'NumberTitle','off','Visible','off', 'colormap', jet(64), 'CloseRequestFcn', 'locke_05b_network(''close'')');
LoadingTime;
pos = get(figNumber, 'Position');
aspect = 1.2;
pos(3) = pos(4) * aspect;
set(figNumber, 'Position', pos);
LoadingTime;
colordef(figNumber,'black');
LoadingTime;
%===================================
% Information for all buttons
labelColor=[0.8 0.8 0.8];
btnLen=0.175;
btnWid=0.075;
% Spacing between the button and the next command's label
spacing=0.025;
%====================================
% The CONSOLE frames
frmBorder=0.02;
yPos=0.05;
frmPos=[0.025 0.025 0.225 0.95];
h=uicontrol( ...
'Style','frame', ...
'Units','normalized', ...
'Position',frmPos, ...
'BackgroundColor',[0.50 0.50 0.50]);
%====================================
% The START button
btnNumber=1;
yPos=0.90-(btnNumber-1)*(btnWid+spacing);
labelStr='Start';
callbackStr='locke_05b_network(''start'');';
% Generic button information
btnPos=[0.05 0.04 btnLen/4 0.0625];
startHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',btnPos, ...
'CData', GetImage(labelStr), ...
'BackgroundColor', btncol, ...
'Callback',callbackStr);
%====================================
% The STOP button
btnNumber=2;
yPos=0.90-(btnNumber-1)*(btnWid+spacing);
labelStr='Stop';
% Setting userdata to -1 (=stop) will stop the demo.
callbackStr='locke_05b_network(''stop'');';
% Generic button information
btnPos=[0.05 + btnLen * 0.5 0.04 btnLen/4 0.0625];
stopHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',btnPos, ...
'Enable','off', ...
'BackgroundColor', btncol, ...
'CData', GetImage(labelStr), ...
'Callback',callbackStr);
%========================================
%pause button
labelStr='Pause';
callbackStr='locke_05b_network(''pause'');';
% Generic button information
btnPos=[0.05 + btnLen/4 0.04 btnLen/4 0.0625];
pauseHndl=uicontrol( ...
'Style','togglebutton', ...
'Units','normalized', ...
'Position',btnPos, ...
'Enable','off', ...
'BackgroundColor', btncol, ...
'CData', GetImage(labelStr), ...
'Value',0, ...
'Callback',callbackStr);
%========================================
%record button
labelStr='RecordOff';
callbackStr='locke_05b_network(''record'');';
% Generic button information
btnPos=[0.05 + btnLen*0.75 0.04 btnLen/4 0.0625];
recHndl=uicontrol( ...
'Style','togglebutton', ...
'Units','normalized', ...
'Position',btnPos, ...
'Enable','on', ...
'BackgroundColor', btncol, ...
'CData', GetImage(labelStr), ...
'Max', 1, 'Min', 0, ...
'Value',0, ...
'Callback',callbackStr);
%=========================================
%select files
h=uicontrol( ...
'Style','frame', ...
'Units','normalized', ...
'Position',[0.0375 0.63 0.2 0.33], ...
'BackgroundColor',innerframecol);
labelHndl=uicontrol('Style', 'text','Units','normalized','position',[0.05 0.905 btnLen 0.05],'string','Parameters File','BackgroundColor', innerframecol, 'ForegroundColor', 'w');
callbackStr='locke_05b_network(''changePfile'')';
pFilesHndl=uicontrol( ...
'Style','popup', ...
'Units','normalized', ...
'String', listOfPFiles, ...
'position',[0.0475 0.875 btnLen 0.05], ...
'call',callbackStr);
% The parameters listbox
callbackStr='locke_05b_network(''param'')';
pHndl=uicontrol( ...
'Style','listbox', ...
'Units','normalized', ...
'position',[0.0475 0.77 btnLen 0.1], ...
'call',callbackStr);
callbackStr='locke_05b_network(''paramValKeyPress'')';
valHndl=uicontrol( ...
'Style','edit',...
'Units','normalized', ...
'position',[0.0475 + btnLen*0.2 0.71 btnLen*0.4 0.05], ...
'Enable','on', ...
'HorizontalAlignment', 'right', ...
'call',callbackStr);
callbackStr='locke_05b_network(''pValUp'')';
pValUpHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.0475 + btnLen*0.6 0.71 btnLen/5 0.05], ...
'String','>', ...
'Callback',callbackStr);
callbackStr='locke_05b_network(''pValDown'')';
pValDownHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.0475 0.71 btnLen/5 0.05], ...
'String','<', ...
'Callback',callbackStr);
%default button
callbackStr='locke_05b_network(''setdef'')';
defHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.0475+ btnLen*0.8 0.71 btnLen/5 0.05], ...
'String','D', ...
'Callback',callbackStr);
callbackStr='locke_05b_network(''applyPChange'')';
ApplyPHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.0475 0.6475 btnLen 0.0625], ...
'String','Apply', ...
'Callback',callbackStr);
%============================================
%env controls
h=uicontrol( ...
'Style','frame', ...
'Units','normalized', ...
'Position',[0.0375 0.165 0.2 0.44], ...
'BackgroundColor',innerframecol);
labelHndl=uicontrol('Style', 'text','Units','normalized','position',[0.05 0.55 btnLen 0.05],'string','Environment File','BackgroundColor', innerframecol, 'ForegroundColor', 'w');
callbackStr='locke_05b_network(''changeEfile'')';
eFilesHndl=uicontrol( ...
'Style','popup', ...
'Units','normalized', ...
'String', listOfEFiles, ...
'position',[0.05 0.52 btnLen 0.05], ...
'call',callbackStr);
% The LD listbox
btnNumber=3;
ypos=0.90-(btnNumber-1)*(btnWid+spacing);
callbackStr='locke_05b_network(''env'')';
envHndl=uicontrol( ...
'Style','popup', ...
'Units','normalized', ...
'String', modelEnvs, ...
'position',[0.05 0.465 btnLen*0.75 0.05], ...
'call',callbackStr);
callbackStr='locke_05b_network(''plotEnv'')';
eplotHndl=uicontrol( ...
'Style','togglebutton', ...
'Units','normalized', ...
'Position',[0.05 + btnLen*0.75 0.465 btnLen/4 0.05], ...
'String','P', ...
'Value', 0, 'Max', 1, 'Min', 0, ...
'Callback',callbackStr);
callbackStr='locke_05b_network(''envParams'')';
envparamsHndl=uicontrol( ...
'Style','listbox', ...
'Units','normalized', ...
'position',[0.05 0.36 btnLen 0.1], ...
'call',callbackStr);
callbackStr='locke_05b_network(''envValKeyPress'')';
envValHndl=uicontrol( ...
'Style','edit',...
'Units','normalized', ...
'position',[0.05 + btnLen*0.2 0.3 btnLen*0.4 0.05], ...
'Enable','on', ...
'HorizontalAlignment', 'right', ...
'call',callbackStr);
callbackStr='locke_05b_network(''eValUp'')';
eValUpHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.05 + btnLen*0.6 0.3 btnLen/5 0.05], ...
'String','>', ...
'Callback',callbackStr);
callbackStr='locke_05b_network(''eValDown'')';
eValDownHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.05 0.3 btnLen/5 0.05], ...
'String','<', ...
'Callback',callbackStr);
%default button
callbackStr='locke_05b_network(''setedef'')';
edefHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.05+ btnLen*0.8 0.3 btnLen/5 0.05], ...
'String','D', ...
'Callback',callbackStr);
callbackStr='locke_05b_network(''applyEChange'')';
ApplyEHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.05 0.2375 btnLen 0.0625], ...
'String','Apply', ...
'Callback',callbackStr);
%pulse button
callbackStr='locke_05b_network(''pulse'')';
pulseHndl=uicontrol( ...
'Style','pushbutton', ...
'Units','normalized', ...
'Position',[0.05 0.1775 btnLen 0.0625], ...
'String','Pulse', ...
'Enable','off', ...
'Callback',callbackStr);
%====================================
% The Axes buttons
labelStr='Auto';
callbackStr='locke_05b_network(''scale'')';
scaleHndl=uicontrol( ...
'Style','push', ...
'Units','normalized', ...
'position',[0.935 0.05 0.05 0.05], ...
'string',labelStr, ...
'Enable', 'off', ...
'call',callbackStr);
labelStr='E';
callbackStr='locke_05b_network(''enlargeScale'')';
enlargeHndl=uicontrol( ...
'Style','push', ...
'Units','normalized', ...
'position',[0.935 0.15 0.05 0.05], ...
'string',labelStr, ...
'Enable', 'off', ...
'call',callbackStr);
labelStr='R';
callbackStr='locke_05b_network(''reduceScale'')';
reduceHndl=uicontrol( ...
'Style','push', ...
'Units','normalized', ...
'position',[0.935 0.1 0.05 0.05], ...
'string',labelStr, ...
'Enable', 'off', ...
'call',callbackStr);
lbs = cell(0);
lbs = [lbs; {'All'}; {'X'}; {'Y'}];
axSelectHndl=uicontrol( ...
'Style','popup', ...
'Units','normalized', ...
'position',[0.935 0.2 0.05 0.05], ...
'string',lbs, ...
'Enable', 'off', ...
'HorizontalAlignment', 'right', ...
'Value', 1);
LoadingTime;
%====================================
% The speed slider
labelStr='Speed';
callbackStr='locke_05b_network(''speed'')';
speedHndl=uicontrol( ...
'Style','slider',...
'Units','normalized', ...
'Value', 0.5, ...
'position',[0.05 0.11 btnLen 0.025], ...
'string',labelStr, ...
