function varargout = MT_GUI(varargin)
% MT_GUI M-file for MT_GUI.fig
%      MT_GUI, by itself, creates a new MT_GUI or raises the existing
%      singleton*.
%
%      H = MT_GUI returns the handle to a new MT_GUI or the handle to
%      the existing singleton*.
%
%      MT_GUI('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in MT_GUI.M with the given input arguments.
%
%      MT_GUI('Property','Value',...) creates a new MT_GUI or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before MT_GUI_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to MT_GUI_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help MT_GUI

% Last Modified by GUIDE v2.5 07-Aug-2006 12:23:47

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                  'gui_Singleton',  gui_Singleton, ...
                  'gui_OpeningFcn', @MT_GUI_OpeningFcn, ...
                  'gui_OutputFcn',  @MT_GUI_OutputFcn, ...
                  'gui_LayoutFcn',  [] , ...
                  'gui_Callback',   []);
if nargin && ischar(varargin{1})
   gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
   [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
   gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before MT_GUI is made visible.
function MT_GUI_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to MT_GUI (see VARARGIN)

clc;

global a c c_tot cpu L N_MT_max MT_length MT_state step bad_input_warning;

L = 10; % microns
Lz = 1; % microns

% The length of a heterodimer is 8nm; there are usually 13 protofilaments
% in the MT. Hence to grow by 1 micron the MT needs 13*10^-6/8*10^-9 = 1625
% dimers. Then the concentration of free Tu, c, will drop by 1625/V
% heterodimers per micron^3 (V is measured in micron^3).
% 1 microM = 10^-21*N_A heterodimers/micron^3, where N_A = 6.022*10^23.
% Therefore, change in c, expressed in microM, is 1625/(10^-21*N_A*V(in
% micron^3)). We denote this quantity by cpu. We also assume that the cell
% has a cylindrical shape, with radius L and height Lz.
% polymerization of unit length (micron) reduces the free Tu concentration c by:
cpu = 1625/(602*pi*L^2*Lz); % microM per micron

% initialization:
% make of maximal size in order to be able to change N_MT after hitting
% "Stop", and then to run again (to continue).
MT_length = zeros(N_MT_max,1); % in microns
MT_state = ones(N_MT_max,1); % 1 - growth state, 2 - shortening state
c_tot = c; % because initially have no MTs
step = 0;
bad_input_warning = 0;

a = linspace(0,2*pi);
clr = ['b','r']; % colors of growing and shortening MTs
plot(L*cos(a),L*sin(a),'k','LineWidth',3); axis off; axis square;


% Choose default command line output for MT_GUI
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes MT_GUI wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = MT_GUI_OutputFcn(hObject, eventdata, handles)
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;
disp('Hello! You have started the simple simulation GUI for MTs.');


function c_Callback(hObject, eventdata, handles)
% hObject    handle to c (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of c as text
%        str2double(get(hObject,'String')) returns contents of c as a double

global c c_tot N_MT MT_length cpu bad_input_warning L;
c_new = str2num(get(hObject,'String'));
if isempty(c_new) || c_new < 0 || ~isreal(c_new) % the input is invalid
   bad_input_warning = 1;
   text(-L*1.1,-L*1.05,'The input value discarded. The input should be a non-negative number.','Color','r');
   set(hObject,'string',num2str(c)); % to restore the previous value in the box.
else % have a valid input
   c = c_new;
   % when I change c I have to recalculate c_tot:
   c_tot = c + sum(MT_length(1:N_MT))*cpu;
end



% --- Executes during object creation, after setting all properties.
function c_CreateFcn(hObject, eventdata, handles)
% hObject    handle to c (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
   set(hObject,'BackgroundColor','white');
end

global c hObject_c;
% set the initial value of c:
c = 10;
set(hObject,'string',num2str(c));
hObject_c = hObject; % need this in order to update the value of c in the box from another function.



function k_g_Callback(hObject, eventdata, handles)
% hObject    handle to k_g (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of k_g as text
%        str2double(get(hObject,'String')) returns contents of k_g as a double

global k_g bad_input_warning L;
k_g_new = str2num(get(hObject,'String'));
if isempty(k_g_new) || k_g_new < 0 || ~isreal(k_g_new) % the input is invalid
   bad_input_warning = 1;
   text(-L*1.1,-L*1.05,'The input value discarded. The input should be a non-negative number.','Color','r');
   set(hObject,'string',num2str(k_g));
else % have a valid input
   k_g = k_g_new;
end



