function varargout = ProExtract_V2p4(varargin)
% PROEXTRACT_V2P4 M-file for ProExtract_V2p4.fig
%      PROEXTRACT_V2P4, by itself, creates a new PROEXTRACT_V2P4 or raises the existing
%      singleton*.
%
%      H = PROEXTRACT_V2P4 returns the handle to a new PROEXTRACT_V2P4 or the handle to
%      the existing singleton*.
%
%      PROEXTRACT_V2P4('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in PROEXTRACT_V2P4.M with the given input arguments.
%
%      PROEXTRACT_V2P4('Property','Value',...) creates a new PROEXTRACT_V2P4 or
%      raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before ProExtract_V2p4_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to ProExtract_V2p4_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 ProExtract_V2p4

% Last Modified by GUIDE v2.5 25-Aug-2011 23:21:05

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @ProExtract_V2p4_OpeningFcn, ...
                   'gui_OutputFcn',  @ProExtract_V2p4_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 ProExtract_V2p4 is made visible.
function ProExtract_V2p4_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 ProExtract_V2p4 (see VARARGIN)

% Choose default command line output for ProExtract_V2p4
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes ProExtract_V2p4 wait for user response (see UIRESUME)
% uiwait(handles.figure1);

% --- Outputs from this function are returned to the command line.
function varargout = ProExtract_V2p4_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 HSSPradio2.
function HSSPradio2_Callback(hObject, eventdata, handles)
% hObject    handle to HSSPradio2 (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 HSSPradio2
set(handles.HSSPradio1, 'Value',0);
set(handles.HSSPradio2, 'Value',1);
set(handles.HSSPradio3, 'Value',0);
set(handles.HSSPinput2, 'Enable', 'on');
set(handles.HSSPinput3, 'Enable','off');
set(handles.HSSPbrowse2, 'Enable', 'on');


function HSSPinput2_Callback(hObject, eventdata, handles)
% hObject    handle to HSSPinput2 (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 HSSPinput2 as text
%        str2double(get(hObject,'String')) returns contents of HSSPinput2 as a double


% --- Executes during object creation, after setting all properties.
function HSSPinput2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to HSSPinput2 (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


% --- Executes on button press in HSSPbrowse2.
function HSSPbrowse2_Callback(hObject, eventdata, handles)
% hObject    handle to HSSPbrowse2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

[FileName,PathName,FilterIndex] = uigetfile('*.*','MultiSelect','off');
set(handles.HSSPinput2,'String',[PathName FileName]);

% --- Executes on button press in HSSPradio3.
function HSSPradio3_Callback(hObject, eventdata, handles)
% hObject    handle to HSSPradio3 (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 HSSPradio3
set(handles.HSSPradio1, 'Value',0);
set(handles.HSSPradio2, 'Value',0);
set(handles.HSSPradio3, 'Value',1);
set(handles.HSSPinput2, 'Enable', 'off');
set(handles.HSSPinput3, 'Enable','on');
set(handles.HSSPbrowse2, 'Enable', 'off');



function HSSPinput3_Callback(hObject, eventdata, handles)
% hObject    handle to HSSPinput3 (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 HSSPinput3 as text
%        str2double(get(hObject,'String')) returns contents of HSSPinput3 as a double


% --- Executes during object creation, after setting all properties.
function HSSPinput3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to HSSPinput3 (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 PDBfileInput_Callback(hObject, eventdata, handles)
% hObject    handle to PDBfileInput (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 PDBfileInput as text
%        str2double(get(hObject,'String')) returns contents of PDBfileInput as a double


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

PDBpath = [cd '\PDB\'];
set(hObject,'String',PDBpath);


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

[FileName,PathName,FilterIndex] = uigetfile('','MultiSelect','off');
set(handles.PDBfileInput,'String',PathName);



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


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

HSSPpath = [cd '\hssp\'];
set(hObject,'String',HSSPpath);


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

[FileName,PathName,FilterIndex] = uigetfile('','MultiSelect','off');
set(handles.HSSPfileInput,'String',PathName);


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

switch 1
    case get(handles.HSSPradio1,'Value')
        GetMode = 1;
        FileList = '';
    case get(handles.HSSPradio2,'Value')
        GetMode = 2;
        FileList = get(handles.HSSPinput2,'String');
    case get(handles.HSSPradio3,'Value')
        GetMode = 3;
        FileList = get(handles.HSSPinput3,'String');
end
PDBpath = get(handles.PDBfileInput,'String');
HSSPpath = get(handles.HSSPfileInput,'String');
ExProStructPath = get(handles.SaveExProStructFolder,'String');

DebugMode = get(handles.DebugMode,'Value');
UnknownHault = get(handles.UnknownHault,'Value');
DoValidate = get(handles.DoValidate,'Value');

ProfileOn = get(handles.DebugOn,'Value');

OnlyMissing = get(handles.OnlyMissing,'Value');

if ProfileOn,
    profile on
end
CreateExProStruct(GetMode,FileList,PDBpath,HSSPpath,ExProStructPath,DebugMode,UnknownHault,DoValidate,OnlyMissing);
if ProfileOn
    profile viewer
    profile clear
    profile off
end

% --- Executes on button press in AlignmentsCheck.
function AlignmentsCheck_Callback(hObject, eventdata, handles)
% hObject    handle to AlignmentsCheck (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 AlignmentsCheck
if get(hObject,'Value'),
    set(handles.MinIDcut,'Enable','on');

%    set(handles.Distance1, 'Value',0);
%    set(handles.Distance2, 'Value',0);
%    set(handles.Distance3, 'Value',1);
%    set(handles.Distance4, 'Value',0);
    
%    set(handles.Distance1, 'Enable', 'off');
%    set(handles.Distance2, 'Enable', 'off');
%    set(handles.Distance4, 'Enable', 'off');
else
    set(handles.MinIDcut,'Enable','off');
    
%    set(handles.Distance1, 'Enable', 'on');
%    set(handles.Distance2, 'Enable', 'on');
%    set(handles.Distance4, 'Enable', 'on');
end


% --- Executes on button press in CommulativeCheck.
function CommulativeCheck_Callback(hObject, eventdata, handles)
% hObject    handle to CommulativeCheck (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 CommulativeCheck


% --- Executes on button press in pushbutton5.
function pushbutton5_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton5 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


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


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

ExProStructFP = [cd '\ExProStruct\'];
set(hObject,'String',ExProStructFP);



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

[FileName,PathName,FilterIndex] = uigetfile('','MultiSelect','off');
set(handles.ExProStructFolderPath,'String',PathName);



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

switch 1
    case get(handles.ExProStructRadio1,'Value')
        GetMode = 1;
        ChainsSpecified = 0;
        FileList = '';
    case get(handles.ExProStructRadio2,'Value')
        GetMode = 2;
        ChainsSpecified = get(handles.ChainsSpecified,'Value');
        FileList = get(handles.ExProStructInput2,'String');
    case get(handles.ExProStructRadio3,'Value')
        GetMode = 3;
        ChainsSpecified = 0;
        FileList = get(handles.ExProStructInput3,'String');
end
ExProStructPath = get(handles.ExProStructFolderPath,'String');
UpdateText = DoUpdateSelection(GetMode,FileList,ExProStructPath);
set(handles.CurrentSelection,'String',UpdateText);


% --- Executes during object creation, after setting all properties.
function edit15_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit15 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called



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


% --- Executes during object creation, after setting all properties.
function AcMin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to AcMin (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 AcMax_Callback(hObject, eventdata, handles)
% hObject    handle to AcMax (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 AcMax as text
%        str2double(get(hObject,'String')) returns contents of AcMax as a double


% --- Executes during object creation, after setting all properties.
function AcMax_CreateFcn(hObject, eventdata, handles)
% hObject    handle to AcMax (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 AcRes_Callback(hObject, eventdata, handles)
% hObject    handle to AcRes (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 AcRes as text
%        str2double(get(hObject,'String')) returns contents of AcRes as a double


% --- Executes during object creation, after setting all properties.
function AcRes_CreateFcn(hObject, eventdata, handles)
% hObject    handle to AcRes (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 DistMin_Callback(hObject, eventdata, handles)
% hObject    handle to DistMin (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 DistMin as text
%        str2double(get(hObject,'String')) returns contents of DistMin as a double


% --- Executes during object creation, after setting all properties.
function DistMin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to DistMin (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 DistMax_Callback(hObject, eventdata, handles)
% hObject    handle to DistMax (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 DistMax as text
%        str2double(get(hObject,'String')) returns contents of DistMax as a double


% --- Executes during object creation, after setting all properties.
function DistMax_CreateFcn(hObject, eventdata, handles)
% hObject    handle to DistMax (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 DistRes_Callback(hObject, eventdata, handles)
% hObject    handle to DistRes (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 DistRes as text
%        str2double(get(hObject,'String')) returns contents of DistRes as a double