'call',callbackStr);
labelHndl=uicontrol('Style', 'text','Units','normalized','position',[0.05 0.135 btnLen 0.025],'string','Speed','BackgroundColor', [0.5 0.5 0.5], 'ForegroundColor', 'w');
timeHndl=uicontrol('FontSize', 10,'Style', 'text','Units','normalized','position',[0.8 0.95 0.2 0.05],'BackgroundColor', [0.2 0.2 0.2], 'ForegroundColor', 'w');
%menu
% plotMenuHndl = uimenu('Label', 'Plot');
% showLegendSubMenu = uimenu(plotMenuHndl, 'Label', 'Show Legend', 'Checked', 'on', 'Callback', 'locke_05b_plot(''ShowLegend'');');
% showMarkersSubMenu = uimenu(plotMenuHndl, 'Label', 'Show Markers', 'Checked', 'on', 'Callback', 'locke_05b_plot(''ShowMarkers'');');
% ShowMarkers = 1;
% ShowLegend = 1;
%==============================
%fill controls
FillParamsControls
FillEnvControls;
LoadingTime;
time_to_plot = GetCP * numCycles; %time to show in one block on time series
xmin = 0;xmax=time_to_plot;
ymin=0;ymax=2;
set(eplotHndl, 'Value', 0);
%draw model
naxHndl = axes( ...
'Units','normalized', 'Position',[0.325 0.25 0.6 0.7],'Visible','on');
set(naxHndl, ...
'XLim',[0 1],'YLim',[0 1], ...
'Drawmode','fast', ...
'Visible','on', ...
'NextPlot','add', 'visible', 'off');
axHndl = axes( ...
'Units','normalized', 'Position',[0.325 0.05 0.6 0.2],'Visible','on');
set(axHndl, ...
'XLim',[xmin xmax],'YLim',[ymin ymax], ...
'Drawmode','fast', ...
'Visible','on', ...
'NextPlot','add');
[Blocks, SubBlocks, BlockPosition, BlockIndexes, SubBlockIndexes, light, lightidx, temperature, Arrows, ArrowHeads, LightArrowHeads] = DrawModel;
% Uncover the figure
y_ops = zeros(1,size(Blocks,2)); %one for each op, 0 - hidden, 1 -show
y_ops(1)=1;
hndlList=[startHndl stopHndl envHndl speedHndl pHndl valHndl envparamsHndl envValHndl pulseHndl pauseHndl defHndl pFilesHndl eFilesHndl pValUpHndl pValDownHndl ApplyPHndl eValUpHndl eValDownHndl ApplyEHndl edefHndl timeHndl eplotHndl scaleHndl enlargeHndl reduceHndl axSelectHndl axHndl naxHndl recHndl];
if isempty(LIGHT_COLS) & TEMPERATURE == 0
set([eFilesHndl envHndl envparamsHndl envValHndl pulseHndl eValUpHndl eValDownHndl ApplyEHndl edefHndl eplotHndl],'Enable','off');
end
set(figNumber,'Visible','on', ...
'UserData',hndlList);
watchoff(oldFigNumber);
figure(figNumber);
LoadingTime('finished');
elseif strcmp(action,'start'),
cla(axHndl);
pulseOn = zeros(size(modelEnvs,1),1);
figNumber=gcf;
hndlList=get(figNumber,'UserData');
startHndl=hndlList(1);
stopHndl=hndlList(2);
envHndl=hndlList(3);
speedHndl=hndlList(4);
pHndl = hndlList(5);
valHndl = hndlList(6);
envparamsHndl = hndlList(7);
envValHndl = hndlList(8);
pulseHndl = hndlList(9);
pauseHndl = hndlList(10);
defHndl = hndlList(11);
pFilesHndl = hndlList(12);
eFilesHndl = hndlList(13);
pValUpHndl = hndlList(14);
pValDownHndl = hndlList(15);
ApplyPHndl = hndlList(16);
eValUpHndl = hndlList(17);
eValDownHndl = hndlList(18);
ApplyEHndl = hndlList(19);
edefHndl = hndlList(20);
timeHndl = hndlList(21);
eplotHndl = hndlList(22);
scaleHndl = hndlList(23);
enlargeHndl = hndlList(24);
reduceHndl = hndlList(25);
axSelectHndl = hndlList(26);
axHndl = hndlList(27);
naxHndl = hndlList(28);
recHndl = hndlList(29);
%need blocks in this list to detect clicks
set([startHndl pFilesHndl eFilesHndl],'Enable','off');
set([stopHndl speedHndl pauseHndl scaleHndl enlargeHndl reduceHndl axSelectHndl],'Enable','on');
PlotEnv = get(eplotHndl,'Value');
if ~isempty(LIGHT_COLS) | TEMPERATURE > 0
set(pulseHndl, 'Enable', 'on');
end
sp = resolution/maxres;
set(speedHndl, 'Value', sp);
pmode = 'play';
% ====== Start of Demo
set(figNumber,'Backingstore','off');
xmin = 0; xmax = time_to_plot;
cp = GetCP;
tv = [xmin:cp:xmax];
set(axHndl,'XLim',[xmin xmax]);
set(axHndl, 'XTick', tv);
y = y0(:);
xlabel('Time');
ylabel('Output Level');
SetAxes;
t0=0;
pow = 1/3;
tol = 0.001;
t = t0;
hmax = (tfinal - t)/5; %step sizes
hmin = (tfinal - t)/200000; % 0.05 s
h = (tfinal - t)/100;
t_toplot = t;
y_toplot = y;
env_toplot = 0;
lastDay = [t0;y];
rates = [];
effectOfLight = [];
tau = tol * max(norm(y,'inf'),1); %allowed error
resolution = floor(maxres * get(speedHndl, 'Value'));
if resolution < 1
resolution=1;
end
minValue = zeros(1, size(Blocks,2));
maxValue = ones(1, size(Blocks,2));
minRate = zeros(1, size(Arrows,1));
maxRate = ones(1, size(Arrows,1));
minLight = zeros(size(light,1), size(light,2));
maxLight = ones(size(light,1), size(light,2));
% The main loop
num_points = 0;
fnum = 0;
% if recording == 1
% opfile = avifile(GetAVIName);
%end
Mv = [];
while (strcmp(pmode, 'play'))
if t + h > tfinal, h = tfinal - t; end
% Compute the slopes
try
[ld_val day] = GetLD(t);
[t_val tempday] = GetTemp(t);
s1 = equations(t, y, pValues, ld_val, t_val); %derrivatives
s2 = equations(t+h, y+h*s1, pValues, ld_val, t_val);
s3 = equations(t+h/2, y+h*(s1+s2)/4, pValues, ld_val, t_val);
% Estimate the error and the acceptable error
delta = norm(h*(s1 - 2*s3 + s2)/3,'inf');
tau = tol*max(norm(y,'inf'),1.0);
% Update the solution only if the error is acceptable
ts = t;
ys = y;
if delta <= tau
num_points = num_points + 1;
t = t + h;
y = y + h*(s1 + 4*s3 + s2)/6;
if mod(num_points, resolution) == 0
y_toplot = [y_toplot y];
t_toplot = [t_toplot t];
%see if light values same as last timepoint
% match = 1;
%for i = 2:size(env_toplot,1)
% if env_plot
%end
rates = [rates ArrowSizes];
%save last 48 hours to calc axis limits required
data = [t; y];
lastDay = [lastDay data];
effectOfLight = [effectOfLight LightSizes];
toremove = find(lastDay(1,:) <= (t - 2*GetCP));
lastDay(:,toremove) = [];
rates(:,toremove) = [];
effectOfLight(:,toremove) = [];
%find range of vlaues for each output over last 2 days
for i = 1:size(BlockIndexes,1)
idx = BlockIndexes{i} + 1; %plus one as row 1 is time
m = lastDay(idx,:);
if size(m,1) > 1
m = sum(m);%sum of 1 or more ops for each timepoint
end
minValue(i) = min(m);
maxValue(i) = max(m);
end
%same for rates
for i = 1:size(Arrows,1)
idx = Arrows(i,2);
m = rates(idx,:);
if size(m,1) > 1
m = sum(m);%sum of 1 or more ops for each timepoint
end
minRate(i) = min(m);
maxRate(i) = max(m);
end
%and light arrows
for i = 1:size(light,1)
for j = 1:size(light,2)
idx = lightidx(i,j);
m = effectOfLight(idx,:);
if size(m,1) > 1
m = sum(m);%sum of 1 or more
end
minLight(i,j) = min(m);
maxLight(i,j) = max(m);
end
end
%set box size
for i = 1:size(Blocks,2)
idx = BlockIndexes{i};
currentSize = sum(y(idx));
if currentSize < minValue(i)
currentSize = 0.1;
elseif currentSize > maxValue(i)
currentSize = 1;
elseif maxValue(i) == minValue(i)
currentSize = 0.5; %constant
else
currentSize = (currentSize - minValue(i))/(maxValue(i) - minValue(i));
