function varargout = virtualPCR(varargin)
% VIRTUALPCR M-file for virtualPCR.fig
% VIRTUALPCR, by itself, creates a new VIRTUALPCR or raises the existing
% singleton*.
%
% H = VIRTUALPCR returns the handle to a new VIRTUALPCR or the handle to
% the existing singleton*.
%
% VIRTUALPCR('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIRTUALPCR.M with the given input arguments.
%
% VIRTUALPCR('Property','Value',...) creates a new VIRTUALPCR or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before virtualPCR_OpeningFunction gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to virtualPCR_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% This GUI is based on the virtualPCR algorithm which is located in
% the doRTReaction.m file. If you want to tweak parameters in this
% algorithm
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Copyright 2002-2003 The MathWorks, Inc.
% Edit the above text to modify the response to help virtualPCR
% Last Modified by GUIDE v2.5 12-Sep-2007 17:23:09
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @virtualPCR_OpeningFcn, ...
'gui_OutputFcn', @virtualPCR_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
%Call global
% --- Executes just before virtualPCR is made visible.
function virtualPCR_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 virtualPCR (see VARARGIN)
%Show welcome message
clc;
disp(' ');
disp(' ');
disp(' ');
disp(' ');
disp('***********************************');
disp('* virtualPCR - (c)2007 University of Antwerp ');
disp('* Author: Gie Spaepen');
disp('* ');
disp('* University of Antwerp');
disp('* Dept. of Medicine');
disp('* ');
disp('* Email: gie.spaepen@ua.ac.be');
disp('* ');
disp('***********************************');
disp(' ');
disp(' ');
disp(' ');
disp(' ');
%Reset global values
global vSamples;
vSamples = {'Name','Cycles','Eff','dNTP','Primers/Probe','RIN','cDNA'};
% Choose default command line output for virtualPCR
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes virtualPCR wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = virtualPCR_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 selection change in lbSamples.
function lbSamples_Callback(hObject, eventdata, handles)
% hObject handle to lbSamples (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 lbSamples contents as cell array
% contents{get(hObject,'Value')} returns selected item from lbSamples
% --- Executes during object creation, after setting all properties.
function lbSamples_CreateFcn(hObject, eventdata, handles)
% hObject handle to lbSamples (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox 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 txtName_Callback(hObject, eventdata, handles)
% hObject handle to txtName (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 txtName as text
% str2double(get(hObject,'String')) returns contents of txtName as a double
% --- Executes during object creation, after setting all properties.
function txtName_CreateFcn(hObject, eventdata, handles)
% hObject handle to txtName (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 txtCDNA_Callback(hObject, eventdata, handles)
% hObject handle to txtCDNA (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 txtCDNA as text
% str2double(get(hObject,'String')) returns contents of txtCDNA as a double
% --- Executes during object creation, after setting all properties.
function txtCDNA_CreateFcn(hObject, eventdata, handles)
% hObject handle to txtCDNA (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 txtEff_Callback(hObject, eventdata, handles)
% hObject handle to txtEff (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 txtEff as text
% str2double(get(hObject,'String')) returns contents of txtEff as a double
% --- Executes during object creation, after setting all properties.
function txtEff_CreateFcn(hObject, eventdata, handles)
% hObject handle to txtEff (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 txtCycles_Callback(hObject, eventdata, handles)
% hObject handle to txtCycles (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 txtCycles as text
% str2double(get(hObject,'String')) returns contents of txtCycles as a double
% --- Executes during object creation, after setting all properties.
function txtCycles_CreateFcn(hObject, eventdata, handles)
% hObject handle to txtCycles (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 txtPrimers_Callback(hObject, eventdata, handles)
% hObject handle to txtPrimers (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 txtPrimers as text
% str2double(get(hObject,'String')) returns contents of txtPrimers as a double
% --- Executes during object creation, after setting all properties.
function txtPrimers_CreateFcn(hObject, eventdata, handles)
% hObject handle to txtPrimers (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
% --- Executes on button press in btAdd.