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


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

switch 1
    case get(handles.ExProStructRadio1,'Value')
        GetMode = 1;
        ChainsSpecified = 0;
        FileList = '';
    case get(handles.ExProStructRadio2,'Value')
        GetMode = 2;
        ChainsSpecified = get(handles.ChainsSpecified,'Value');        
        FileList = get(handles.ExProStructInput2,'String');
    case get(handles.ExProStructRadio3,'Value')
        GetMode = 3;
        ChainsSpecified = 0;
        FileList = get(handles.ExProStructInput3,'String');
end

ExProStructPath = get(handles.ExProStructFolderPath,'String');

AcMin = str2num(get(handles.AcMin,'String'))/100;
AcMax = str2num(get(handles.AcMax,'String'))/100;
AcRes = str2num(get(handles.AcRes,'String'))/100;

DistMin = str2num(get(handles.DistMin,'String'));
DistMax = str2num(get(handles.DistMax,'String'));
DistRes = str2num(get(handles.DistRes,'String'));

CLMin = str2num(get(handles.CLmin,'String'));
CLMax = str2num(get(handles.CLmax,'String'));
CLRes = str2num(get(handles.CLres,'String'));

MinIDcut = str2num(get(handles.MinIDcut,'String'))/100;


switch 1
    case get(handles.Distance1,'Value')
        DistMode = 1;
    case get(handles.Distance2,'Value')
        DistMode = 2;
    case get(handles.Distance3,'Value')
        DistMode = 3;
    case get(handles.Distance4,'Value')
        DistMode = 4;
end

MultiChain = get(handles.MultiChainCheck,'Value');
UseAlign = get(handles.AlignmentsCheck,'Value');
UseComulative = get(handles.CommulativeCheck,'Value');

OutputFolder = get(handles.OutputFolder,'String');
OutputName = get(handles.OutputName,'String');

DebugMode = get(handles.DebugMode,'Value');
UnknownHault = get(handles.UnknownHault,'Value');
DoValidate = get(handles.DoValidate,'Value');
ProfileOn = get(handles.DebugOn,'Value');

CreateIndex = get(handles.CreateIndexSet,'Value');
IncludeFromOther = get(handles.IncludeFromOtherCheck,'Value');
ReferencePath = get(handles.ReferencePath,'String');


if ProfileOn,
    profile on
end

%if frac(sym((AcMax-AcMin)/AcRes)) ~= 0,
%    fprintf(1,'Difference between AcMax and AcMin must be divisible by AcRes');
%elseif frac(sym((DistMax-DistMin)/DistRes)) ~= 0,
%    fprintf(1,'Difference between DistMax and DistMin must be divisible by DistRes');
%else
    OutputPath = [OutputFolder OutputName '.mat'];
    fprintf(1,'Creating dataset file and saving preliminary variables.\n');
    save(OutputPath,'AcMin','AcMax','AcRes','DistMin','DistMax','DistRes','DistMode','UseAlign','UseComulative','MinIDcut','CLMin','CLMax','CLRes','MultiChain');
    fprintf(1,'Datasetfile created.\n');
    if get(handles.checkbox10,'Value')
        ScrambleMode = 'None';
        ScrambleNum = 1;
        CreateDataset(GetMode,FileList,ExProStructPath,AcMin,AcMax,AcRes,DistMin,DistMax,DistRes,DistMode,UseAlign,UseComulative,MinIDcut,CLMin,CLMax,CLRes,MultiChain,OutputPath,DebugMode,UnknownHault,DoValidate,ScrambleMode,ScrambleNum,CreateIndex,ChainsSpecified);
    end
    if get(handles.checkbox11,'Value'),
        if IncludeFromOther,
            load(ReferencePath,'Naboref');
            save(OutputPath,'-append','Naboref');
            clear Naboref
        else
            if get(handles.checkbox9,'Value'),
                ScrambleMode = 'SA';
            else
                ScrambleMode = 'All';
            end
            ScrambleNum = str2num(get(handles.edit36,'String'));
            CreateDataset(GetMode,FileList,ExProStructPath,AcMin,AcMax,AcRes,DistMin,DistMax,DistRes,DistMode,UseAlign,UseComulative,MinIDcut,CLMin,CLMax,CLRes,MultiChain,OutputPath,DebugMode,UnknownHault,DoValidate,ScrambleMode,ScrambleNum,0,ChainsSpecified);
        end
    end
    %end
    
    if ProfileOn
    profile viewer
    profile clear
    profile off
end


% --- Executes on button press in HSSPradio1.
function HSSPradio1_Callback(hObject, eventdata, handles)
% hObject    handle to HSSPradio1 (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 HSSPradio1
set(handles.HSSPradio1, 'Value',1);
set(handles.HSSPradio2, 'Value',0);
set(handles.HSSPradio3, 'Value',0);
set(handles.HSSPinput2, 'Enable', 'off');
set(handles.HSSPinput3, 'Enable','off');
set(handles.HSSPbrowse2, 'Enable', 'off');




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


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

HSSPpath = [cd '\ExProStruct\'];
set(hObject,'String',HSSPpath);

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

[FileName,PathName,FilterIndex] = uigetfile('','MultiSelect','off');
set(handles.SaveExProStructFolder,'String',PathName);



% --- Executes on button press in Distance1.
function Distance1_Callback(hObject, eventdata, handles)
% hObject    handle to Distance1 (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 Distance1

set(handles.Distance1, 'Value',1);
set(handles.Distance2, 'Value',0);
set(handles.Distance3, 'Value',0);
set(handles.Distance4, 'Value',0);

% --- Executes on button press in Distance2.
function Distance2_Callback(hObject, eventdata, handles)
% hObject    handle to Distance2 (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 Distance2

set(handles.Distance1, 'Value',0);
set(handles.Distance2, 'Value',1);
set(handles.Distance3, 'Value',0);
set(handles.Distance4, 'Value',0);

% --- Executes on button press in Distance3.
function Distance3_Callback(hObject, eventdata, handles)
% hObject    handle to Distance3 (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 Distance3

set(handles.Distance1, 'Value',0);
set(handles.Distance2, 'Value',0);
set(handles.Distance3, 'Value',1);
set(handles.Distance4, 'Value',0);

% --- Executes on button press in Distance4.
function Distance4_Callback(hObject, eventdata, handles)
% hObject    handle to Distance4 (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 Distance4

set(handles.Distance1, 'Value',0);
set(handles.Distance2, 'Value',0);
set(handles.Distance3, 'Value',0);
set(handles.Distance4, 'Value',1);


% --- Executes on button press in ExProStructRadio2.
function ExProStructRadio2_Callback(hObject, eventdata, handles)
% hObject    handle to ExProStructRadio2 (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 ExProStructRadio2

set(handles.ExProStructRadio1, 'Value',0);
set(handles.ExProStructRadio2, 'Value',1);
set(handles.ExProStructRadio3, 'Value',0);
set(handles.ExProStructInput2, 'Enable', 'on');
set(handles.ExProStructInput3, 'Enable','off');
set(handles.ExProStructBrowse2, 'Enable', 'on');
set(handles.ChainsSpecified, 'Enable', 'on');


function ExProStructInput2_Callback(hObject, eventdata, handles)
% hObject    handle to ExProStructInput2 (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 ExProStructInput2 as text
%        str2double(get(hObject,'String')) returns contents of ExProStructInput2 as a double


% --- Executes during object creation, after setting all properties.
function ExProStructInput2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to ExProStructInput2 (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


% --- Executes on button press in ExProStructBrowse2.
function ExProStructBrowse2_Callback(hObject, eventdata, handles)
% hObject    handle to ExProStructBrowse2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

[FileName,PathName,FilterIndex] = uigetfile('*.*','MultiSelect','off');
set(handles.ExProStructInput2,'String',[PathName FileName]);


% --- Executes on button press in ExProStructRadio3.
function ExProStructRadio3_Callback(hObject, eventdata, handles)
% hObject    handle to ExProStructRadio3 (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 ExProStructRadio3

set(handles.ExProStructRadio1, 'Value',0);
set(handles.ExProStructRadio2, 'Value',0);
set(handles.ExProStructRadio3, 'Value',1);
set(handles.ExProStructInput2, 'Enable', 'off');
set(handles.ExProStructInput3, 'Enable','on');
set(handles.ExProStructBrowse2, 'Enable', 'off');
set(handles.ChainsSpecified, 'Enable', 'off');

function ExProStructInput3_Callback(hObject, eventdata, handles)
% hObject    handle to ExProStructInput3 (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 ExProStructInput3 as text
%        str2double(get(hObject,'String')) returns contents of ExProStructInput3 as a double


% --- Executes during object creation, after setting all properties.
function ExProStructInput3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to ExProStructInput3 (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


% --- Executes on button press in ExProStructRadio1.
function ExProStructRadio1_Callback(hObject, eventdata, handles)
% hObject    handle to ExProStructRadio1 (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 ExProStructRadio1

set(handles.ExProStructRadio1, 'Value',1);
set(handles.ExProStructRadio2, 'Value',0);
set(handles.ExProStructRadio3, 'Value',0);
set(handles.ExProStructInput2, 'Enable', 'off');
set(handles.ExProStructInput3, 'Enable','off');
set(handles.ExProStructBrowse2, 'Enable', 'off');
set(handles.ChainsSpecified, 'Enable', 'off');