end
if currentSize < 0.1
currentSize = 0.1;
end
if ~isreal(currentSize)
currentSize = real(currentSize);
end
currentSize = currentSize * maxSize;
set(Blocks(1,i), 'Position', [BlockPosition(i,1) - currentSize/2 BlockPosition(i,2) - currentSize/2 currentSize currentSize]);
%sub blocks
subBlockidx = Blocks(2,i);
%ratio of sub to main block
if subBlockidx > 0
subidx = SubBlockIndexes{subBlockidx};
subSize = (sum(y(subidx)) / sum(y(idx)));
if subSize < 0.01
subSize = 0.01;
end
subSize = currentSize * subSize;
set(SubBlocks(subBlockidx), 'Position', [BlockPosition(i,1) - currentSize/2 BlockPosition(i,2) + currentSize/2 - subSize currentSize subSize]);
end
end
%set arrow thicknesses
for i = 1:size(Arrows,1)
idx = Arrows(i,2);
currentSize = sum(ArrowSizes(idx));
if currentSize < minRate(i)
currentSize = 0.1;
elseif currentSize > maxRate(i)
currentSize = 1;
elseif maxRate(i) == minRate(i)
currentSize = 0.5; %constant
else
currentSize = (currentSize - minRate(i))/(maxRate(i) - minRate(i));
end
if currentSize < 0.1
currentSize = 0.1;
end
if ~isreal(currentSize)
currentSize = real(currentSize);
end
if Arrows(i,3) > 0
cs = currentSize * maxSize;
xc = get(ArrowHeads(Arrows(i,3)), 'XData');
yc = get(ArrowHeads(Arrows(i,3)), 'YData');
d = get(ArrowHeads(Arrows(i,3)), 'Tag');
if d == 'd' %down arrow
set(ArrowHeads(Arrows(i,3)), 'XData', [xc(1); xc(1) + cs/2; xc(1) - cs/2], 'YData', [yc(1); yc(1) + cs/2; yc(1) + cs/2]);
%line end
lc = get(Arrows(i,1),'YData');
lc(2) = yc(1) + cs/2;
set(Arrows(i,1), 'YData', lc);
elseif d == 'l' %left facing
set(ArrowHeads(Arrows(i,3)), 'XData', [xc(1); xc(1) + cs/2; xc(1) + cs/2], 'YData', [yc(1); yc(1) - cs/2; yc(1) + cs/2]);
%line end
lc = get(Arrows(i,1),'XData');
lc(2) = xc(1) + cs/2;
set(Arrows(i,1), 'XData', lc);
elseif d == 'u' %up facing
set(ArrowHeads(Arrows(i,3)), 'XData', [xc(1); xc(1) - cs/2; xc(1) + cs/2], 'YData', [yc(1); yc(1) - cs/2; yc(1) - cs/2]);
%line end
lc = get(Arrows(i,1),'YData');
lc(2) = yc(1) - cs/2;
set(Arrows(i,1), 'YData', lc);
elseif d == 'r' %right facing
set(ArrowHeads(Arrows(i,3)), 'XData', [xc(1); xc(1) - cs/2; xc(1) - cs/2], 'YData', [yc(1); yc(1) + cs/2; yc(1) - cs/2]);
%line end
lc = get(Arrows(i,1),'XData');
lc(2) = xc(1) - cs/2;
set(Arrows(i,1), 'XData', lc);
elseif d == 'ir' %vertcal inhibitory
ml = (yc(1) + yc(2))/2;
set(ArrowHeads(Arrows(i,3)), 'XData', [xc(1); xc(2); xc(1) - cs/4; xc(1) - cs/4], 'YData', [ml - cs/2; ml + cs/2; ml + cs/2; ml - cs/2]);
%line end
lc = get(Arrows(i,1),'XData');
lc(2) = xc(1) - cs/4;
set(Arrows(i,1), 'XData', lc);
elseif d == 'il' %vertcal inhibitory
ml = (yc(1) + yc(2))/2;
set(ArrowHeads(Arrows(i,3)), 'XData', [xc(4) + cs/4; xc(4) + cs/4; xc(3); xc(4)], 'YData', [ml - cs/2; ml + cs/2; ml + cs/2; ml - cs/2]);
%line end
lc = get(Arrows(i,1),'XData');
lc(2) = xc(4) + cs/4;
set(Arrows(i,1), 'XData', lc);
end
end
set(Arrows(i,1), 'LineWidth', linewidth * currentSize);
end
%light
for j = 1:size(day,1)
for i = 1:size(light,2)
colour = eval(get(light(j,i), 'Tag'));
dv = day(j);
if dv > 1
dv = 1;
end
colour = colour * dv;
idx = lightidx(j,i);
currentSize = sum(LightSizes(idx));
if currentSize < minLight(j,i)
currentSize = 0.1;
elseif currentSize > maxLight(j,i)
currentSize = 1;
elseif maxLight(i) == minLight(i)
currentSize = 0.5; %constant
else
currentSize = (currentSize - minLight(i))/(maxLight(i) - minLight(i));
end
if currentSize < 0.1
currentSize = 0.1;
end
if ~isreal(currentSize)
currentSize = real(currentSize);
end
cs = currentSize * maxSize;
xc = get(LightArrowHeads(j,i), 'XData');
yc = get(LightArrowHeads(j,i), 'YData');
d = get(LightArrowHeads(j,i), 'Tag');
if d == 'ld' %left-down arrow
set(LightArrowHeads(j,i), 'XData', [xc(1); xc(1) + cs; xc(3)], 'YData', [yc(1); yc(2); yc(1) + cs], 'FaceColor', colour, 'EdgeColor', colour);
%line end
lcy = get(light(j,i),'YData');
lcx = get(light(j,i),'XData');
lcy(2) = yc(1) + cs/2;
lcx(2) = xc(1) + cs/2;
set(light(j,i), 'YData', lcy, 'XData', lcx);
elseif d == 'ru' %right-up arrow
set(LightArrowHeads(j,i), 'XData', [xc(1); xc(1) - cs; xc(3)], 'YData', [yc(1); yc(2); yc(1) - cs], 'FaceColor', colour, 'EdgeColor', colour);
%line end
lcy = get(light(j,i),'YData');
lcx = get(light(j,i),'XData');
lcy(2) = yc(1) - cs/2;
lcx(2) = xc(1) - cs/2;
set(light(j,i), 'YData', lcy, 'XData', lcx);
end
set(light(j,i), 'color', colour, 'LineWidth',linewidth * currentSize );
end
end
if tempday ~= 0
for i = 1:size(temperature,1)
set(temperature(i), 'Visible', 'on');
end
else
for i = 1:size(temperature,1)
set(temperature(i), 'Visible', 'off');
end
end
str =sprintf('Time = %5.1f', t);
set(timeHndl, 'String', str);
%update plot
%add the selected env cycle
lv = [];
e = get(envHndl,'Value');
offVal = envValues(e,5);
for i = 1:size(ld_val,1)
if ld_val(i) > offVal
lv = [lv; ymin + (ymax-ymin)/10;];
else
lv = [lv; ymin+ (ymax-ymin)/100];
end
end
env_toplot = [env_toplot lv];
if ~isempty(envValues) & PlotEnv ~=0
envColour = envCols(e,:);
for e = 1:size(env_toplot,1)
set(envLine,'Parent', axHndl,'color',envColour, 'Visible', 'on', 'YData', env_toplot(e,:), 'XData', t_toplot);
end
end
for i = 1:size(y_ops,2)
if y_ops(i) ~= 0
plotdata = y_toplot(BlockIndexes{i},:);
if size(plotdata,1) > 1
plotdata = sum(plotdata);%block is sum of 2 ops
end
% if (day > 0 | tempday > 0) & (min(plotdata) <= envYval) & PlotEnv ~= 0
% lineColour = 'k';
% else
%set marker depending on whether block is
%ellipse or rectange
lineColour = get(Blocks(1,i), 'FaceColor');
% end
set(head(i),'parent', axHndl,'color',lineColour,'MarkerEdgeColor', lineColour, 'MarkerFaceColor', lineColour,'xdata',t,'ydata',plotdata(end)) %current time point
set(tail(i),'parent', axHndl,'color',lineColour,'xdata',t_toplot,'ydata',plotdata) %rest
end
end
if recording
%fnum = fnum+1;
pos = get(figNumber, 'Position');
Mv = [Mv;getframe(figNumber, [pos(3) * 0.325 pos(4) * 0.05 pos(3) * 0.6 pos(4) * 0.9])];
%ned to reset file nam ebetween runs
%imwrite(Mv.cdata, strcat('img', '.tiff'), 'tiff', 'WriteMode', 'append', 'Compression', 'packbits', 'Resolution', 72);
%opfile = addframe(opfile, naxHndl);
end
%update x axis
if t > xmax
xmin = xmax;
xmax = xmin + time_to_plot;
set(axHndl, 'XLim',[xmin xmax]);
cp = time_to_plot/5;
tv = [xmin:cp:xmax];
set(axHndl, 'XTick', tv);
t_toplot = t;
y_toplot = y;
env_toplot = 0;
end
drawnow;
end
end
% Update the step size
if delta ~= 0.0
h = min(hmax, 0.9*h*(tau/delta)^pow);
end
catch
[msg id] = lasterr;
ShowError(strcat({'Error evaluating the model file. '},msg, '.'));
vc('stop');
end
end; % Main loop ...
