mbetoolbox_dnapars(varargin)

function varargout = mbetoolbox_dnapars(varargin)
% MBETOOLBOX_DNAPARS M-file for mbetoolbox_dnapars.fig
%      MBETOOLBOX_DNAPARS, by itself, creates a new MBETOOLBOX_DNAPARS or raises the existing
%      singleton*.
%
%      H = MBETOOLBOX_DNAPARS returns the handle to a new MBETOOLBOX_DNAPARS or the handle to
%      the existing singleton*.
%
%      MBETOOLBOX_DNAPARS('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in MBETOOLBOX_DNAPARS.M with the given input arguments.
%
%      MBETOOLBOX_DNAPARS('Property','Value',...) creates a new MBETOOLBOX_DNAPARS or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before mbetoolbox_dnapars_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to mbetoolbox_dnapars_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

% Matlab Molecular Biology & Evolution Toolbox, (C) 2004,
% Written by James J. Cai

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

% Last Modified by GUIDE v2.5 19-May-2004 01:08:30

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @mbetoolbox_dnapars_OpeningFcn, ...
                   'gui_OutputFcn',  @mbetoolbox_dnapars_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin & isstr(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 mbetoolbox_dnapars is made visible.
function mbetoolbox_dnapars_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 mbetoolbox_dnapars (see VARARGIN)

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

% Update handles structure
guidata(hObject, handles);

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

if (size(varargin,1)>0)
	totalspecies = varargin{1};
if (isnumeric(totalspecies))	
	set(handles.outgrno, 'String', num2str([1:totalspecies]'));
end
end




% --- Outputs from this function are returned to the command line.
function varargout = mbetoolbox_dnapars_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;


% --- Executes on button press in Toption1.
function Toption1_Callback(hObject, eventdata, handles)
% hObject    handle to Toption1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of Toption1
set(handles.Toption1, 'Value', 1);
set(handles.Toption2, 'Value', 0);
set(handles.Toption3, 'Value', 0);




% --- Executes on button press in Toption2.
function Toption2_Callback(hObject, eventdata, handles)
% hObject    handle to Toption2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of Toption2
set(handles.Toption1, 'Value', 0);
set(handles.Toption2, 'Value', 1);
set(handles.Toption3, 'Value', 0);


% --- Executes on button press in Toption3.
function Toption3_Callback(hObject, eventdata, handles)
% hObject    handle to Toption3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of Toption3
set(handles.Toption1, 'Value', 0);
set(handles.Toption2, 'Value', 0);
set(handles.Toption3, 'Value', 1);


% --- 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)

optionstr = '';
i_Toption1 = get(handles.Toption1, 'Value');
i_Toption2 = get(handles.Toption2, 'Value');
i_Toption3 = get(handles.Toption3, 'Value');

if (i_Toption1==1)
    optionstr = [optionstr, ' -u1'];       
elseif(i_Toption2==1)
    optionstr = [optionstr, ' -u2'];
elseif(i_Toption3==1)
    optionstr = [optionstr, ' -u3'];
end

s_maxtree = get(handles.maxtree, 'String');
    optionstr = [optionstr, ' -m', s_maxtree];
    
i_jumbleYES = get(handles.jumbleYES, 'Value');
i_jumbleNO = get(handles.jumbleNO, 'Value');
s_njumble = get(handles.njumble, 'String');

if (i_jumbleYES==1)
    optionstr = [optionstr, ' -j', s_njumble];
    optionstr = [optionstr, ' -s', num2str(i_oddseed)];
end

optionstr = [optionstr, ' -o', num2str(get(handles.outgrno,'Value'))];

i_threshYES = get(handles.threshYES, 'Value');
i_threshNO = get(handles.threshNO, 'Value');
s_threshold = get(handles.threshold, 'String');

if (i_threshYES==1)
    optionstr = [optionstr, ' -t', s_threshold];        
end



i_transvpYES = get(handles.transvpYES, 'Value');
i_transvpNO = get(handles.transvpNO, 'Value');

if (i_transvpYES==1)
    optionstr = [optionstr, ' -v'];
end

 
 if (exist('mbetoolbox_dnapars.fig','file')==2 && exist('mbetoolbox_dnapars.m','file')==2 && exist('mbetoolbox_dnapars.exe','file')==2) 
		cmd = 'mbetoolbox_dnapars.exe';
		dirstr=chdir2where(cmd);

		outtree = [dirstr,'\outtree'];
		outfile = [dirstr,'\outfile'];

	 if ((exist(outtree,'file')==2 & exist(outfile,'file')==2))

		option = questdlg('The file outfile/outtree already exist. Do you want to replace it?', ...
				   'File(s) Overwrite', ...
				  'Yes','No','No');
		switch option,
			case 'Yes', 
			
			case 'No',
			return;
		end
	end

		cmd = [cmd, ' ', optionstr];
		disp(cmd)
		[s,w] = system(cmd);
if (s==0)
		disp(w)
	set(handles.frameMASK,'Visible','on');
	set(handles.textMASK,'Visible','on');
	set(handles.checkboxOUTFILE,'Visible','on');
	set(handles.checkboxTREEFILE,'Visible','on');
	set(handles.pushbuttonView,'Visible','on');
	set(handles.pushbuttonClose,'Visible','on');


    set(handles.outgrno,'Visible','off');
    set(handles.text5,'Visible','off');
    set(handles.transvpNO,'Visible','off');
    set(handles.transvpYES,'Visible','off');
    set(handles.RUN,'Visible','off');
    set(handles.CLOSE,'Visible','off');    
else
    errordlg('Error occurred when running the third part program!');
    close;
end


	else
		errordlg('ERROR: File required not found.');
	end

    