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


% --- Executes during object creation, after setting all properties.
function MinIDcut_CreateFcn(hObject, eventdata, handles)
% hObject    handle to MinIDcut (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 CLmin_Callback(hObject, eventdata, handles)
% hObject    handle to CLmin (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 CLmin as text
%        str2double(get(hObject,'String')) returns contents of CLmin as a double


% --- Executes during object creation, after setting all properties.
function CLmin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to CLmin (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 CLmax_Callback(hObject, eventdata, handles)
% hObject    handle to CLmax (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 CLmax as text
%        str2double(get(hObject,'String')) returns contents of CLmax as a double


% --- Executes during object creation, after setting all properties.
function CLmax_CreateFcn(hObject, eventdata, handles)
% hObject    handle to CLmax (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 CLres_Callback(hObject, eventdata, handles)
% hObject    handle to CLres (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 CLres as text
%        str2double(get(hObject,'String')) returns contents of CLres as a double


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



% --- Executes on button press in MultiChainCheck.
function MultiChainCheck_Callback(hObject, eventdata, handles)
% hObject    handle to MultiChainCheck (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 MultiChainCheck





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


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

DatasetPath = [cd '\Dataset\'];
set(hObject,'String',DatasetPath);


% --- Executes on button press in pushbutton13.
function pushbutton13_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton13 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

[FileName,PathName,FilterIndex] = uigetfile('*.*','MultiSelect','off');
set(handles.OutputFolder,'String',[PathName FileName]);


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


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




% --- Executes on button press in DebugMode.
function DebugMode_Callback(hObject, eventdata, handles)
% hObject    handle to DebugMode (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 DebugMode


% --- Executes on button press in UnknownHault.
function UnknownHault_Callback(hObject, eventdata, handles)
% hObject    handle to UnknownHault (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 UnknownHault


% --- Executes on button press in DoValidate.
function DoValidate_Callback(hObject, eventdata, handles)
% hObject    handle to DoValidate (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 DoValidate



% --- Executes on button press in DebugOn.
function DebugOn_Callback(hObject, eventdata, handles)
% hObject    handle to DebugOn (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 DebugOn




% --- Executes on button press in OnlyMissing.
function OnlyMissing_Callback(hObject, eventdata, handles)
% hObject    handle to OnlyMissing (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 OnlyMissing





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


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

ExProStructFP = [cd '\Dataset\'];
set(hObject,'String',ExProStructFP);


% --- Executes on button press in ConvertBrowse1.
function ConvertBrowse1_Callback(hObject, eventdata, handles)
% hObject    handle to ConvertBrowse1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

[FileName,PathName,FilterIndex] = uigetfile('','MultiSelect','off');
set(handles.ConvertRawDataset,'String',[PathName FileName]);


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


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

ExProStructFP = [cd '\Dataset\'];
set(hObject,'String',ExProStructFP);


% --- Executes on button press in ConvertBrowse2.
function ConvertBrowse2_Callback(hObject, eventdata, handles)
% hObject    handle to ConvertBrowse2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

[FileName,PathName,FilterIndex] = uigetfile('','MultiSelect','off');
set(handles.ConvertOutputFolder,'String',PathName);


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


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


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

ConvertRawDataset = get(handles.ConvertRawDataset,'String');
ConvertOutputFolder = get(handles.ConvertOutputFolder,'String');
ConvertOutputName = get(handles.ConvertOutputName,'String');

ConvertOutputPath = [ConvertOutputFolder ConvertOutputName '.mat'];

Converter(ConvertRawDataset,ConvertOutputPath);


function edit36_Callback(hObject, eventdata, handles)
% hObject    handle to edit36 (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 edit36 as text
%        str2double(get(hObject,'String')) returns contents of edit36 as a double


% --- Executes during object creation, after setting all properties.
function edit36_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit36 (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


% --- Executes on button press in checkbox9.
function checkbox9_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox9 (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 checkbox9




% --- Executes on button press in checkbox10.
function checkbox10_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox10 (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 checkbox10

if ~ get(handles.checkbox11,'Value'),
    set(handles.checkbox10,'Value',1);
end

% --- Executes on button press in checkbox11.
function checkbox11_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox11 (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 checkbox11

if ~ get(handles.checkbox10,'Value'),
    set(handles.checkbox11,'Value',1);
end


if get(handles.checkbox11,'Value'),
    set(handles.IncludeFromOtherCheck,'Enable','on');
    if get(handles.IncludeFromOtherCheck,'Value'),
        set(handles.ReferencePath,'Enable','on');
        set(handles.edit36,'Enable','off');
        set(handles.checkbox9,'Enable','off');
    else
        set(handles.ReferencePath,'Enable','off');
        set(handles.edit36,'Enable','on');
        set(handles.checkbox9,'Enable','on');
    end
else
    set(handles.IncludeFromOtherCheck,'Enable','off');
    set(handles.ReferencePath,'Enable','off');
    set(handles.edit36,'Enable','off');
    set(handles.checkbox9,'Enable','off');
end


% --- Executes on button press in CreateIndexSet.
function CreateIndexSet_Callback(hObject, eventdata, handles)
% hObject    handle to CreateIndexSet (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 CreateIndexSet


% --- Executes on button press in IncludeFromOtherCheck.
function IncludeFromOtherCheck_Callback(hObject, eventdata, handles)
% hObject    handle to IncludeFromOtherCheck (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 IncludeFromOtherCheck


if get(handles.IncludeFromOtherCheck,'Value'),
    set(handles.ReferencePath,'Enable','on');
    set(handles.edit36,'Enable','off');
    set(handles.checkbox9,'Enable','off');
else
    set(handles.ReferencePath,'Enable','off');
    set(handles.edit36,'Enable','on');
    set(handles.checkbox9,'Enable','on');
end

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


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



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

[FileName,PathName,FilterIndex] = uigetfile('*.*','MultiSelect','off');
set(handles.ReferencePath,'String',[PathName FileName]);



% --- Executes on button press in ChainsSpecified.
function ChainsSpecified_Callback(hObject, eventdata, handles)
% hObject    handle to ChainsSpecified (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 ChainsSpecified


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function CreateExProStruct(GetMode,FileList,PDBpath,HSSPpath,ExProStructPath,DebugMode,UnknownHault,DoValidate,OnlyMissing)
%Function loads the HSSPload and PDBload and saves the combined output to
%file for every file in argument list HSSPfileList \SBH

global ErrorCount %Keeps track of certain types of errors to determine if logfile shold be rewritten or appended
ErrorCount(1:2) = 0; %Sets starting values to 0, when error occures, switches value to 1 for certain error type
OldFiles = dir(ExProStructPath);

%Switching between the three modes for inputs: 1 - All files in folder, 2 -
%List of files, 3 - files written in field

Statusfile = fopen('Status.txt','w');
IgnoredFiles = 0;
SavedFiles = 0;

switch GetMode
    case 1
        HSSPdir = dir(HSSPpath);
        TotalFiles = size(HSSPdir,1)-2;
        fprintf(1,'-----Creating ExProStruct from %d entries.-----\n',TotalFiles)
        tic
        %Do for every file in the directory
        for i = 3:size(HSSPdir,1);
            ThisHSSP = HSSPdir(i).name;
            Exists = 0;
            for j = 3:size(OldFiles,1);
                if strcmp(OldFiles(j).name(1:4),upper(ThisHSSP(1:4)))
                    Exists = 1;
                    break
                end
            end
            if ~ (OnlyMissing && Exists)
                fprintf(1,'Loading %s, file %d of %d. %d percent complete.\n',ThisHSSP,i-2,TotalFiles,round((i-3)/TotalFiles*100));
                try
                    fprintf(1,'Loading HSSP data.\n');
                    [PDBid,ExProStruct] = HSSPload([HSSPpath ThisHSSP]); %Load the HSSP file
                catch ME
                    idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                    switch idSegLast,
                        case 'InvalidFid'
                            Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                            fprintf(1, ['Invalid HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        case {'nonExistentField', 'alignmentMismatch', 'subsassignnumelmismatch','index_assign_element_count_mismatch','badsubscript','unassignedOutputs'}
                            Logfile = ErrorLogging(1,['Corrupted file :' ThisHSSP]);
                            fprintf(1, ['HSSP file ' ThisHSSP ' is corrupted. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        otherwise
                            if UnknownHault,
                                for p = 1:length(ME.stack),
                                    errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                    fprintf(1,sprintf(errmsg));
                                end