pmode = 'stopped';
% ====== End of Demo
% if recording == 1
% close(opfile);
% opfile = 0;
%end
if ~isempty(Mv) %no resizin gif recording
movie2avi(Mv,GetAVIName);
% save('d:\Movie1', 'Mv');
end
set([startHndl pFilesHndl],'Enable','on');
if ~isempty(LIGHT_COLS) | TEMPERATURE > 0
set(eFilesHndl,'Enable','on');
end
set([stopHndl pulseHndl pauseHndl scaleHndl enlargeHndl reduceHndl axSelectHndl],'Enable','off');
feature ('javafigures',1);
elseif strcmp(action,'speed')
resolution=floor(get(speedHndl, 'Value') * maxres);
if resolution < 1
resolution=1;
end
elseif strcmp(action, 'param') %select a param
p = get(pHndl, 'Value');
set(valHndl, 'String',pValues(p));
elseif strcmp(action, 'envParams') %env listbox
%move slider
p = get(envparamsHndl, 'Value'); %parameter
e = get(envHndl, 'Value'); %cycle eg 'white'
set(envValHndl, 'String',envValues(e,p));
elseif strcmp(action, 'pulse') %pulse button
pulseOn(get(envHndl, 'Value')) = t;
elseif strcmp(action, 'pause') %pulse button
ps = get(pauseHndl, 'Value');
while ps > 0
pause(1);
ps = get(pauseHndl, 'Value');
end
elseif strcmp(action, 'stop')
set(pauseHndl, 'Value', 0);
pmode = 'stopped';
elseif strcmp(action, 'close')
locke_05b_network('stop');
feature ('javafigures',1);
delete(gcf);
elseif strcmp(action, 'setdef')
p = get(pHndl, 'Value');
set(valHndl, 'String', pDefValues(p));
elseif strcmp(action, 'changePfile')
p = get(pFilesHndl, 'Value');
p = listOfPFiles{p};
SetParamsFile(paramFile, p)
FillParamsControls;
elseif strcmp(action, 'changeEfile')
p = get(eFilesHndl, 'Value');
p = listOfEFiles{p};
SetEnvFile(envFile, p)
FillEnvControls(get(envHndl,'Value'));
elseif strcmp(action, 'env')
FillEnvControls(get(envHndl,'Value'));
elseif strcmp(action, 'applyPChange')
p = get(pHndl, 'Value');
pv = get(valHndl, 'String');
to_remove = [];
for i = 1:size(pv,2)
if ~isstrprop(pv(i), 'digit') & ~strcmp('.', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
dps = find(pv == '.');
if size(dps,2) > 1
pv(dps(2:end)) = [];
end
if isempty(pv) | str2double(pv) < 0
pv = '0';
end
set(valHndl, 'String', pv);
pValues(p) = str2double(pv);
%update listbox view
str = get(pHndl, 'String');
ln = char(str(p));
idx = strfind(ln, char(spaces));
param_name = ln(1:idx - 1);
str(p) = strcat(param_name, spaces, num2str(pValues(p)));
set(pHndl, 'String', str);
elseif strcmp(action, 'pValUp')
p = get(pHndl, 'Value');
pv = get(valHndl, 'String');
%ensure a valid number in text box
to_remove = [];
for i = 1:size(pv,2)
if ~isstrprop(pv(i), 'digit') & ~strcmp('.', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
dps = find(pv == '.');
if size(dps,2) > 1
pv(dps(2:end)) = [];
end
if isempty(pv) | str2double(pv) < 0
pv = '0';
end
%increment by 10% of default value
if pDefValues(p) ~= 0
newval = str2double(pv) + (pDefValues(p)/10);
else
newval = str2double(pv) + 0.1;
end
pv = num2str(newval);
set(valHndl, 'String', pv);
elseif strcmp(action, 'pValDown')
p = get(pHndl, 'Value');
pv = get(valHndl, 'String');
%ensure a valid number in text box
to_remove = [];
for i = 1:size(pv,2)
if ~isstrprop(pv(i), 'digit') & ~strcmp('.', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
dps = find(pv == '.');
if size(dps,2) > 1
pv(dps(2:end)) = [];
end
if isempty(pv) | str2double(pv) < 0
pv = '0';
end
%decrement by 10% of default value
if pDefValues(p) ~= 0
newval = str2double(pv) - (pDefValues(p)/10);
else
newval = str2double(pv) - 0.1;
end
if newval < 0
newval = 0;
end
pv = num2str(newval);
set(valHndl, 'String', pv);
elseif strcmp(action, 'eValDown')
p = get(envparamsHndl, 'Value'); %parameter eg time on
e = get(envHndl, 'Value'); %cycle eg 'white'
pv = get(envValHndl, 'String');%value
to_remove = [];
for i = 1:size(pv,2)
if ~isstrprop(pv(i), 'digit') & ~strcmp('.', pv(i)) & ~strcmp('-', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
%only allow '-' in first position
to_remove = [];
for i = 2:size(pv,2)
if strcmp('-', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
dps = find(pv == '.');
if size(dps,2) > 1
pv(dps(2:end)) = [];
end
if isempty(pv)
pv = '0';
end
%increment value
newVal = str2double(pv);
if p == 1 %cp
if newVal >= 3
newVal = newVal - 1;
else
newVal = 2;
end
elseif p == 2 | p == 3 | p == 7 %dawn/dusk pulselength
if newVal >= 1
newVal = newVal - 1;
else
newVal = 0;
end
elseif p == 5 | p == 4 | p == 6 %Ioff Ion, pulse size
if ~isempty(LIGHT_COLS)
if e <= size(LIGHT_COLS,1)
%light selected
if newVal >= 0.1
newVal = newVal - 0.1;
else
newVal = 0;
end
else
%temp
newVal = newVal - 1;
end
else
%temp
newVal = newVal - 1;
end
end
pv = num2str(newVal);
set(envValHndl, 'String', pv);
elseif strcmp(action, 'eValUp')
p = get(envparamsHndl, 'Value'); %parameter eg time on
e = get(envHndl, 'Value'); %cycle eg 'white'
pv = get(envValHndl, 'String');%value
to_remove = [];
for i = 1:size(pv,2)
if ~isstrprop(pv(i), 'digit') & ~strcmp('.', pv(i)) & ~strcmp('-', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
%only allow '-' in first position
to_remove = [];
for i = 2:size(pv,2)
if strcmp('-', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
dps = find(pv == '.');
if size(dps,2) > 1
pv(dps(2:end)) = [];
end
if isempty(pv)
pv = '0';
end
%increment value
newVal = str2double(pv);
if p == 1 | p == 2 | p == 3 | p == 7 %cp dawn/dusk pulselength
newVal = newVal + 1;
elseif p == 5 | p == 4 | p == 6 %Ioff Ion, pulse size
if ~isempty(LIGHT_COLS)
if e <= size(LIGHT_COLS,1)
%light selected
newVal = newVal + 0.1;
else
%temp
newVal = newVal + 1;
end
else
%temp
newVal = newVal + 1;
end
end
pv = num2str(newVal);
set(envValHndl, 'String', pv);
elseif strcmp(action, 'applyEChange')
p = get(envparamsHndl, 'Value'); %parameter eg time on
e = get(envHndl, 'Value'); %cycle eg 'white'
pv = get(envValHndl, 'String');%value
to_remove = [];
for i = 1:size(pv,2)
if ~isstrprop(pv(i), 'digit') & ~strcmp('.', pv(i)) & ~strcmp('-', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
%only allow '-' in first position
to_remove = [];
for i = 2:size(pv,2)
if strcmp('-', pv(i))
to_remove = [to_remove i];
end
end
pv(to_remove) = [];
dps = find(pv == '.');
if size(dps,2) > 1
pv(dps(2:end)) = [];
end
if isempty(pv)
pv = '0';
end
set(envValHndl, 'String', pv);
envValues(e,p) = str2double(pv);
%validate change
if p == 1
%if a light cp changed, change for all lights
if ~isempty(LIGHT_COLS)
if e <= size(LIGHT_COLS,1)
envValues(1:size(LIGHT_COLS,1),1) = str2double(pv);
%reduce any on of off times greater than cp
tooLarge = find(envValues(1:size(LIGHT_COLS,1),2) > str2double(pv));
envValues(tooLarge,2) = str2double(pv);
tooLarge = find(envValues(1:size(LIGHT_COLS,1),3) > str2double(pv));
envValues(tooLarge,3) = str2double(pv);
end
end
if e > size(LIGHT_COLS,1)
if envValues(e,2) > str2double(pv)
envValues(e,2) = str2double(pv);
end
if envValues(e,3) > str2double(pv)
envValues(e,3) = str2double(pv);
end
end
elseif p == 2 %time on so mak esure cp and time off are at least equal to this
if ~isempty(LIGHT_COLS)
if e <= size(LIGHT_COLS,1)
if envValues(e,1) < str2double(pv)
envValues(1:size(LIGHT_COLS,1),1) = str2double(pv);
end
end
end
if e > size(LIGHT_COLS,1)
if envValues(e,1) < str2double(pv)
envValues(e,1) = str2double(pv);
end
end
if envValues(e,3) < str2double(pv)
envValues(e,3) = str2double(pv);
end
elseif p == 3 %time off so make sure cp at least equal to this, and time on no greater
if ~isempty(LIGHT_COLS)
if e <= size(LIGHT_COLS,1)
if envValues(e,1) < str2double(pv)
envValues(1:size(LIGHT_COLS,1),1) = str2double(pv);
end
end
end
if e > size(LIGHT_COLS,1)
if envValues(e,1) < str2double(pv)
envValues(e,1) = str2double(pv);
end
end
if envValues(e,2) > str2double(pv)
envValues(e,2) = str2double(pv);
end
elseif p == 4 %ion value, ensure ioff value no greater
if envValues(e,5) > str2double(pv)
envValues(e,5) = str2double(pv);
end
elseif p == 5 %ioff value, ensure ion is not less
if envValues(e,4) < str2double(pv)
envValues(e,4) = str2double(pv);
end
end
%update listbox view
str = get(envparamsHndl, 'String');
for i = 1:size(str,1)
ln = char(str(i));
idx = strfind(ln, char(spaces));
env_name = ln(1:idx - 1);
str(i) = strcat(env_name, spaces, num2str(envValues(e,i)));
end
set(envparamsHndl, 'String', str);
elseif strcmp(action, 'setedef')
p = get(envparamsHndl, 'Value'); %parameter eg time on
e = get(envHndl, 'Value'); %cycle eg 'white'
set(envValHndl, 'String', envDefValues(e,p));%value
elseif strcmp(action, 'plotEnv')
PlotEnv = get(eplotHndl,'Value');
elseif strcmp(action, 'scale') %auto set scale
%find last cycle of data, usually 24 hours
ymin = -1;
ymax = -1;
for i = 1:size(y_ops,2)
if y_ops(1,i) > 0
idx = BlockIndexes{i} + 1; %plus one as row 1 is time
m = lastDay(idx,:);
if size(m,1) > 1
m = sum(m);%sum of 1 or more ops for each timepoint
end
if ymin > min(m) | ymin < 0
ymin = min(m);
end
if ymax < max(m)
ymax = max(m);
end
end
end
if ymax <= ymin
ymax = ymin + 1;
end
set(axHndl, 'YLim',[ymin ymax]);
elseif strcmp(action, 'reduceScale')
ax = get(axSelectHndl, 'Value');
if (ax == 1 | ax == 2) %x axis
time_to_plot = (xmax-xmin) * 2;
xmin = floor(t);
xmax = xmin + time_to_plot;
cp = ((xmax-xmin)/5);
tv = [xmin:cp:xmax];
set(axHndl, 'XTick', tv);
set(axHndl, 'XLim',[xmin xmax]);
t_toplot = t_toplot(end);
y_toplot = y_toplot(:,end);
env_toplot = env_toplot(end);
end
if (ax == 1 | ax == 3)
ymin = ymin / 2;
ymax = ymax * 2;
set(axHndl, 'YLim',[ymin ymax]);
end
elseif strcmp(action, 'enlargeScale')
ax = get(axSelectHndl, 'Value');
if (ax == 1 | ax == 2)
time_to_plot = (xmax-xmin) / 2;
xmin = floor(t);
xmax = xmin + time_to_plot;
cp = ((xmax-xmin)/5);
tv = [xmin:cp:xmax];
set(axHndl, 'XTick', tv);
if xmax <= xmin
xmax = xmin + 1;
end
set(axHndl, 'XLim',[xmin xmax]);
t_toplot = t_toplot(end);
y_toplot = y_toplot(:,end);
env_toplot = env_toplot(end);
end
if (ax == 1 | ax == 3)
ymin = ymin * 2;
ymax = ymax / 2;
if ymax <= ymin
ymax = ymin + 1;
end
set(axHndl, 'YLim',[ymin ymax]);
end
elseif strcmp(action, 'record')
r = get(recHndl, 'Value');
if r == 0
recording = 0;
set(recHndl, 'CData', GetImage('RecordOff'));
% feature ('javafigures',1);
else
recording = 1;
set(recHndl, 'CData', GetImage('RecordOn'));
% feature ('javafigures',0);
end
elseif isnumeric(action)
if y_ops(1,action) > 0
y_ops(1,action) = 0;
set(head(action), 'visible', 'off');
set(tail(action), 'visible', 'off');
else
y_ops(1,action) = 1;
set(head(action), 'visible', 'on');
set(tail(action), 'visible', 'on');
end
end; % if strcmp(action, ...
