choose_file_type.m

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

% Last Modified by GUIDE v2.5 12-May-2014 16:08:59

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @choose_file_type_OpeningFcn, ...
                   'gui_OutputFcn',  @choose_file_type_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 choose_file_type is made visible.
function choose_file_type_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 choose_file_type (see VARARGIN)

% Choose default command line output for choose_file_type
handles.output = [];
handles.output.num_treat=1;
handles.output.num_ctr=1;
handles.output.build='hg19';
% Update handles structure
guidata(hObject, handles);

% Insert custom Title and Text if specified by the user
% Hint: when choosing keywords, be sure they are not easily confused 
% with existing figure properties.  See the output of set(figure) for
% a list of figure properties.
if(nargin > 3)
    for index = 1:2:(nargin-3),
        if nargin-3==index, break, end
        switch lower(varargin{index})
         case 'title'
          set(hObject, 'Name', varargin{index+1});
         case 'string'
          set(handles.title, 'String', varargin{index+1});
        end
    end
end

% Determine the position of the dialog - centered on the callback figure
% if available, else, centered on the screen
FigPos=get(0,'DefaultFigurePosition');
OldUnits = get(hObject, 'Units');
set(hObject, 'Units', 'pixels');
OldPos = get(hObject,'Position');
FigWidth = OldPos(3);
FigHeight = OldPos(4);
if isempty(gcbf)
    ScreenUnits=get(0,'Units');
    set(0,'Units','pixels');
    ScreenSize=get(0,'ScreenSize');
    set(0,'Units',ScreenUnits);

    FigPos(1)=1/2*(ScreenSize(3)-FigWidth);
    FigPos(2)=2/3*(ScreenSize(4)-FigHeight);
else
    GCBFOldUnits = get(gcbf,'Units');
    set(gcbf,'Units','pixels');
    GCBFPos = get(gcbf,'Position');
    set(gcbf,'Units',GCBFOldUnits);
    FigPos(1:2) = [(GCBFPos(1) + GCBFPos(3) / 2) - FigWidth / 2, ...
                   (GCBFPos(2) + GCBFPos(4) / 2) - FigHeight / 2];
end
FigPos(3:4)=[FigWidth FigHeight];
set(hObject, 'Position', FigPos);
set(hObject, 'Units', OldUnits);



% Make the GUI modal
set(handles.figure1,'WindowStyle','modal')

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

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

% The figure can be deleted now
delete(handles.figure1);


% --- Executes when user attempts to close figure1.
function figure1_CloseRequestFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if isequal(get(hObject, 'waitstatus'), 'waiting')
    % The GUI is still in UIWAIT, us UIRESUME
    uiresume(hObject);
else
    % The GUI is no longer waiting, just close it
    delete(hObject);
end


% --- Executes on key press over figure1 with no controls selected.
function figure1_KeyPressFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
   
    
if isequal(get(hObject,'CurrentKey'),'return')
    uiresume(handles.figure1);
end    


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

contents = cellstr(get(hObject,'String'));
handles.output.sample_type = contents{get(hObject,'Value')};

% Update handles structure
guidata(hObject, handles);

% Use UIRESUME instead of delete because the OutputFcn needs
% to get the updated handles structure.
%uiresume(handles.figure1);


% --- Executes during object creation, after setting all properties.
function exp_list_CreateFcn(hObject, eventdata, handles)
% hObject    handle to exp_list (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 && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end
set(hObject,'String',{'Select data type...','Screen data','Gene expression data'})


% --- Executes on button press in pushbutton3.
function pushbutton3_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

uiresume(handles.figure1);


% --- Executes during object creation, after setting all properties.
function figure1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called


% --- Executes on selection change in popupmenu3.
function popupmenu3_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu3 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu3
contents = cellstr(get(hObject,'String'));
handles.output.build = contents{get(hObject,'Value')};

% Update handles structure
guidata(hObject, handles);

% --- Executes during object creation, after setting all properties.
function popupmenu3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu3 (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 && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end
set(hObject,'String',{'Select organism...','hg19','mm9'})



function edit2_Callback(hObject, eventdata, handles)
% hObject    handle to edit2 (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 edit2 as text
%        str2double(get(hObject,'String')) returns contents of edit2 as a double
n=str2num(get(hObject,'String'));
if isempty(n), alert('String','Please enter a valid number...'), return; end
handles.output.num_treat=n;
guidata(hObject, handles);

% --- Executes during object creation, after setting all properties.
function edit2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit2 (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



function edit3_Callback(hObject, eventdata, handles)
% hObject    handle to edit3 (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 edit3 as text
%        str2double(get(hObject,'String')) returns contents of edit3 as a double
n=str2num(get(hObject,'String'));
if isempty(n), alert('String','Please enter a valid number...'), return; end
handles.output.num_ctr=n;
guidata(hObject, handles);

% --- Executes during object creation, after setting all properties.
function edit3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit3 (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