% --- Executes during object creation, after setting all properties.
function k_g_CreateFcn(hObject, eventdata, handles)
% hObject    handle to k_g (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
   set(hObject,'BackgroundColor','white');
end

global k_g;
k_g = .005;
set(hObject,'string',num2str(k_g));



function v_s_Callback(hObject, eventdata, handles)
% hObject    handle to v_s (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of v_s as text
%        str2double(get(hObject,'String')) returns contents of v_s as a double

global v_s bad_input_warning L;
v_s_new = str2num(get(hObject,'String'));
if isempty(v_s_new) || v_s_new < 0 || ~isreal(v_s_new) % the input is invalid
   bad_input_warning = 1;
   text(-L*1.1,-L*1.05,'The input value discarded. The input should be a non-negative number.','Color','r');
   set(hObject,'string',num2str(v_s));
else % have a valid input
   v_s = v_s_new;
end


% --- Executes during object creation, after setting all properties.
function v_s_CreateFcn(hObject, eventdata, handles)
% hObject    handle to v_s (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
   set(hObject,'BackgroundColor','white');
end

global v_s;
v_s = .7;
set(hObject,'string',num2str(v_s));



function k_cat_Callback(hObject, eventdata, handles)
% hObject    handle to k_cat (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of k_cat as text
%        str2double(get(hObject,'String')) returns contents of k_cat as a double

global k_cat bad_input_warning L;
k_cat_new = str2num(get(hObject,'String'));
if isempty(k_cat_new) || k_cat_new < 0 || ~isreal(k_cat_new) % the input is invalid
   bad_input_warning = 1;
   text(-L*1.1,-L*1.05,'The input value discarded. The input should be a non-negative number.','Color','r');
   set(hObject,'string',num2str(k_cat));
else % have a valid input
   k_cat = k_cat_new;
end


% --- Executes during object creation, after setting all properties.
function k_cat_CreateFcn(hObject, eventdata, handles)
% hObject    handle to k_cat (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
   set(hObject,'BackgroundColor','white');
end

global k_cat;
k_cat = 3;
set(hObject,'string',num2str(k_cat));



function k_res_Callback(hObject, eventdata, handles)
% hObject    handle to k_res (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of k_res as text
%        str2double(get(hObject,'String')) returns contents of k_res as a double

global k_res bad_input_warning L;
k_res_new = str2num(get(hObject,'String'));
if isempty(k_res_new) || k_res_new < 0 || ~isreal(k_res_new) % the input is invalid
   bad_input_warning = 1;
   text(-L*1.1,-L*1.05,'The input value discarded. The input should be a non-negative number.','Color','r');
   set(hObject,'string',num2str(k_res));
else % have a valid input
   k_res = k_res_new;
end


% --- Executes during object creation, after setting all properties.
function k_res_CreateFcn(hObject, eventdata, handles)
% hObject    handle to k_res (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
   set(hObject,'BackgroundColor','white');
end

global k_res;
k_res = .007;
set(hObject,'string',num2str(k_res));


% --- Executes on slider movement.
function N_MT_Callback(hObject, eventdata, handles)
% hObject    handle to N_MT (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

global N_MT N_MT_max MT_length c c_tot cpu;
N_MT = round(get(hObject,'Value'));
set(hObject,'Value',N_MT); % correct slider position, because rounded the value.
% If reduce the number of MTs  - assume all the extra MTs get
% depolymerized, i.e., all the extra MTs become zero length:
MT_length(N_MT+1:N_MT_max) = 0;
% If change N_MT also have to ensure the conservation of tubulin:
c = c_tot - sum(MT_length(1:N_MT))*cpu;



% --- Executes during object creation, after setting all properties.
function N_MT_CreateFcn(hObject, eventdata, handles)
% hObject    handle to N_MT (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
   set(hObject,'BackgroundColor',[.9 .9 .9]);
end

global N_MT N_MT_min N_MT_max;
N_MT_min = 1;
N_MT_max = 200;
N_MT = 60;

set(hObject,'Min',N_MT_min);
set(hObject,'Max',N_MT_max);
set(hObject,'Value',N_MT);



% --- Executes on button press in Run.
function Run_Callback(hObject, eventdata, handles)
% hObject    handle to Run (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global a c c_tot cpu k_g v_s k_cat k_res L N_MT MT_length MT_state stop step hObject_c bad_input_warning;