%============================================
function v = GetParamValues(pFile, m)
[Names, Values] = textread(strcat(pFile, '.pv'),'%[^=]%*c%f');
v = zeros(size(m, 1),1);
for i = 1:size(m,1);
for j = 1:size(Names, 1); %search names for a match with state name
%when found, get corresponding value
if strcmp(Names(j), m(i)) ~= 0;
v(i) = Values(j);
end
end
end
%============================================
function SetParamsFile(fp, pFile)
global pnames;
global y0;
global pValues;
global pDefValues;
global pValues;
global modelname;
global spaces;
global pHndl;
global valHndl;
%read initial states and constants from values file made by interface file
opkeys = textread(strcat(modelname, '.sts'),'%*d,%[^,]%*[^\n]');
y0 = GetParamValues(strcat(fp, pFile), opkeys); %remove ox states???
pnames = textread(strcat(modelname, '.prm'),'%*d,%[^,]%*[^\n]');
pValues = GetParamValues(strcat(fp, pFile), pnames);
for i = 1:size(pnames,1)
pnames{i} = char(strcat(pnames{i}, spaces, num2str(pValues(i))));
end
pDefValues = pValues;
%===========================================
function SetEnvFile(fp, eFile)
global envDefValues;
global envValues;
global envparamsHndl;
global envValHndl;
global envParams;
global LIGHT_COLS
global TEMPERATURE;
global spaces;
global modelEnvs;
global defpulselen;
global defldcp ;
global defon;
global defoff;
global defion;
global defioff;
global defion;
global deftcp;
global defton;
global deftoff;
global defhtemp;
global deflowtemp;
global defhtemp;
global defpulselen;
global envNames;
%get default env params from file
try
if ~isempty(LIGHT_COLS) | TEMPERATURE > 0
fid = fopen(strcat(fp,eFile, '.env'), 'rt');
end
if ~isempty(LIGHT_COLS)
defon = zeros(size(LIGHT_COLS,1),1);
defoff = ones(size(LIGHT_COLS,1),1) * 12;
defion = ones(size(LIGHT_COLS,1),1);
defioff = zeros(size(LIGHT_COLS,1),1);
i = [];
while isempty(i) & ~feof(fid)
str = fgets(fid);
i= strfind(str, '(ld=');
end
type = str(i+4:end-1);
num_col = size(LIGHT_COLS,1);
ldvals = [];
str = fgets(fid);
while str(1) ~= '(' & ~feof(fid)
if strncmp(str, 'Regime1', 7) %only bother with first regime
temp.Name = str(1:strfind(str, '=') - 1);
temp.Value = str2double(str(strfind(str, '=') + 1:end));
ldvals = [ldvals temp];
end
str = fgets(fid);
end
for j = 1:size(ldvals,2)
if strcmp(ldvals(j).Name, 'Regime1CP') ~= 0
defldcp = ldvals(j).Value;
end
end
for col = 1:num_col
search_str = strcat('Regime1', char(LIGHT_COLS{col})); %RegimeXColour
for j = 1:size(ldvals,2)
if strcmp(ldvals(j).Name, strcat(search_str, 'On')) ~= 0
defon(col) = ldvals(j).Value;
elseif strcmp(ldvals(j).Name, strcat(search_str, 'Off')) ~= 0
defoff(col) = ldvals(j).Value;
elseif strcmp(ldvals(j).Name, strcat(search_str, 'Ion')) ~= 0
defion(col) = ldvals(j).Value;
elseif strcmp(ldvals(j).Name, strcat(search_str, 'Ioff')) ~= 0
defioff(col) = ldvals(j).Value;
end
end
end
end
if TEMPERATURE > 0
defton = 0;
deftoff = 12;
defhtemp = 25;
deflowtemp = 10;
i = [];
frewind(fid);
while isempty(i) & ~feof(fid)
str = fgets(fid);
i= strfind(str, '(temp=');
end
type = str(i+6:end-1);
tempvals = [];
str = fgets(fid);
while str(1) ~= '(' & ~feof(fid)
if strncmp(str, 'TempRegime1', 11) %
temp.Name = str(1:strfind(str, '=') - 1);
temp.Value = str2double(str(strfind(str, '=') + 1:end));
tempvals = [tempvals temp];
end
str = fgets(fid);
end
for j = 1:size(tempvals,2)
if strcmp(tempvals(j).Name, 'TempRegime1CP') ~= 0
deftcp = tempvals(j).Value;
end
end
search_str = 'TempRegime1';
for j = 1:size(tempvals,2)
if strcmp(tempvals(j).Name, strcat(search_str, 'TemperatureOn')) ~= 0
defton = tempvals(j).Value;
elseif strcmp(tempvals(j).Name, strcat(search_str, 'TemperatureOff')) ~= 0
deftoff = tempvals(j).Value;
elseif strcmp(tempvals(j).Name, strcat(search_str, 'TemperatureTon')) ~= 0
defhtemp = tempvals(j).Value;
elseif strcmp(tempvals(j).Name, strcat(search_str, 'TemperatureToff')) ~= 0
deflowtemp = tempvals(j).Value;
end
end
end
if ~isempty(LIGHT_COLS) | TEMPERATURE > 0
status = fclose(fid);
end
catch
ShowError(strcat({'The environemt file '}, eFile, {' cannot be read. Using default values instead'}));
status = fclose(fid);
if ~isempty(LIGHT_COLS)
defldcp = 24;
defon = zeros(size(LIGHT_COLS,1),1);
defoff = ones(size(LIGHT_COLS,1),1) * 12;
defion = ones(size(LIGHT_COLS,1),1);
defioff = zeros(size(LIGHT_COLS,1),1);
end
if TEMPERATURE > 0
deftcp = 24;
defton = 0;
deftoff = 12;
defhtemp = 25;
deflowtemp = 10;
end
end
modelEnvs = cell(0);
envValues = [];
defpulselen = 1;
if ~isempty(LIGHT_COLS)
for i = 1:size(LIGHT_COLS,1)
envValues = [envValues; defldcp defon(i) defoff(i) defion(i) defioff(i) defion(i) defpulselen];
modelEnvs = [modelEnvs; LIGHT_COLS(i)];
end
end
if TEMPERATURE > 0
envValues = [envValues; deftcp defton deftoff defhtemp deflowtemp defhtemp defpulselen];
modelEnvs = [modelEnvs; {'Temperature'}];
end
if isempty(modelEnvs)
modelEnvs = {'NA'};
end
envDefValues = envValues;
%============================================
function ShowError(msg)
msgbox(msg,'An Error Has Occurred','error','modal');
%============================================
function result = SplitString(ln)
%returns col vector of names, can't cope with multiple consecutive spaces.