                                Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                keyboard
                            else
                                Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            end
                    end
                    if DebugMode,
                        for p = 1:length(ME.stack),
                            errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                            fprintf(1,sprintf(errmsg));
                        end
                        fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                        keyboard
                    end
                    clear ExProStruct
                    IgnoredFiles = IgnoredFiles + 1;
                    continue
                end

                try
                    fprintf(1,'Loading PDB data.\n');
                    ExProStruct = PDBload([PDBpath 'pdb' PDBid '.ent'],ExProStruct); %Load the PDB file
                catch ME
                    idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                    switch idSegLast,
                        case 'BadPDBFile'
                            Logfile = ErrorLogging(2,['File not found:' PDBid]);
                            fprintf(1, ['Invalid PDB ID ' PDBid '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        otherwise
                            if UnknownHault,
                                for p = 1:length(ME.stack),
                                    errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                    fprintf(1,sprintf(errmsg));
                                end

                                Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                keyboard
                            else
                                Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            end
                    end
                    if DebugMode,
                        for p = 1:length(ME.stack),
                            errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                            fprintf(1,sprintf(errmsg));
                        end
                        fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                        keyboard
                    end
                    clear ExProStruct
                    IgnoredFiles = IgnoredFiles + 1;
                    continue
                end
                if DoValidate,
                    try
                        fprintf(1,'Validating structure.\n');
                        ExProStruct = ValidateExProStruct(ExProStruct);
                    catch ME
                        idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                        switch idSegLast,
                            case {'CAundef','Atom'}
                                Logfile = ErrorLogging(2,['Corrupted file: ' PDBid]);
                                fprintf(1, ['PDB file ' PDBid ' is corrupted. ' ME.message '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            case {'ResType','SecStruct','SA','PDBres','Aligns'}
                                Logfile = ErrorLogging(1,['Corrupted file :' ThisHSSP]);
                                fprintf(1, ['HSSP file ' ThisHSSP ' is corrupted. ' ME.message '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            otherwise
                                if UnknownHault,
                                    for p = 1:length(ME.stack),
                                        errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                        fprintf(1,sprintf(errmsg));
                                    end

                                    Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                    fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                    keyboard
                                else
                                    Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                    fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                                end
                        end
                        if DebugMode,
                            for p = 1:length(ME.stack),
                                errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                fprintf(1,sprintf(errmsg));
                            end
                            fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                            keyboard
                        end
                        clear ExProStruct
                        IgnoredFiles = IgnoredFiles + 1;
                        continue
                    end
                end
                save([ExProStructPath PDBid '.mat'],'ExProStruct');
                SavedFiles = SavedFiles + 1;
                elapsed = toc;
                tleft = elapsed*(TotalFiles-(i-2))/(i-2);

                fprintf(1,'ExProStruct has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n%d files successfully saved. %d files ignored due to errors.\n\n', PDBid,sec2time(elapsed),sec2time(tleft),SavedFiles,IgnoredFiles);
                fprintf(Statusfile,'ExProStruct has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n%d files successfully saved. %d files ignored due to errors.\n\n', PDBid,sec2time(elapsed),sec2time(tleft),SavedFiles,IgnoredFiles);
            else
                fprintf(1,'ExProStruct for %s already exists\n',ThisHSSP);
            end
            clear ExProStruct
        end
    case 2
        FileOfIDs = fopen(FileList);
        TotalFiles = 0
        while 1
            if ~ischar(Line)
                break
            end
            fgetl(FileOfIDs)
            TotalFiles = TotalFiles + 1;
        end
        fclose(FileOfIDs);
        tic
        keyboard
        fprintf(1,'-----Creating ExProStruct from %d entries.-----\n',TotalFiles)
        FileOfIDs = fopen(FileList);
        Line = fgetl(FileOfIDs);
        i = 1;
        while 1
            if ~ischar(Line)
                break
            end
            fprintf(1,'Loading %s, file %d of %d. %d percent complete.\n',ThisHSSP,i,TotalFiles,round((i-1)/TotalFiles*100));
            ThisHSSP = Line
            Exists = 0;
            for j = 3:size(OldFiles,1);
                if strcmp(OldFiles(j).name(1:4),upper(ThisHSSP(1:4)))
                    Exists = 1;
                    break
                end
            end
            if ~ (OnlyMissing && Exists)
                i = i + 1
                try
                    fprintf(1,'Loading HSSP data.\n');
                    [PDBid,ExProStruct] = HSSPload([HSSPpath ThisHSSP '.hssp']);
                catch ME
                    idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                    switch idSegLast,
                        case 'InvalidFid'
                            Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                            fprintf(1, ['Invalid HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        case {'nonExistentField', 'alignmentMismatch', 'subsassignnumelmismatch','index_assign_element_count_mismatch','badsubscript','unassignedOutputs'}
                            Logfile = ErrorLogging(1,['Corrupted file :' ThisHSSP]);
                            fprintf(1, ['HSSP file ' ThisHSSP ' is corrupted. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        otherwise
                            if UnknownHault,
                                for p = 1:length(ME.stack),
                                    errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                    fprintf(1,sprintf(errmsg));
                                end

                                Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                keyboard
                            else
                                Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            end
                    end
                    if DebugMode,
                        for p = 1:length(ME.stack),
                            errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                            fprintf(1,sprintf(errmsg));
                        end
                        fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                        keyboard
                    end
                    clear ExProStruct
                    IgnoredFiles = IgnoredFiles + 1;
                    continue
                end

                try
                    fprintf(1,'Loading PDB data.\n');
                    ExProStruct = PDBload([PDBpath 'pdb' PDBid '.ent'],ExProStruct);
                catch ME
                    idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                    switch idSegLast,
                        case 'BadPDBFile'
                            Logfile = ErrorLogging(2,['File not found:' PDBid]);
                            fprintf(1, ['Invalid PDB ID ' PDBid '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        otherwise
                            if UnknownHault,
                                for p = 1:length(ME.stack),
                                    errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                    fprintf(1,sprintf(errmsg));
                                end

                                Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                keyboard
                            else
                                Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            end
                    end
                    if DebugMode,
                        for p = 1:length(ME.stack),
                            errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                            fprintf(1,sprintf(errmsg));
                        end
                        fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                        keyboard
                    end
                    clear ExProStruct
                    IgnoredFiles = IgnoredFiles + 1;
                    continue
                end
                if DoValidate,
                    try
                        fprintf(1,'Validating structure.\n');
                        ExProStruct = ValidateExProStruct(ExProStruct);
                    catch ME
                        idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                        switch idSegLast,
                            case {'CAundef','Atom'}
                                Logfile = ErrorLogging(2,['Corrupted file: ' PDBid]);
                                fprintf(1, ['PDB file ' PDBid ' is corrupted. ' ME.message '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            case {'ResType','SecStruct','SA','PDBres','Aligns'}
                                Logfile = ErrorLogging(1,['Corrupted file :' ThisHSSP]);
                                fprintf(1, ['HSSP file ' ThisHSSP ' is corrupted. ' ME.message '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            otherwise
                                if UnknownHault,
                                    for p = 1:length(ME.stack),
                                        errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                        fprintf(1,sprintf(errmsg));
                                    end

                                    Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                    fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                    keyboard
                                else
                                    Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                    fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                                end
                        end
                        if DebugMode,
                            for p = 1:length(ME.stack),
                                errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                fprintf(1,sprintf(errmsg));
                            end
                            fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                            keyboard
                        end
                        clear ExProStruct
                        IgnoredFiles = IgnoredFiles + 1;
                        continue
                    end
                end
                save([ExProStructPath PDBid '.mat'],'ExProStruct');
                SavedFiles = SavedFiles + 1;
                elapsed = toc;
                tleft = elapsed*(TotalFiles-i)/i;
                fprintf(1,'ExProStruct has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n%d files successfully saved. %d files ignored due to errors.\n\n', PDBid,sec2time(elapsed),sec2time(tleft),SavedFiles,IgnoredFiles);
                fprintf(Statusfile,'ExProStruct has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n%d files successfully saved. %d files ignored due to errors.\n\n', PDBid,sec2time(elapsed),sec2time(tleft),SavedFiles,IgnoredFiles);

            else
                fprintf(1,'ExProStruct for %s already exists\n',ThisHSSP);
            end


            clear ExProStruct
            Line = fgetl(FileOfIDs);
        end
        fclose(FileOfIDs);
    case 3
        SeperateIndices = findstr(FileList,';');
        TotalFiles = length(SeperateIndices) + 1;
        tic
        fprintf(1,'-----Creating ExProStruct from %d entries.-----\n',TotalFiles)
        for i = 0:length(SeperateIndices),
            if length(SeperateIndices) == 0,
                ThisHSSP = FileList;
            elseif i == 0,
                ThisHSSP = FileList(1:SeperateIndices(1)-1);
            elseif i == length(SeperateIndices),
                ThisHSSP = FileList(SeperateIndices(i)+1:length(FileList));
            else
                ThisHSSP = FileList(SeperateIndices(i)+1:SeperateIndices(i+1)-1);
            end
            Exists = 0;
            for j = 3:size(OldFiles,1);
                if strcmp(OldFiles(j).name(1:4),upper(ThisHSSP(1:4)))
                    Exists = 1;
                    break
                end
            end
            if ~ (OnlyMissing && Exists)

                fprintf(1,'Loading %s, file %d of %d. %d percent complete.\n',ThisHSSP,i+1,TotalFiles,round((i)/TotalFiles*100));

                try
                    fprintf(1,'Loading HSSP data.\n');
                    [PDBid,ExProStruct] = HSSPload([HSSPpath ThisHSSP '.hssp']);
                catch ME
                    idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                    switch idSegLast,
                        case 'InvalidFid'
                            Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                            fprintf(1, ['Invalid HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        case {'nonExistentField', 'alignmentMismatch', 'subsassignnumelmismatch','index_assign_element_count_mismatch','badsubscript','unassignedOutputs'}
                            Logfile = ErrorLogging(1,['Corrupted file :' ThisHSSP]);
                            fprintf(1, ['HSSP file ' ThisHSSP ' is corrupted. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        otherwise
                            if UnknownHault,
                                for p = 1:length(ME.stack),
                                    errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                    fprintf(1,sprintf(errmsg));
                                end