%disp(['k_g = ',num2str(k_g),',  v_s = ',num2str(v_s),',  k_cat = ',num2str(k_cat),',  k_res = ',num2str(k_res)]);

stop = 0;

v_g = inline('k_g*c','k_g','c');
f_cat = inline('k_cat/c^2','k_cat','c');
f_res = inline('k_res*c','k_res','c');


STEPS = 10000; % each step runs through all the MTs

while step < STEPS && ~stop
   step = step + 1;

   if bad_input_warning
       disp('Input value discarded. The input should be a non-negative number.');
       text(-L*1.1,-L*1.05,'The input value discarded. The input should be a non-negative number.','Color','r');
       pause(3);
       bad_input_warning = 0;
   end

   dt = .3/(k_res*c_tot); % time step; this is inside the loop in case I change
                          % c_tot (through changing c) or k_res while running.
   for n = 1:N_MT
       if MT_state(n) == 1 % if in the growth state

           % disp(['c = ',num2str(c),',  k_cat = ',num2str(k_cat)]);

           if c == 0 || rand > exp(-dt*f_cat(k_cat,c)) % if have catastrophe
               MT_state(n) = 2;
           else % continue growth
               % dl is the length increment; MT length cannot be > L;
               % also, because growth reduces free Tu concentration c,
               % it cannot become negative. The factor of (.5+rand) in
               % front of the velocity is not necessary, but is used here
               % to introduce some randomness.
               dl = min([(.5+rand)*v_g(k_g,c)*dt,L-MT_length(n),c/cpu]);
               MT_length(n) = MT_length(n) + dl;
               c = c - dl*cpu;
           end
       else % if in the shortening state, i.e., MT_state(n) = 2
           if rand > exp(-dt*f_res(k_res,c)) % if have rescue
               MT_state(n) = 1;
           else % continue shortening
               dl = min([(.5+rand)*v_s*dt,MT_length(n)]);
               MT_length(n) = MT_length(n) - dl;
               c = c + dl*cpu;
           end
       end
   end % for n = 1:N_MT
   % make a check:
   if c > (1.00000000001)*c_tot || c < 0
       disp(['ERROR: wrong concentration of free Tu: ',num2str(c)]);
       return;
   elseif c > c_tot
       c = c_tot;
   end

   err = c_tot - c - sum(MT_length(1:N_MT))*cpu;
   if abs(err/c_tot) > 1e-10
       disp('ERROR: There is no concervation of tubulin!');
       disp(['step ',num2str(step),': c_tot - c - sum(MT_length(1:N_MT))*cpu = ',num2str(err)]);
       return;
   else % make a correction:
       c = c + err;
   end

   % updating the value of c in the GUI box:
   set(hObject_c,'string',num2str(c));

   % drawing:
   clr = ['b','r']; % colors of growing and shortening MTs
   hold off;
   plot(L*cos(a),L*sin(a),'k','LineWidth',3); axis off; axis square; hold on;
   for n = 1:N_MT
       plot([0 MT_length(n)*cos(2*pi*n/N_MT)],[0 MT_length(n)*sin(2*pi*n/N_MT)],clr(MT_state(n)));
   end
   title([num2str(N_MT),' MTs;  step ',num2str(step),': \Deltat = ',num2str(dt,3),'s, c_{tot} = ',num2str(c_tot,3),', c = ',num2str(c,3)]);
   pause(.01);
end
if step == STEPS
   disp('Reached the maximal allowed number of steps. Click ''Reset'' to proceed.');
   text(-L*1.1,-L*1.05,'Reached the maximal allowed number of steps. Click ''Reset'' to proceed.','Color','r');
end



% --- Executes on button press in Stop.
function Stop_Callback(hObject, eventdata, handles)
% hObject    handle to Stop (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global stop;
stop = 1;


% --- Executes on button press in Reset.
function Reset_Callback(hObject, eventdata, handles)
% hObject    handle to Reset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global a L N_MT N_MT_max MT_length MT_state c c_tot step;
% initialization:
MT_length = zeros(N_MT_max,1);
MT_state = ones(N_MT_max,1); % 1 - growth state, 2 - shortening state
c = c_tot;
step = 0;

hold off;
plot(L*cos(a),L*sin(a),'k','LineWidth',3); axis off; axis square;



% --- Executes on button press in Quit.
function Quit_Callback(hObject, eventdata, handles)
% hObject    handle to Quit (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

disp('Good bye!');
% first need to stop, then quit; if don't stop then quit with errors.
global stop
stop = 1;
close(handles.output);