%remove trailing blanks
line = char(ln);
if size(line,2) <= 1 %no colours
result = {};
else
while isspace(line(size(line,2))) & size(line,2) > 1
line = line(1:size(line,2)-1);
end
%remove any leading blanks
while isspace(line(1)) & size(line,2) > 1
line = line(2:size(line,2));
end
%split
spaces = isspace(line);
start = find(spaces); %location of spaces in the list
result = cell(size(start,2)+1,1);
%first name has no space at start
if size(start,2) == 0 %only 1 colour
result(1,1) = {line};
else %more than 1
result(1,1) = {line(1:start(1)-1)};
for i = 1:size(start,2)-1
result(i+1,1) = {line(start(i)+1:start(i+1)-1)};
end
%last name has no space at end
result(size(result,1),1) = {line(start(size(start,2))+1:size(line,2))};
end
end
%======================================================
function [val, day] = GetLD(t)
global LIGHT_COLS;
global pulseOn;
global envHndl;
global envValues;
if isempty(LIGHT_COLS)
val = [];
day = 0;
else
day = zeros(size(LIGHT_COLS,1));
currentLight = get(envHndl, 'Value');%one selected
%vector with entry for each colour
val = zeros(size(LIGHT_COLS,1));
for i = 1:size(LIGHT_COLS,1)
%for each colour
cp = envValues(i,1); %cp for that colour
dawn = envValues(i,2);
dusk = envValues(i,3);
onVal = envValues(i,4);
offVal = envValues(i,5);
pulseVal = envValues(i,6);
pulseLen= envValues(i,7);
if dusk > cp
dusk = cp;
end
if dawn > dusk
dawn = dusk;
end
if pulseOn(i) > 0 & t >= pulseOn(i) & t < (pulseOn(i) + pulseLen)
val(i) = pulseVal;
else
if mod(t,cp) >= dawn & mod(t,cp) < dusk
val(i) = onVal;
else
val(i) = offVal;
end
end
day(i) = val(i)/onVal;
end
end
%======================================================
function [val, day] = GetTemp(t)
global TEMPERATURE;
global envValues;
global pulseOn;
global envHndl;
global modelEnvs;
if TEMPERATURE == 0
val = [];
day = 0;
else
day = 0;
cp = envValues(end,1); %cp for that colour
dawn = envValues(end,2);
dusk = envValues(end,3);
onVal = envValues(end,4);
offVal = envValues(end,5);
pulseVal = envValues(end,6);
pulseLen= envValues(end,7);
if dusk > cp
dusk = cp;
end
if dawn > dusk
dawn = dusk;
end
if pulseOn(end) > 0 & t >= pulseOn(end) & t < (pulseOn(end) + pulseLen)
val = pulseVal;
else
if mod(t,cp) >= dawn & mod(t,cp) < dusk
val = onVal;
else
val = offVal;
end
end
currentEnv = get(envHndl, 'Value');%one selected
if (currentEnv == size(modelEnvs,1)) & val ~= offVal
day = 1;
end
end
%========================================================
function val = GetCP() %cp of colour selected
global envValues;
global envHndl;
if ~isempty(envValues)
currentEnv = get(envHndl, 'Value');%one selected
val = envValues(currentEnv,1);
else
val = 24;%model has no ld or temp
end
%==========================================================
function FillParamsControls()
global pHndl;
global pnames;
global valHndl;
global pValues;
set(pHndl,'String', pnames);
set(pHndl,'Value', 1);
set(valHndl,'String', pValues(1));
%===========================================================
function FillEnvControls(idx)
global envparamsHndl;
global envParams;
global envValHndl;
global envValues;
global TEMPERATURE;
global defpulselen;
global LIGHT_COLS;
global defldcp ;
global defon;
global defoff;
global defion;
global defioff;
global defion;
global deftcp;
global defton;
global deftoff;
global defhtemp;
global deflowtemp;
global defhtemp;
global defpulselen;
global spaces;
if nargin < 1
idx = 1;
end
defpulselen = 1;
if ~isempty(LIGHT_COLS)
if idx <= size(LIGHT_COLS,1)
%light selected
selected = 'ld';
elseif TEMPERATURE > 0
%temp
selected = 'temp';
else
% no env
selected = 'none';
end
elseif TEMPERATURE > 0
selected = 'temp';
else
%no env
selected = 'none';
end
envParamsList = cell(7);
if strcmp(selected,'ld')
envParamsList = [{char(strcat('LD Cycle Period',spaces,num2str(envValues(idx,1))))}; ...
{char(strcat('On Time',spaces,num2str(envValues(idx,2))))}; ...
{char(strcat('Off Time',spaces,num2str(envValues(idx,3))))}; ...
{char(strcat('On Value',spaces,num2str(envValues(idx,4))))}; ...
{char(strcat('Off Value',spaces,num2str(envValues(idx,5))))}; ...
{char(strcat('Pulse Value',spaces,num2str(envValues(idx,6))))}; ...
{char(strcat('Pulse Length',spaces,num2str(envValues(idx,7))))}];
elseif strcmp(selected,'temp')
envParamsList = [{char(strcat('Temp Cycle Period',spaces,num2str(envValues(idx,1))))}; ...
{char(strcat('On Time',spaces,num2str(envValues(idx,2))))}; ...
{char(strcat('Off Time',spaces,num2str(envValues(idx,3))))}; ...
{char(strcat('High Value',spaces,num2str(envValues(idx,4))))}; ...
{char(strcat('Low Value',spaces,num2str(envValues(idx,5))))}; ...
{char(strcat('Pulse Value',spaces,num2str(envValues(idx,6))))}; ...
{char(strcat('Pulse Length',spaces,num2str(envValues(idx,7))))}];
end
if ~strcmp(selected,'none')
set(envparamsHndl,'String', envParamsList);
set(envparamsHndl,'Value', 1);
set(envValHndl,'String', envValues(idx,1));
end
%==========================================================
function img = GetImage(idx)
global btncol;
img = ones(16,16,3);
for i = 1:16
for j = 1:16
img(i,j,:) = btncol;
end
end
if strcmp(idx, 'Start')
for i = 1:15 %start button arrow
for j = 0:(7 - abs(8 - i))
img(i,5+j,:) = [ 0 0 1];
end
end
elseif strcmp(idx, 'Stop')
for i = 5:12
for j = 5:12
img(i,j,:) = [ 0 0 1];
end
end
elseif strcmp(idx, 'RecordOff')
for i = 5:12
for j = 5:12
img(i,j,:) = [ 0 0 1];
end
end
for j = 7:10
img(4,j,:) = [0 0 1];
img(13,j,:) = [0 0 1];
end
for i = 7:10
img(i,4,:) = [0 0 1];
img(i,13,:) = [0 0 1];
end
elseif strcmp(idx, 'RecordOn')
for i = 5:12
for j = 5:12
img(i,j,:) = [1 0 0 ];
end
end
for j = 7:10
img(4,j,:) = [1 0 0];
img(13,j,:) = [1 0 0];
end
for i = 7:10
img(i,4,:) = [1 0 0];
img(i,13,:) = [1 0 0];
end
else
for i = 5:12
img(i,5,:) = [0 0 1];
img(i,6,:) = [0 0 1];
img(i,11,:) = [0 0 1];
img(i,12,:) = [0 0 1];
end
end
%====================================================
function LoadingTime(p)
persistent fg;
persistent progbar;
if nargin == 0
%increment
p = get(progbar, 'Position');
p(3) = p(3) + 0.075;
set(progbar, 'Position', p);
drawnow;
elseif strcmp(p, 'init')
scrsz = get(0,'ScreenSize');
pos = [scrsz(3)* (3/8) scrsz(4)* (11/24) scrsz(3)/4 scrsz(4)/12];
fg=figure( 'Name','Loading...','Position', pos, 'NumberTitle','off','Visible','on', ...
'Menubar', 'none', 'Resize', 'off', 'Toolbar', 'none');
progbar=uicontrol( ...
'Style','frame', ...
'Units','normalized', ...
'Position',[0.125 0.333 0.075 0.333], ...