                                Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                keyboard
                            else
                                Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            end
                    end
                    if DebugMode,
                        for p = 1:length(ME.stack),
                            errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                            fprintf(1,sprintf(errmsg));
                        end
                        fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                        keyboard
                    end
                    clear ExProStruct
                    IgnoredFiles = IgnoredFiles + 1;
                    continue
                end

                try
                    fprintf(1,'Loading PDB data.\n');
                    ExProStruct = PDBload([PDBpath 'pdb' PDBid '.ent'],ExProStruct);
                catch ME
                    idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                    switch idSegLast,
                        case 'BadPDBFile'
                            Logfile = ErrorLogging(2,['File not found:' PDBid]);
                            fprintf(1, ['Invalid PDB ID ' PDBid '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                        otherwise
                            if UnknownHault,
                                for p = 1:length(ME.stack),
                                    errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                    fprintf(1,sprintf(errmsg));
                                end

                                Logfile = ErrorLogging(2,['Unknown error in file: ' PDBid]);
                                fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                keyboard
                            else
                                Logfile = ErrorLogging(2,['File not found:' PDBid]);
                                fprintf(1, ['Unknown error in PDB ID ' PDBid '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            end
                    end
                    if DebugMode,
                        for p = 1:length(ME.stack),
                            errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                            fprintf(1,sprintf(errmsg));
                        end
                        fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                        keyboard
                    end
                    clear ExProStruct
                    IgnoredFiles = IgnoredFiles + 1;
                    continue
                end
                if DoValidate,
                    try
                        fprintf(1,'Validating structure.\n');
                        ExProStruct = ValidateExProStruct(ExProStruct);
                    catch ME
                        idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
                        switch idSegLast,
                            case {'CAundef','Atom'}
                                Logfile = ErrorLogging(2,['Corrupted file: ' PDBid]);
                                fprintf(1, ['PDB file ' PDBid ' is corrupted. ' ME.message '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            case {'ResType','SecStruct','SA','PDBres','Aligns'}
                                Logfile = ErrorLogging(1,['Corrupted file :' ThisHSSP]);
                                fprintf(1, ['HSSP file ' ThisHSSP ' is corrupted. ' ME.message '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                            otherwise
                                if UnknownHault,
                                    for p = 1:length(ME.stack),
                                        errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                        fprintf(1,sprintf(errmsg));
                                    end

                                    Logfile = ErrorLogging(1,['Unknown error in file: ' ThisHSSP]);
                                    fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                                    keyboard
                                else
                                    Logfile = ErrorLogging(1,['File not found:' ThisHSSP]);
                                    fprintf(1, ['Unknown error in HSSP ID ' ThisHSSP '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                                end
                        end
                        if DebugMode,
                            for p = 1:length(ME.stack),
                                errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                                fprintf(1,sprintf(errmsg));
                            end
                            fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                            keyboard
                        end
                        clear ExProStruct
                        IgnoredFiles = IgnoredFiles + 1;
                        continue
                    end
                end
                save([ExProStructPath PDBid '.mat'],'ExProStruct');
                SavedFiles = SavedFiles + 1;
                elapsed = toc;
                tleft = elapsed*(TotalFiles-(i+1))/(i+1);
                fprintf(1,'ExProStruct has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n%d files successfully saved. %d files ignored due to errors.\n\n', PDBid,sec2time(elapsed),sec2time(tleft),SavedFiles,IgnoredFiles);
                fprintf(Statusfile,'ExProStruct has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n%d files successfully saved. %d files ignored due to errors.\n\n', PDBid,sec2time(elapsed),sec2time(tleft),SavedFiles,IgnoredFiles);
            else
                fprintf(1,'ExProStruct for %s already exists\n',ThisHSSP);
            end
            clear ExProStruct
        end
end

fclose(Statusfile);

elapsed = toc;
fprintf(1,'-----Finished creating ExProStruct. Total elapsed time: %s-----\n',sec2time(elapsed));

function [PDBid,ExProStruct] = HSSPload(FileName)
%Function loading residues from HSSP file. For each residue, defines
%residue type, secondary structure, solvent acc., number in pdb, alignment
%from hssp. \SBH

%Opens the HSSP file, and defines variables
HSSPfile = fopen(FileName,'r');


HeaderProtein = '## PROTEINS';
Header = '## ALIGNMENTS';

g = 0; %Number of times residues have been run thrught, that is how many times has "## ALIGNMENTS" been reached

%Loop running through every line in file, until EOF has been reached
while 1,
    Line = fgetl(HSSPfile);
    if ~ischar(Line) %Testing for EOF
        break;
    end
    %Extracts name of matching pdb file, returns as function output
    if length(Line)>6,
        if Line(1:5) == 'PDBID'
            PDBid = upper(Line(12:15));
        end
    end

    if length(Line)>=length(HeaderProtein),
        if strcmp(Line(1:length(HeaderProtein)),HeaderProtein),
            i = 1;
            Line = fgetl(HSSPfile);
            Line = fgetl(HSSPfile);
            while Line(1:2) ~= '##',
                ExProStruct(1).AlignIde(i) = str2num(Line(29:32));
                i = i + 1;
                Line = fgetl(HSSPfile);
            end
        end
    end

    %Runs a loop everytime "Header" is reached, that is "## ALIGNMENTS,
    %ends the loop when file holds no more allignments
    if length(Line)>=length(Header),
        while strcmp(Line(1:length(Header)),Header),
            %Defines some running variables
            g = g + 1;
            i = 0; %Current residue position
            Chain = 0; %Current chain...
            OldChain = '';
            Line = fgetl(HSSPfile);
            Line = fgetl(HSSPfile);

            %Runs loop untill no more residues in this ## Alignment tab
            while Line(1:2) ~= '##',
                if strcmp('!',Line(15));
                    Line = fgetl(HSSPfile);
                end

                PDBchain = Line(13);

                %Tests if new chain is reached, and adjusts variables if
                %that is the case                
                if ~strcmp(OldChain,PDBchain),
                    if Chain > 0,
                        ExProStruct(Chain).ChainLength = PDBres;
                    end
                    Chain = Chain + 1;
                    i = 0;
                end
                OldChain = PDBchain;
                
                %Identifies number of same residue in pdb file
                PDBres = str2num(Line(8:11));
                
                if isempty(PDBres)
                    Line = fgetl(HSSPfile);
                    continue
                end

                i = i + 1;

                %Tests if this is the first runthrough of residues, if so,
                %saves some standard values into ExProStruct
                if g == 1,
                    HSSPsa = str2num(Line(37:39));
                    ResType = aa2int(Line(15));
                    switch Line(18),
                        case 'H'
                            SecStruct = 1;
                        case 'E'
                            SecStruct = 2;
                        case 'T'
                            SecStruct = 3;
                        otherwise
                            SecStruct = 4;
                    end

                    ExProStruct(Chain).Residue(i).ResType = ResType;
                    ExProStruct(Chain).Residue(i).SecStruct = SecStruct;
                    ExProStruct(Chain).Residue(i).SA = HSSPsa;
                    ExProStruct(Chain).Residue(i).PDBres = PDBres;
                    ExProStruct(Chain).Residue(i).PDBchain = PDBchain;
                end

                %Tests if current residue pdbnumber matches that of the one
                %in the ExProStruct, just to make sure. If this is the
                %case, changes alignment value for this residue to 1.
                if ExProStruct(Chain).Residue(i).PDBres == PDBres,
                    if length(ExProStruct(1).AlignIde) - (g-1)*70 >= 70
                        MaxJ = 70;
                    else
                        MaxJ = length(ExProStruct(1).AlignIde) - (g-1)*70;
                    end
                    for j = 1:MaxJ,
                        if length(Line)-51 >= j,
                            Subst = Line(51+j);
                            AAnum = aa2int(Subst);
                        else
                            AAnum = 0;
                        end
                        if AAnum > 20,
                            AAnum = 0;
                        end
                        ExProStruct(Chain).Residue(i).Align(j+70*(g-1)) = AAnum;
                    end
                else
                    error('HSSPload:alignmentMismatch','Error in matching allignments pdbid %d in block on %d',PDBres,g);
                end