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

% --- Executes during object creation, after setting all properties.
function maxtree_CreateFcn(hObject, eventdata, handles)
% hObject    handle to maxtree (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
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end



function maxtree_Callback(hObject, eventdata, handles)
% hObject    handle to maxtree (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 maxtree as text
%        str2double(get(hObject,'String')) returns contents of maxtree as a double


% --- Executes during object creation, after setting all properties.
function threshold_CreateFcn(hObject, eventdata, handles)
% hObject    handle to threshold (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
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end



function threshold_Callback(hObject, eventdata, handles)
% hObject    handle to threshold (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 threshold as text
%        str2double(get(hObject,'String')) returns contents of threshold as a double


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

% Hint: get(hObject,'Value') returns toggle state of jumbleYES
set(handles.jumbleYES, 'Value', 1);
set(handles.jumbleNO, 'Value', 0);
set(handles.njumble, 'Enable', 'On');


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

% Hint: get(hObject,'Value') returns toggle state of jumbleNO
set(handles.jumbleYES, 'Value', 0);
set(handles.jumbleNO, 'Value', 1);
set(handles.njumble, 'Enable', 'Off');


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

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


% --- Executes on selection change in outgrno.
function outgrno_Callback(hObject, eventdata, handles)
% hObject    handle to outgrno (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = get(hObject,'String') returns outgrno contents as cell array
%        contents{get(hObject,'Value')} returns selected item from outgrno


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

% Hint: get(hObject,'Value') returns toggle state of transvpYES
set(handles.transvpYES, 'Value', 1);
set(handles.transvpNO, 'Value', 0);
set(handles.threshold, 'Enable', 'on');

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

% Hint: get(hObject,'Value') returns toggle state of transvpNO
set(handles.transvpYES, 'Value', 0);
set(handles.transvpNO, 'Value', 1);
set(handles.threshold, 'Enable', 'off');

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

% Hint: get(hObject,'Value') returns toggle state of threshYES
set(handles.threshYES, 'Value', 1);
set(handles.threshNO, 'Value', 0);
set(handles.threshold, 'Enable','on');

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

% Hint: get(hObject,'Value') returns toggle state of threshNO
set(handles.threshYES, 'Value', 0);
set(handles.threshNO, 'Value', 1);
set(handles.threshold, 'Enable','off');


% --- Executes during object creation, after setting all properties.
function njumble_CreateFcn(hObject, eventdata, handles)
% hObject    handle to njumble (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
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end



function njumble_Callback(hObject, eventdata, handles)
% hObject    handle to njumble (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 njumble as text
%        str2double(get(hObject,'String')) returns contents of njumble as a double


% --- Executes on button press in radiobutton14.
function radiobutton14_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton14 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton14


% --- Executes on button press in radiobutton15.
function radiobutton15_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton15 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton15


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

% Hint: get(hObject,'Value') returns toggle state of checkboxOUTFILE


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

% Hint: get(hObject,'Value') returns toggle state of checkboxTREEFILE


% --- Executes on button press in pushbuttonView.
function pushbuttonView_Callback(hObject, eventdata, handles)
% hObject    handle to pushbuttonView (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
   		cmd = 'mbetoolbox_dnapars.exe';

		dirstr = fileparts(which(cmd));

		outtree = [dirstr,'\outtree'];
		outfile = [dirstr,'\outfile'];

    i_checkboxOUTFILE = get(handles.checkboxOUTFILE, 'Value');
    i_checkboxTREEFILE = get(handles.checkboxTREEFILE, 'Value');
    
    if (i_checkboxOUTFILE==1) 
       	 system(['notepad.exe ', '"', outfile, '" &']);
     end
     
     if (i_checkboxTREEFILE==1) 
       	 system(['njplot.exe ', '"', outtree, '" &']);
     end




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


function [dirstr]=chdir2where(cmd)
% CHDIR2WHERE             Jump to a specified file
%
% CHDIR2WHERE filename changes MATLAB current directory to the one containing
% filename.  filename must be on the MATLAB path.  goto uses the first
% instance of filename that it finds (a la WHICH).
%
% SEE ALSO:  WHICH

% Matlab Molecular Biology & Evolution Toolbox, (C) 2004,
% Written by James J. Cai

cmd_full = which(cmd);
% 5/17/2004 Replace dirstr = cmd_full(1:size(cmd_full,2)-size(cmd,2)); with dirstr = fileparts(cmd_full);
% based on: Scott Hirsch, [e-mail], http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=3145&objectType=file
dirstr = fileparts(cmd_full);
cd(dirstr);