'BackgroundColor',[0 0 1]);
drawnow;
elseif strcmp(p, 'finished')
set(progbar, 'Position', [0.125 0.333 0.75 0.333]);
drawnow;
delete(fg);
if exist('Launching.txt', 'file') == 2
delete('Launching.txt');
end
end
%======================================================
function [idximg, colmap] = RGBtoIndx(img)
%converts an rgb image to an indexed image and colourmap
persistent lastimg;
persistent lastidximg;
persistent map;
if 1%isempty(lastimg)
map = zeros(256,3);
idximg = zeros(size(img,1), size(img,2));
for row = 1:size(img,1)
for col = 1:size(img,2)
pc = [0 0 0];
pc(1) = img(row,col,1);
pc(2) = img(row,col,2);
pc(3) = img(row,col,3);
if sum(pc == [0 0 0]) < 3
for i = 2:size(map,1)
mc = [0 0 0];
mc(1) = map(i,1);
mc(2) = map(i,2);
mc(3) = map(i,3);
if sum(mc == [0 0 0]) == 3
map(i,1) = pc(1);
map(i,2) = pc(2);
map(i,3) = pc(3);
idximg(row,col) = i;
break;
elseif mc == pc
idximg(row,col) = i;
break;
end
end
end
end
end
lastimg = img;
lastidximg = idximg;
for row = 1:size(map,1)
for col = 1:size(map,2)
if map(row,col) > 1
map = map./255;
colmap = map;
return;
end
end
end
colmap = map;
else
idximg = lastidximg;
for row = 1:size(img,1)
for col = 1:size(img,2)
if sum(img(row,col,:) == lastimg(row,col,:)) < 3
%changed since last frame
if sum(img(row,col,:)) == 0
idximg(row,col) = 1;
else
for i = 2:size(map,1)
if map(i,1) == img(row,col,1) & map(i,2) == img(row,col,2) & map(i,3) == img(row,col,3)
idximg(row,col) = i;
break;
elseif sum(map(i,:)) == 0
map(i,1) = img(row,col,1);
if map(i,1) > 1
map(i,1) = map(i,1) / 255;
end
map(i,2) = img(row,col,2);
if map(i,2) > 1
map(i,2) = map(i,2) / 255;
end
map(i,3) = img(row,col,3);
if map(i,3) > 1
map(i,3) = map(i,3) / 255;
end
idximg(row,col) = i;
break;
end
end
end
end
end
end
lastimg = img;
lastidximg = idximg;
colmap = map;
end
%========================================================
function SetAxes
global y_ops;
global head;
global tail;
global envLine;
global PlotEnv;
global Blocks;
head = [];
tail = [];
for i = 1:size(y_ops,2)
if y_ops(i) ~= 0
v = 'on';
else
v = 'off'; %visibility of lines
end
if strcmp(get(Blocks(1,i), 'Tag'),'e')
mk = '.';
mks = 21;
else
mk = 's';
mks=7;
end
head = [head; line('Marker', mk, 'MarkerSize', mks,'erase','xor', 'xdata', [], 'ydata', [], 'zdata', [],'Visible', v)];
tail = [tail; line('LineStyle','-', 'erase','xor', 'xdata', [], 'ydata', [],'zdata', [], 'Visible', v)];
envLine = line('LineStyle','-', 'erase','xor', 'xdata', [], 'ydata', [], 'Visible', v);
end
if PlotEnv == 0
v = 'off';
end
%===================================================
function s = GetAVIName()
r = 1;
while exist(strcat('recording', num2str(r), '.avi'), 'file') == 2
r = r + 1;
end
s = strcat('recording', num2str(r), '.avi');
%====================================================
function dydt = equations(t, y, pPV, pLD, pTEMP)
global ArrowSizes;
global LightSizes;
global NumStates;
P = pPV;
LD_VAL = pLD;
TEMP_VAL = pTEMP;
NumStates = size(y,1);
%TO DO : INSERT EQUATIONS HERE
Dark = 1 - LD_VAL(1);
if Dark < 0
Dark = 0;
end
LHYox = y(14);
TOC1ox = y(15);
Xox = y(16);
Yox = y(17);
dydt = zeros(17,1);
% cLm - Level of LHY mRNA
dydt(1) = LD_VAL(1)*P(1)*y(13)+(P(2)*(y(9))^P(3))/(P(4)^P(3) + (y(9))^P(3)) - (P(5)*y(1))/(P(6) + y(1));
% cLc - Level of cytoplasmic LHY protein
dydt(2) = P(66)*LHYox+P(7)*y(1) - P(8)*y(2) + P(9)*y(3) - (P(10)*y(2))/(P(11) + y(2));
% cLn - Level of nuclear LHY protein
dydt(3) = P(8)*y(2) - P(9)*y(3) - (P(12)*y(3))/(P(13) + y(3));
% cTm - Level of TOC1 mRNA
dydt(4) = ( (P(14)*(y(12)^P(15))) / (P(16)^P(15) + y(12)^P(15)) ) * ((P(17)^P(18)) / (P(17)^P(18) + y(3)^P(18))) - (P(19)*y(4))/(P(20) + y(4));
% cTc - Level of cytoplasmic TOC1 protein
dydt(5) = P(67)*TOC1ox+P(21)*y(4) - P(22)*y(5) + P(23)*y(6) - (Dark * P(24) + P(25)) * ((y(5)) /(P(26) + y(5)) );
% cTn - Level of nuclear TOC1 protein
dydt(6) = P(22)*y(5) - P(23)*y(6)- (Dark * P(27) + P(28)) * ((y(6))/ (P(29) + y(6)));
% cXm - Level of X mRNA
dydt(7) = (P(30) * (y(6))^P(31))/(P(32)^P(31) + (y(6))^P(31)) - (P(33) * y(7))/(P(34) + y(7));
% cXc - Level of cytoplasmic protein X
dydt(8) = P(68)*Xox+P(35)*y(7) - P(36)*y(8) + P(37)*y(9) - (P(38) * y(8))/(P(39) + y(8));
% cXn - Level of nuclear protein X
dydt(9) = P(36)*y(8) - P(37)*y(9) - (P(40)*y(9))/(P(41) + y(9));
% cYm - Level of Y mRNA
dydt(10) = (LD_VAL(1)*P(42)*y(13) + ((LD_VAL(1)*P(43) + P(44))*(P(45)^P(48)) /( P(45)^P(48) + y(6)^P(48)))) * ((P(46)^P(47)) / (P(46)^P(47) + y(3)^P(47))) - (P(49)*y(10))/(P(50) + y(10));
% cYc - Level of cytoplasmic protein Y
dydt(11) = P(69)*Yox+P(51)*y(10) - P(52)*y(11) + P(53)*y(12) - (P(54)*y(11))/(P(55) + y(11));
% cYn - Level of nuclear protein Y
dydt(12) = P(52)*y(11) - P(53)*y(12) - (P(56)*y(12))/(P(57)+y(12));
% cPn - Level of nuclear protein P
dydt(13) = P(70)+ Dark * P(58) - (P(61)*y(13))/(P(59) + y(13)) - P(60) * LD_VAL(1)* y(13);
% cLmox - Level of LHY mRNA from constitutive gene
dydt(14) = P(62)-(P(5)*LHYox)/(P(6)+LHYox);
% cTmox - Level of TOC1 mRNA from constitutive gene
dydt(15) = P(63)-(P(19)*TOC1ox)/(P(20)+TOC1ox);
% cXmox - Level of protein X mRNA from constitutive gene
dydt(16) = P(64) - (P(33)*Xox)/(Xox + P(34));
% cYmox - Level of protein Y mRNA from constitutive gene
dydt(17) = P(65) - (P(49)*Yox)/(Yox + P(50));
%Rates control arrow thicknesses
ArrowSizes = [P(66)*LHYox+P(7)*y(1); ...
1/(((P(17)^P(18)) / (P(17)^P(18) + y(3)^P(18)))); ...
1/(((P(46)^P(47)) / (P(46)^P(47) + y(3)^P(47)))); ...
P(67)*TOC1ox+P(21)*y(4); ...
1/(((LD_VAL(1)*P(43) + P(44))*(P(45)^P(48)) /( P(45)^P(48) + y(6)^P(48)))); ...
P(69)*Yox+P(51)*y(10); ...
( (P(14)*(y(12)^P(15))) / (P(16)^P(15) + y(12)^P(15)) ); ...
(P(30) * (y(6))^P(31))/(P(32)^P(31) + (y(6))^P(31)); ...
P(68)*Xox+P(35)*y(7); ...
(P(2)*(y(9))^P(3))/(P(4)^P(3) + (y(9))^P(3))
];
a =LD_VAL(1)*P(42)*y(13) + ((LD_VAL(1)*P(43) + P(44))*(P(45)^P(48)) /( P(45)^P(48) + y(6)^P(48)));
LightSizes = [LD_VAL(1)*y(13); LD_VAL(1); a];
%==============================================================
function [blocks, subblocks, positions, indexes, subindexes, light, lightidx, temp, arrows, arrowheads, lightarrowheads] = DrawModel()
global maxSize;
global maxHeadSize;
global linewidth;
global colours;
global lcolours;
global dcolours;
global opIndexes;
global naxHndl;
%% Create figure
%figure1 = gcf;
linecol = [1 1 1]; %white
linewidth = 10;
maxHeadSize = 30;
colours = [1 1 0; 0 1 1; 0 1 0;1 0 1; 1 0 0;0 0 1; 1 1 1]; %yellow, cyan, green, magenta, red, blue, white
lcolours = [1 1 0; 0 1 1; 0 1 0;1 0 1; 1 0 0;0 0 1; 1 1 1]; %yellow, cyan, green, magenta, red, blue, white
dcolours = [0.5 0.5 0; 0 0.5 0.5; 0 0.5 0;0.5 0 0.5; 0.5 0 0;0 0 0.5; 0.5 0.5 0.5]; %yellow, cyan, green, magenta, red, blue, white
%blocks = [];subblocks = [];positions =[];indexes = [];subindexes = []; light = [];lightidx = [];temp=[];arrows=[];return;
%% Create lines
%col 1 is handle to arrow, col 2 indicates what controls its thickness
arrows = [ ...
line('Parent', naxHndl,'XData', [0.55 0.95],'YData', [0.95 0.95],'LineWidth',linewidth,'Color',linecol, 'Tag', 'l') 1 0; ...
line('Parent', naxHndl,'XData', [0.95 0.95],'YData',[0.675 0.05],'LineWidth',linewidth,'Color',linecol, 'Tag', 'l') 3 0; ...
line('Parent', naxHndl,'XData', [0.95 0.95],'YData',[0.675 0.5],'LineWidth',linewidth,'Color',linecol, 'Tag', 'l') 2 0; ...
line('Parent', naxHndl,'XData', [0.05 0.05],'YData',[0.05 0.45],'LineWidth',linewidth,'Color',linecol, 'Tag', 'l') 5 0; ...
];
%arrows, col2 is index controlling what sets the thickness of the arrow
arrows = [arrows; ...
line('Parent', naxHndl,'XData', [0.95 0.95],'YData',[0.95 0.875],'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 1 1; ...
line('Parent', naxHndl,'XData', [0.05 0.05],'YData',[0.55 0.575],'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 8 3; ...
line('Parent', naxHndl,'XData', [0.45 0.2],'YData',[0.5 0.5],'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 4 2; ...
line('Parent', naxHndl,'XData', [0.05 0.05],'YData',[0.775 0.8],'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 9 4; ...
line('Parent', naxHndl,'XData', [0.1 0.35],'YData',[0.95 0.95],'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 10 5; ...
line('Parent', naxHndl,'XData', [0.5 0.5],'YData',[0.1 0.125],'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 6 8; ...
line('Parent', naxHndl,'XData', [0.5 0.5],'YData',[0.325 0.35],'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 7 9; ...
];
%inhibitory arrows
arrows = [arrows; ...
line('Parent', naxHndl,'XData', [0.95 0.55],'YData', [0.5 0.5], 'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 2 10; ...
line('Parent', naxHndl,'XData',[0.95 0.55],'YData', [0.05 0.05], 'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 3 7; ...
line('Parent', naxHndl,'XData',[0.05 0.45],'YData', [0.05 0.05], 'LineWidth',linewidth,'Color',linecol, 'Tag', 'a') 5 6; ...