                Line = fgetl(HSSPfile);
            end
            ExProStruct(Chain).ChainLength = PDBres;
        end
    end
end
fclose(HSSPfile);


function ExProStruct = PDBload(FileName,ExProStruct)
%Function loads PDB file into array, and transfers coordinates and pdb-id
%for residues into ProExtract_V2p4 Structure array. \SBH
%Opens the PDB file in pdbread-structure

PDBStruct = pdbread(FileName);

if isfield(PDBStruct,'Title'),
    ExProStruct(1).Title = PDBStruct.Title;
else
    ExProStruct(1).Title = 'Undefined';
end

if isfield(PDBStruct,'Header'),
    if isfield(PDBStruct.Header,'classification'),
        ExProStruct(1).Classification = PDBStruct.Header.classification;
    else
        ExProStruct(1).Classification = 'Undefined';
    end
else
    ExProStruct(1).Classification = 'Undefined';
end

if isfield(PDBStruct,'Keywords'),
    ExProStruct(1).Keywords = PDBStruct.Keywords;
else
    ExProStruct(1).Keywords = 'Undefined';
end

if isfield(PDBStruct,'Source'),
    ExProStruct(1).Source = PDBStruct.Source;
else
    ExProStruct(1).Source = 'Undefined';
end

%Finding number of atoms in model, starting residue position (pdb) and
%defining variables

Chains = size(ExProStruct,2);
NumAtoms = size(PDBStruct.Model(1,1).Atom,2);
OldResNr = -1000;

%Looping through all atoms, if not hydrogen executes inner code
for i = 1:NumAtoms,
    if ~strcmp(PDBStruct.Model(1,1).Atom(1,i).AtomName,'H'),
        PDBres = PDBStruct.Model(1,1).Atom(1,i).resSeq; %Residue # in PDB
        PDBchain = PDBStruct.Model(1,1).Atom(1,i).chainID;
        if PDBres ~= OldResNr, %Checks if new residue has been reached
            CurrentAtom = 1;
        else
            CurrentAtom = CurrentAtom + 1;
        end
        %Loops through all residues in ExProStruct searching for one with
        %PDBres equal to the one found here, if present in HSSP, should be
        %present in the structure as well. When found, saves coordinates of
        %atoms and atom names.
        for j = 1:size(ExProStruct,2)
            for k = 1:size(ExProStruct(j).Residue,2)
                if (ExProStruct(j).Residue(k).PDBres == PDBres) && strcmpi(ExProStruct(j).Residue(k).PDBchain,PDBchain),
                    %Extracting coordinates from PDB
                    X = PDBStruct.Model(1,1).Atom(1,i).X;
                    Y = PDBStruct.Model(1,1).Atom(1,i).Y;
                    Z = PDBStruct.Model(1,1).Atom(1,i).Z;
                    AtomName = PDBStruct.Model(1,1).Atom(1,i).AtomName;
                    
                    %Writing to structure
                    ExProStruct(j).Residue(k).Atom(CurrentAtom).ID = AtomName;
                    ExProStruct(j).Residue(k).Atom(CurrentAtom).X = X;
                    ExProStruct(j).Residue(k).Atom(CurrentAtom).Y = Y;
                    ExProStruct(j).Residue(k).Atom(CurrentAtom).Z = Z;
                end
            end
        end
        OldResNr = PDBres;
    end
end

function ExProStruct = ValidateExProStruct(ExProStruct)
%Validates the structure obtained to check that all fields that should
%contain data does so.
NumAligns = length(ExProStruct(1).AlignIde);
RunToChain = size(ExProStruct,2);
DeletedChain = 0;
for Chain = 1:RunToChain
    ChainDeleted = 0;
    Deleted = 0;
    RunTo = size(ExProStruct(Chain - DeletedChain).Residue,2);
    for i = 1:RunTo
        Delete = 0;
        ResTypeUndefined = 0;
        ResType = ExProStruct(Chain - DeletedChain).Residue(i - Deleted).ResType;
        SecStruct = ExProStruct(Chain - DeletedChain).Residue(i - Deleted).SecStruct;
        SA = ExProStruct(Chain - DeletedChain).Residue(i - Deleted).SA;
        PDBres = ExProStruct(Chain - DeletedChain).Residue(i - Deleted).PDBres;
        PDBchain = ExProStruct(Chain - DeletedChain).Residue(i - Deleted).PDBchain;
        Align = ExProStruct(Chain - DeletedChain).Residue(i - Deleted).Align;
        ChainLength = ExProStruct(Chain - DeletedChain).ChainLength;
        try
            Atom = ExProStruct(Chain - DeletedChain).Residue(i - Deleted).Atom;
        catch
            Atom = [];
        end
        
        if isempty(Atom),
            fprintf(1,'Atom coordinates undefined for residue %d in chain %d. Residue deleted.\n',i,Chain);
            Delete = 1;
            end
        if isempty(ResType) && ~ Delete,
            fprintf(1,'Residue type undefined for residue %d in chain %d. Residue deleted.\n',i,Chain);
            Delete = 1;
            ResTypeUndefined = 1;
        elseif (ResType == 0 | ResType > 20) && ~ Delete,
            fprintf(1,'Residue type undefined for residue %d in chain %d. Residue deleted.\n',i,Chain);
            Delete = 1;
            ResTypeUndefined = 1;
        end
        if isempty(SecStruct) && ~ Delete,
            fprintf(1,'Secondary structure undefined for residue %d in chain %d. Residue deleted.\n',i,Chain)
            Delete = 1;
        end
        if isempty(SA) && ~ Delete,
            fprintf(1,'Solvent accessibility undefined for residue %d in chain %d. Residue deleted.\n',i,Chain)
            Delete = 1;
        end
        if isempty(PDBchain) && ~ Delete,
            fprintf(1,'PDB chain undefined for residue %d in chain %d. Residue deleted.\n',i,Chain)
            Delete = 1;
        end

        if isempty(PDBres) && ~ Delete,
            fprintf(1,'PDB residue number undefined for residue %d in chain %d. Residue deleted.\n',i,Chain)
            Delete = 1;
        end
        if length(Align) ~= NumAligns && ~ Delete,
            fprintf(1,'One or more allignments undefined for residue %d in chain %d. Residue deleted.\n',i,Chain)
            Delete = 1;
        end
        if isempty(ChainLength) && ~ Delete,
            fprintf(1,'Chainlength undefined for chain %d. Residue deleted.\n',Chain)
            Delete = 1;
        end

        CA = 0;
        FunAtom = 0;
        if ~ ResTypeUndefined && ~ Delete,
            Fatom = FunctAtom(ResType);
            for t=1:length(Fatom),
                FunAtom(t)=0;
                for j=1:size(Atom,2)
                    if strcmp(Atom(j).ID,'CA')
                        CA = 1;
                    end
                    if strcmp(Atom(j).ID,Fatom(t)),
                        FunAtom(t) = 1;
                    end
                end
            end
        elseif ~ Delete,
            for j=1:size(Atom,2)
                if strcmp(Atom(j).ID,'CA')
                    CA = 1;
                end
            end
        end
        if ~ CA && ~ Delete,
            fprintf(1,'Position of CA undefined for residue %d in Chain %d. Residue deleted.\n',i,Chain)
            Delete = 1;
        end
        if ~ min(FunAtom) && ~ Delete,
            fprintf(1,'Position of functional atom undefined for residue %d in Chain %d. Residue deleted.\n',i,Chain)
            Delete = 1;
        end
        

        if Delete,
            k = 1;
            for j = 1:size(ExProStruct(Chain - DeletedChain).Residue,2)
                if j ~= i - Deleted,
                    NewResStruct(k) = ExProStruct(Chain - DeletedChain).Residue(j);
                    k = k + 1;
                end
            end
            if k > 1,
                ExProStruct(Chain - DeletedChain).Residue = NewResStruct;
                clear NewResStruct;
                Deleted = Deleted + 1;
            else
            fprintf('Chain %d is now empty. Chain deleted.\n',Chain - DeletedChain);
            if Chain == 1 && size(ExProStruct,2) > 1,
                ExProStruct(Chain+1).AlignIde = ExProStruct(Chain).AlignIde;
                ExProStruct(Chain+1).Title = ExProStruct(Chain).Title;
                ExProStruct(Chain+1).Classification = ExProStruct(Chain).Classification;
                ExProStruct(Chain+1).Keywords = ExProStruct(Chain).Keywords;
                ExProStruct(Chain+1).Source = ExProStruct(Chain).Source;
            end
                for j = 1:size(ExProStruct,2)
                    if j ~= Chain - DeletedChain,
                        NewStruct(k) = ExProStruct(j);
                        k = k + 1;
                    end
                end
                if k <= 1,
                    fprintf('All chains are now deleted. Structure empty.\n');
                    NewStruct.AlignIde = ExProStruct.AlignIde;
                    NewStruct.Residue = [];
                    NewStruct.ChainLength = ExProStruct.ChainLength;
                end
                ExProStruct = NewStruct;
                clear NewStruct;
                DeletedChain = DeletedChain + 1;
                ChainDeleted = 1;
            end
        end
    end
end