function btAdd_Callback(hObject, eventdata, handles)
% hObject handle to btAdd (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%Call global
global vSamples;
%Get the fields
%try
name = get(handles.txtName,'string');
eff = str2num(get(handles.txtEff,'string'));
cs = str2num(get(handles.txtCycles,'string'));
dntp = str2num(get(handles.txtDNTP,'string'));
pp = str2num(get(handles.txtPrimers,'string'));
rin = str2num(get(handles.txtRIN,'string'));
disp(rin);
cdna = str2num(get(handles.txtCDNA,'string'));
%Compile the sample
sample = {name,eff,cs,dntp,pp,rin,cdna};
%and concatenate
try
vSamples = [vSamples;sample];
catch
sample = {name,eff,cs,dntp,pp,rin,cdna,'',''};
vSamples = [vSamples;sample];
end
%catch
disp('* Some of the parameters are no numbers');
%end
%Set the listbox
set(handles.lbSamples,'string',vSamples(:,1));
% --- Executes on button press in btCalculate.
function btCalculate_Callback(hObject, eventdata, handles)
% hObject handle to btCalculate (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%Call global
global vSamples;
%Set axes
axes(handles.axAmpPlot);
%Clear axes
cla;
%Results
vResults = {'Ct','StDev'};
%Loop through the samples
clc;
disp('***********************************');
disp('* Start PCR Reaction');
disp('***********************************');
disp(' ');
for i=2:size(vSamples,1)
%Get the parameters
name = vSamples{i,1};
eff = vSamples{i,2};
cs = vSamples{i,3};
dntp = vSamples{i,4};
pp = vSamples{i,5};
rin = vSamples{i,6};
cdna = vSamples{i,7};
%Launch the reaction
disp('***********************************');
disp(strcat('* Name:',name));
[rn,ct,ctstdev] = doTripleRT(cdna,dntp,pp,cs,eff,rin,1);
%Concatenate the results
result = {ct,ctstdev};
vResults = [vResults;result];
disp(' ');
end
%Save figure, ask first
%button = questdlg('Save this plot as image?','virtualPCR','Yes','No','No');
%if strcmp(button,'Yes') == 1
% saveas(gcf,'lastrun','jpg');
%end
function txtDNTP_Callback(hObject, eventdata, handles)
% hObject handle to txtDNTP (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 txtDNTP as text
% str2double(get(hObject,'String')) returns contents of txtDNTP as a double
% --- Executes during object creation, after setting all properties.
function txtDNTP_CreateFcn(hObject, eventdata, handles)
% hObject handle to txtDNTP (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
% --- Executes on button press in btClear.
function btClear_Callback(hObject, eventdata, handles)
% hObject handle to btClear (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%Reset the global
global vSamples;
vSamples = {'Name','Cycles','Eff','dNTP','Primers/Probe','RIN','cDNA'};;
%Set axes
axes(handles.axAmpPlot);
%Clear axes
cla;
%Set the listbox
set(handles.lbSamples,'string',vSamples(:,1));
% --- Executes on button press in rbLinear.
function rbLinear_Callback(hObject, eventdata, handles)
% hObject handle to bt_setAxis (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%Set axes
axes(handles.axAmpPlot);
%Change axes
set(gca,'YScale','linear');
% --- Executes on button press in rbLinear.
function rbLog_Callback(hObject, eventdata, handles)
% hObject handle to bt_setAxis (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%Set axes
axes(handles.axAmpPlot);
%Change axes
set(gca,'YScale','log');
% --- Executes on button press in btViewResults.
function btViewResults_Callback(hObject, eventdata, handles)
% hObject handle to btViewResults (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global vSamples;
vSamples
function edit8_Callback(hObject, eventdata, handles)
% hObject handle to edit8 (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 edit8 as text
% str2double(get(hObject,'String')) returns contents of edit8 as a double
% --- Executes during object creation, after setting all properties.
function edit8_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit8 (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 txtRIN_Callback(hObject, eventdata, handles)
% hObject handle to txtRIN (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 txtRIN as text
% str2double(get(hObject,'String')) returns contents of txtRIN as a double
% --- Executes during object creation, after setting all properties.
function txtRIN_CreateFcn(hObject, eventdata, handles)
% hObject handle to txtRIN (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