];
%light handles returned so can be turned on and off
light = [ ...
line('Parent', naxHndl,'XData', [0.275 0.1],'YData', [0.725 0.55],'LineWidth',linewidth,'LineStyle',':','Color',[1 1 0], 'Tag', '[1 1 0]') ...
line('Parent', naxHndl,'XData', [0.275 0.45],'YData', [0.725 0.9],'LineWidth',linewidth,'LineStyle',':','Color',[1 1 0], 'Tag', '[1 1 0]') ...
line('Parent', naxHndl,'XData', [0.725 0.55],'YData', [0.275 0.1],'LineWidth',linewidth,'LineStyle',':','Color',[1 1 0], 'Tag', '[1 1 0]') ...
]; %annotation(figure1,'arrow',[0.475 0.475],[0.95 0.55],'LineWidth',10,'LineStyle',':','Color',[1 1 0],'HeadStyle','rectangle', 'HeadWidth',30,'HeadLength',8, 'Tag', '[1 1 0]') ...
lightarrowheads = [ ...
fill([0.1; 0.2; 0.1] ,[0.55;0.55; 0.65],[1 1 0],'Parent', naxHndl, 'EdgeColor', [1 1 0], 'Tag', 'ld') ...
fill([0.45; 0.35; 0.45] ,[0.9;0.9; 0.8],[1 1 0],'Parent', naxHndl, 'EdgeColor', [1 1 0], 'Tag', 'ru') ...
fill([0.55; 0.65; 0.55] ,[0.1;0.1; 0.2],[1 1 0],'Parent', naxHndl, 'EdgeColor', [1 1 0], 'Tag', 'ld') ...
];
lightidx = [2 1 3];
arrowheads =[ ...
fill([0.95; 1; 0.9] ,[0.775;0.875; 0.875],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'd');
fill([0.1; 0.2; 0.2] ,[0.5;0.45; 0.55],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'l');
fill([0.05; 0; 0.1] ,[0.675;0.575; 0.575],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'u');
fill([0.05; 0; 0.1] ,[0.9;0.8; 0.8],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'u');
fill([0.45; 0.35; 0.35] ,[0.95;1; 0.9],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'r');
fill([0.45; 0.45; 0.4; 0.4] ,[0;0.1;0.1;0],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'ir');
fill([0.6; 0.6; 0.55; 0.55] ,[0;0.1;0.1;0],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'il');
fill([0.5; 0.45; 0.55] ,[0.225;0.125; 0.125],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'u');
fill([0.5; 0.45; 0.55] ,[0.45; 0.35; 0.35],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'u');
fill([0.6; 0.6; 0.55; 0.55] ,[0.45;0.55;0.55;0.45],linecol,'Parent', naxHndl, 'EdgeColor', linecol, 'Tag', 'il');
];
temp = [];
%RNAs
lhyRNA = [0.5 0.95]; %coordinates of center
yRNA = [0.5 0.05];
xRNA = [0.05 0.725];
toc1RNA = [0.5 0.5];
maxSize = 0.1;
hlhyRNA = rectangle('Parent', naxHndl,'Curvature', 1, 'Position',[lhyRNA(1) - maxSize/2 lhyRNA(2) - maxSize/2 maxSize maxSize],'FaceColor',colours(3,:),'LineStyle','none', 'Tag', 'e', 'ButtonDownFcn', 'locke_05b_network(1)');
hxRNA = rectangle('Parent', naxHndl,'Curvature', 1, 'Position',[xRNA(1) - maxSize/2 xRNA(2) - maxSize/2 maxSize maxSize],'FaceColor',colours(1,:),'LineStyle','none', 'Tag', 'e', 'ButtonDownFcn', 'locke_05b_network(5)');
htoc1RNA = rectangle('Parent', naxHndl,'Curvature', 1, 'Position',[toc1RNA(1) - maxSize/2 toc1RNA(2) - maxSize/2 maxSize maxSize],'FaceColor',colours(5,:),'LineStyle','none', 'Tag', 'e', 'ButtonDownFcn', 'locke_05b_network(3)');
hyRNA = rectangle('Parent', naxHndl,'Curvature', 1, 'Position',[yRNA(1) - maxSize/2 yRNA(2) - maxSize/2 maxSize maxSize],'FaceColor',colours(2,:),'LineStyle','none', 'Tag', 'e', 'ButtonDownFcn', 'locke_05b_network(7)');
%labels
fs = 10;
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.5 0.85],'Color',[1 1 1],'HorizontalAlignment','left','String',{'LHY', 'mRNA'},'Interpreter','none');
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.35 0.125],'Color',[1 1 1],'HorizontalAlignment','left','String',{'Y mRNA'},'Interpreter','none');
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.125 0.725],'Color',[1 1 1],'HorizontalAlignment','left','String',{'X mRNA'},'Interpreter','none');
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.45 0.6],'Color',[1 1 1],'HorizontalAlignment','left','String',{'TOC1', 'mRNA'},'Interpreter','none');
%proteins
lhyProtein = [0.95 0.725]; %coordinates of center
yProtein = [0.5 0.275];
xProtein = [0.05 0.95];
toc1Protein = [0.05 0.5];
%pProtein = [0.475 0.5];
%nuclear proteins
nlhyProtein = lhyProtein; %coordinates of center
nyProtein = yProtein;
nxProtein = xProtein;
ntoc1Protein = toc1Protein;
colours = [1 1 0; 0 1 1; 0 1 0;1 0 1; 1 0 0;0 0 1; 1 1 1]; %yellow,
%cyan, green, magenta, red, blue, white
%dark cytoplasmic, light nuclear
hlhyProtein = rectangle('Parent', naxHndl,'Position', [lhyProtein(1) - maxSize/2 lhyProtein(2) - maxSize/2 maxSize maxSize],'FaceColor',dcolours(3,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(2)');
hxProtein = rectangle('Parent', naxHndl,'Position', [xProtein(1) - maxSize/2 xProtein(2) - maxSize/2 maxSize maxSize],'FaceColor',dcolours(1,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(6)');
htoc1Protein = rectangle('Parent', naxHndl,'Position', [toc1Protein(1) - maxSize/2 toc1Protein(2) - maxSize/2 maxSize maxSize],'FaceColor',dcolours(5,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(4)');
hyProtein = rectangle('Parent', naxHndl,'Position', [yProtein(1) - maxSize/2 yProtein(2) - maxSize/2 maxSize maxSize],'FaceColor',dcolours(2,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(8)');
%hpProtein = annotation(figure1,'rectangle',[pProtein(1) - maxSize/2 pProtein(2) - maxSize/2 maxSize maxSize],'FaceColor',[1 0 1],'LineStyle','none');
hnlhyProtein = rectangle('Parent', naxHndl,'Position', [nlhyProtein(1) - maxSize/2 nlhyProtein(2) - maxSize/2 maxSize maxSize],'FaceColor',lcolours(3,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(2)');
hnxProtein = rectangle('Parent', naxHndl,'Position', [nxProtein(1) - maxSize/2 nxProtein(2) - maxSize/2 maxSize maxSize],'FaceColor',lcolours(1,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(6)');
hntoc1Protein = rectangle('Parent', naxHndl,'Position', [ntoc1Protein(1) - maxSize/2 ntoc1Protein(2) - maxSize/2 maxSize maxSize],'FaceColor',lcolours(5,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(4)');
hnyProtein = rectangle('Parent', naxHndl,'Position', [nyProtein(1) - maxSize/2 nyProtein(2) - maxSize/2 maxSize maxSize],'FaceColor',lcolours(2,:),'LineStyle','-', 'Tag', 'r', 'ButtonDownFcn', 'locke_05b_network(8)');
%labels
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.825 0.725],'Color',[1 1 1],'HorizontalAlignment','left','String',{'LHY', 'Protein'},'Interpreter','none');
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.35 0.275],'Color',[1 1 1],'HorizontalAlignment','left','String',{'Y Protein'},'Interpreter','none');
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.125 0.9],'Color',[1 1 1],'HorizontalAlignment','left','String',{'X Protein'},'Interpreter','none');
text('Parent', naxHndl,'FontSize',fs, 'Position',[0.075 0.425],'Color',[1 1 1],'HorizontalAlignment','left','String',{'Toc1 Protein'},'Interpreter','none');
%annotation(figure1,'textbox','FontSize',fs, 'Position',[pProtein(1) - maxSize/2 pProtein(2) - maxSize*1.5 maxSize maxSize],'EdgeColor','none','LineStyle','none','Color',[1 1 1],'FitHeightToText','on','FontWeight','demi','HorizontalAlignment','center','String',{'P Protein'},'Interpreter','none');
%return vector of handels to blocks representing states
blocks = [hlhyRNA hlhyProtein htoc1RNA htoc1Protein hxRNA hxProtein hyRNA hyProtein; ...
0 1 0 2 0 3 0 4]; %sub blocks
subblocks = [hnlhyProtein hntoc1Protein hnxProtein hnyProtein];
positions = [lhyRNA; lhyProtein; toc1RNA; toc1Protein; xRNA; xProtein; yRNA; yProtein];
indexes = cell(8,1); %indicates which block represents which state
indexes{1} = [1];
indexes{2} = [2 3]; %sum of two states
indexes{3} = [4];
indexes{4} = [5 6];
indexes{5} = [7];
indexes{6} = [8 9];
indexes{7} = [10];
indexes{8} = [11 12];
subindexes = cell(4,1); %indicates which block represents which state
subindexes{1} = [3];
subindexes{2} = [6];
subindexes{3} = [9];
subindexes{4} = [12];
%opIndexes = [hlhyRNA;hlhyProtein;hnlhyProtein]; %block for each state
%