function CreateDataset(GetMode,FileList,ExProStructPath,AcMin,AcMax,AcRes,DistMin,DistMax,DistRes,DistMode,UseAlign,UseComulative,MinIDcut,CLMin,CLMax,CLRes,MultiChain,OutputPath,DebugMode,UnknownHault,DoValidate,ScrambleMode,ScrambleNum,CreateIndex,ChainsSpecified)
%Function to create the actual Nabo dataset. The function takes many
%inputs, which are defined by the user in the GUI. Returns output tensor to
%file specified.
%Structure of output tensor is (Residue type 1, Residue type 2, Solvent
%shell #, Distance shell #, Secondary structure residue 1, Secondary
%structure residue 2, Avg. ChainLength)
%Function runs PopulateNabo for each input file

global ErrorCount %Keeps track of certain types of errors to determine if logfile shold be rewritten or appended
ErrorCount(3) = 0; %Sets starting values to 0, when error occures, switches value to 1 for certain error type

global Nabo
global c
global IndexArray

SaSteps = (AcMax-AcMin)/AcRes + 2;
CLSteps = (CLMax-CLMin)/CLRes + 2;
%DistSteps = (DistMax-DistMin)/DistRes + 2;
DistSteps = (DistMax-DistMin)/DistRes + 1;

Nabo = zeros(20,20,SaSteps,DistSteps,4,4,CLSteps,6,'single');
if CreateIndex,
    IndexArray = cell(20,20,SaSteps,DistSteps,4,4,CLSteps,6);
end

whosindexarray = whos('IndexArray');
thesize = whosindexarray.bytes;
fprintf(1,bytestosize(thesize));


c = 0;

%Different modes of inputs, much like in the CreateExProStruct function
switch GetMode
    case 1
        ExProStructDir = dir(ExProStructPath);
        TotalFiles = size(ExProStructDir,1) - 2;
        fprintf(1,'-----Creating dataset from %d entries.-----\n',TotalFiles)
        tic
        for i = 3:size(ExProStructDir,1)
            fprintf(1,'Loading %s, file %d of %d. %d percent complete.\n',ExProStructDir(i).name,i-2,TotalFiles,round((i-3)/TotalFiles*100));
            PopulateNabo([ExProStructPath ExProStructDir(i).name],AcMin,AcMax,AcRes,DistMin,DistMax,DistRes,DistMode,UseAlign,UseComulative,MinIDcut,CLMin,CLMax,CLRes,MultiChain,DebugMode,UnknownHault,DoValidate,ScrambleMode,ScrambleNum,ExProStructDir(i).name(1:4),CreateIndex,'');
            elapsed = toc;
            tleft = elapsed*(TotalFiles-(i-2))/(i-2);
            fprintf(1,'Dataset has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n\n', ExProStructDir(i).name,sec2time(elapsed),sec2time(tleft));
        end
        
    case 2
        FileOfIDs = fopen(FileList);
        if ChainsSpecified,
            Line = fgetl(FileOfIDs);
        end
        Line = fgetl(FileOfIDs);
        TotalFiles = 0;
        while 1
            if ~ischar(Line)
                break
            end
            Line = fgetl(FileOfIDs);
            TotalFiles = TotalFiles + 1;
        end
        fclose(FileOfIDs);
        fprintf(1,'-----Creating dataset from %d entries.-----\n',TotalFiles)
        tic
        FileOfIDs = fopen(FileList);
        Line = fgetl(FileOfIDs);
        if ChainsSpecified,
            Line = fgetl(FileOfIDs);
        end
        i=1;
        while 1
            if ~ischar(Line)
                break
            end
            ll = length(Line);
            if ChainsSpecified,
                TheChain = Line(5);
                Line = Line(1:4);
            else
                TheChain = '';
                Line = Line(ll-3:ll);
            end
            fprintf(1,'Loading %s, file %d of %d. %d percent complete.\n',upper(Line),i,TotalFiles,round((i-1)/TotalFiles*100));
            if ChainsSpecified,
                fprintf(1,'Loading chain %s.\n',TheChain);
            end
            i = i + 1;
            PopulateNabo([ExProStructPath upper(Line(1:4)) '.mat'],AcMin,AcMax,AcRes,DistMin,DistMax,DistRes,DistMode,UseAlign,UseComulative,MinIDcut,CLMin,CLMax,CLRes,MultiChain,DebugMode,UnknownHault,DoValidate,ScrambleMode,ScrambleNum,upper(Line),CreateIndex,TheChain);
            elapsed = toc;
            tleft = elapsed*(TotalFiles-i)/i;
            fprintf(1,'Dataset has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n\n', upper(Line),sec2time(elapsed),sec2time(tleft));
            Line = fgetl(FileOfIDs);            
        end
        fclose(FileOfIDs);
    case 3
        SeperateIndices = findstr(FileList,';');
        TotalFiles = length(SeperateIndices) + 1;
        tic
        fprintf(1,'-----Creating ExProStruct from %d entries.-----\n',TotalFiles)
        for i = 0:length(SeperateIndices),
            if length(SeperateIndices) == 0,
                ThisExProStruct = FileList;
            elseif i == 0,
                ThisExProStruct = FileList(1:SeperateIndices(1)-1);
            elseif i == length(SeperateIndices),
                ThisExProStruct = FileList(SeperateIndices(i)+1:length(FileList));
            else
                ThisExProStruct = FileList(SeperateIndices(i)+1:SeperateIndices(i+1)-1);
            end
            fprintf(1,'Loading %s, file %d of %d. %d percent complete.\n',ThisExProStruct,i,TotalFiles,round((i)/TotalFiles*100));
            PopulateNabo([ExProStructPath upper(ThisExProStruct) '.mat'],AcMin,AcMax,AcRes,DistMin,DistMax,DistRes,DistMode,UseAlign,UseComulative,MinIDcut,CLMin,CLMax,CLRes,MultiChain,DebugMode,UnknownHault,DoValidate,ScrambleMode,ScrambleNum,upper(ThisExProStruct),CreateIndex,'');
            elapsed = toc;
            tleft = elapsed*(TotalFiles-(i+1))/(i+1);
            fprintf(1,'Dataset has been successfully created and saved for %s.\nElapsed time: %s.\nEstimated time left: %s.\n\n', upper(ThisExProStruct),sec2time(elapsed),sec2time(tleft));
            
        end
end
if strcmp(ScrambleMode,'None')
    if CreateIndex,
        save(OutputPath,'-append','Nabo','IndexArray');
    else
        save(OutputPath,'-append','Nabo');
    end
else
    Naboref = Nabo;
    save(OutputPath,'-append','Naboref');
end
fprintf(1,'Nabo has successfully been computed and saved to %s.\nA total of %s pairs were added.\n',OutputPath,num2str(c));
fprintf(1,'-----Finished creating dataset-----\n');
clear global Nabo
clear global IndexArray

function PopulateNabo(ExProStructPath,AcMin,AcMax,AcRes,DistMin,DistMax,DistRes,DistMode,UseAlign,UseComulative,MinIDcut,CLMin,CLMax,CLRes,MultiChain,DebugMode,UnknownHault,DoValidate,ScrambleMode,ScrambleNum,PDBid,CreateIndex,TheChain)
%Function to add data to the output tensor.

global Nabo
global IndexArray
global c

try
    load(ExProStructPath); %Loads the structure file
catch ME
    idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
    ExProStructID = char(regexp(ExProStructPath,'\w+\.\w+$','match'));
    switch idSegLast,
        case 'couldNotReadFile'
            Logfile = ErrorLogging(3,['File not found:' ExProStructID]);
            fprintf(1, ['Invalid ExProStruct ID ' ExProStructID '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
        otherwise
            if UnknownHault,
                for p = 1:length(ME.stack),
                    errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                    fprintf(1,sprintf(errmsg));
                end

                Logfile = ErrorLogging(1,['Unknown error in file: ' ExProStructID]);
                fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                keyboard
            else
                Logfile = ErrorLogging(1,['File not found:' ExProStructID]);
                fprintf(1, ['Unknown error in ExProStruct ID ' ExProStructID '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
            end
    end
    if DebugMode,
        for p = 1:length(ME.stack),
            errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
            fprintf(1,sprintf(errmsg));
        end
        fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
        keyboard
    end
    clear ExProStruct
    return
end

if DoValidate, %Runs validate, if selected
    try
        fprintf(1,'Validating structure.\n');
        ExProStruct = ValidateExProStruct(ExProStruct);
        fprintf(1, 'Structure validation successfull.\n');
    catch ME
        idSegLast = char(regexp(ME.identifier, '(?<=:)\w+$', 'match'));
        ExProStructID = char(regexp(ExProStructPath,'\w+\.\w+$','match'));
        switch idSegLast,
            case {'ResType','SecStruct','SA','PDBres','Aligns','CAundef','Atom'}
                Logfile = ErrorLogging(3,['Corrupted file: ' ExProStructID]);
                fprintf(1, ['ExProStruct file ' ExProStructID ' is corrupted. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
            otherwise
                if UnknownHault,
                    for p = 1:length(ME.stack),
                        errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                        fprintf(1,sprintf(errmsg));
                    end

                    Logfile = ErrorLogging(3,['Unknown error in file: ' ExProStructID]);
                    fprintf(1,'Unknown error encountered, haulting for manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
                    keyboard
                else
                    Logfile = ErrorLogging(3,['File not found:' ExProStructID]);
                    fprintf(1, ['Unknown error in HSSP ID ' ExProStructID '. Saved to log ' regexprep(Logfile,'\','\\\\') '\n']);
                end
        end
        if DebugMode,
            for p = 1:length(ME.stack),
                errmsg = ['Error encountered in line ' num2str(ME.stack(p).line) ' in file ' char(regexp(ME.stack(p).file,'\w+\.\w+$','match')) '\n'];
                fprintf(1,sprintf(errmsg));
            end
            fprintf(1,'Entering manual debugging mode. Type "ME" for error information. "return" to proceed with next file.\n');
            keyboard
        end
        clear ExProStruct
        return
    end
end

for l = 1:ScrambleNum,

    ValAligns = IdentifyValidAligns(ExProStruct(1).AlignIde,MinIDcut);
    
    j = 1;
    
    if MultiChain, %If multichain is selected, puts the chains together to form one long chain
        CombiChain = [ExProStruct.Residue];
        for Chain = 1:size(ExProStruct,2),
            for i = 1:size(ExProStruct(Chain).Residue,2),
                CombiChain(j).ChainLength = ExProStruct(Chain).ChainLength;
                j = j + 1;
            end
        end
    else
        if strcmp(TheChain,''),
            CombiChain = ExProStruct(1).Residue;
            for i = 1:size(ExProStruct(1).Residue,2),
                CombiChain(i).ChainLength = ExProStruct(1).ChainLength;
            end
        else
            for Chain = 1:size(ExProStruct,2),
                if size(ExProStruct(Chain).Residue,2) > 0,
                    if strcmp(ExProStruct(Chain).Residue(1).PDBchain,TheChain),
                        CombiChain = ExProStruct(Chain).Residue;
                        for i = 1:size(ExProStruct(Chain).Residue,2),
                            CombiChain(i).ChainLength = ExProStruct(Chain).ChainLength;
                        end
                    end
                end
            end
        end
    end
    
    a = 0;
    b = 0;
    
    if ~exist('CombiChain'),
        fprintf(1,'No residues in chain, continuing...\n');
        continue
    end
    
    SA = SaBin(CombiChain,AcMin,AcMax,AcRes,UseComulative);
    
       if ~ strcmp(ScrambleMode,'None'),
           TheChain = Scramble(CombiChain,ScrambleMode,AcMin,AcMax,AcRes);
       else
           TheChain = CombiChain;
       end

    fprintf(1,'Calculating data.\n');
    for k = 1:length(SA)
        for i = 1:length(SA(k).Residue)
            for j = (i+1):length(SA(k).Residue)
                Res1 = TheChain(SA(k).Residue(i));
                Res2 = TheChain(SA(k).Residue(j));
                Dist = CalcDist(Res1,Res2,DistMin,DistMax,DistRes,DistMode);

                
                if Dist > DistMax
                    continue,
                end

                CL = mean(Res1.ChainLength,Res2.ChainLength);%HVAD MED DET HER???????
                ChainLength = CLBin(CL,CLMin,CLMax,CLRes);

                if ~ strcmp(ScrambleMode,'None'),
                    Res1Type = Res1.ScrambledResType;
                    Res2Type = Res2.ScrambledResType;
                else
                    Res1Type = Res1.ResType;
                    Res2Type = Res2.ResType;
                end

                SolvAc = k;
                Distance = DistBin(Dist,DistMin,DistMax,DistRes);

                Res1SS = Res1.SecStruct;
                Res2SS = Res2.SecStruct;

                PrimarySeqDiff = abs(Res1.PDBres-Res2.PDBres) + 1;

                if PrimarySeqDiff > 6 || ~ strcmp(Res1.PDBchain,Res2.PDBchain),
                    PrimarySeqDiff = 6;
                end
                
                %Adds 1 to the field in Nabo
                if Res1Type <= size(Nabo,1) && Res2Type <= size(Nabo,2),
                    NaboOld1 = Nabo(Res1Type,Res2Type,SolvAc,Distance,Res1SS,Res2SS,ChainLength,PrimarySeqDiff);
                    Nabo(Res1Type,Res2Type,SolvAc,Distance,Res1SS,Res2SS,ChainLength,PrimarySeqDiff) =  NaboOld1 + 1/ScrambleNum;
                    NaboOld2 = Nabo(Res2Type,Res1Type,SolvAc,Distance,Res2SS,Res1SS,ChainLength,PrimarySeqDiff);
                    Nabo(Res2Type,Res1Type,SolvAc,Distance,Res2SS,Res1SS,ChainLength,PrimarySeqDiff) = NaboOld2 + 1/ScrambleNum;
                    a = a + 1;
                    if CreateIndex,
                        Res1Chain = Res1.PDBchain;
                        Res2Chain = Res2.PDBchain;
                        Res1PDBres = num2str(Res1.PDBres,'%04.0f');
                        Res2PDBres = num2str(Res2.PDBres,'%04.0f');
                        
                        IndexString = [PDBid Res1PDBres Res1Chain Res2PDBres Res2Chain];
                        OldIndex = IndexArray{Res1Type,Res2Type,SolvAc,Distance,Res1SS,Res2SS,ChainLength,PrimarySeqDiff};
                        IndexArray{Res1Type,Res2Type,SolvAc,Distance,Res1SS,Res2SS,ChainLength,PrimarySeqDiff} = [OldIndex;IndexString];
                        
                        IndexString = [PDBid Res2PDBres Res2Chain Res1PDBres Res1Chain];
                        OldIndex = IndexArray{Res2Type,Res1Type,SolvAc,Distance,Res2SS,Res1SS,ChainLength,PrimarySeqDiff};
                        IndexArray{Res2Type,Res1Type,SolvAc,Distance,Res2SS,Res1SS,ChainLength,PrimarySeqDiff} = [OldIndex;IndexString];
                    end
                end
                
                %If using aligns, does the same thing for these
                if UseAlign,
                    for z = 1:length(ValAligns),
                        Res1Type = Res1.Align(ValAligns(z));
                        Res2Type = Res2.Align(ValAligns(z));
                        if (Res1Type ~= 0) && (Res2Type ~=0),
                            Nabo(Res1Type,Res2Type,SolvAc,Distance,Res1SS,Res2SS,ChainLength,PrimarySeqDiff) = Nabo(Res1Type,Res2Type,SolvAc,Distance,Res1SS,Res2SS,ChainLength,PrimarySeqDiff) + 1/ScrambleNum;
                            Nabo(Res2Type,Res1Type,SolvAc,Distance,Res2SS,Res1SS,ChainLength,PrimarySeqDiff) = Nabo(Res2Type,Res1Type,SolvAc,Distance,Res2SS,Res1SS,ChainLength,PrimarySeqDiff) + 1/ScrambleNum;
                            b = b + 1;
                        end
                    end
                end
            end
        end
    end

    c = c + (a + b) / ScrambleNum;

end

fprintf(1,'%s pairs of residues used. %s pairs used from alignments. %s hits added to Nabo.\n',num2str(a),num2str(b),num2str(a+b));

whosindexarray = whos('IndexArray');
thesize = whosindexarray.bytes;
fprintf(1,bytestosize(thesize));


function thesize = bytestosize(numbytes)
kb = floor(numbytes/1024);
mb = floor(kb/1024);
gb = floor(mb/1024);
thesize = ['IndexArray: ' num2str(gb) ' Gb, ' num2str(mb-1024*gb) ' Mb, ' num2str(kb-1024*mb) ' kb, ' num2str(round(numbytes-1024*kb)) ' bytes.\n'];

function ExProStruct = Scramble(Residues,ScrambleMode,AcMin,AcMax,AcRes)

ScrambledStruct = Residues;

if strcmp(ScrambleMode,'All'),
    SA = SaBin(Residues,-1000,1000,2000,0);
elseif strcmp(ScrambleMode,'SA'),
    SA = SaBin(Residues,AcMin,AcMax,AcRes,0);
end

for i = 1:size(SA,2),
    if SA(i).Residue(1) == 0
        ScrambledSA(i).Residue = 0;
        continue
    end
    
    numRes = size(SA(i).Residue,2);
    ResCount = 1:numRes;

    for j=1:numRes,
        randNum = rand;
        thisResPos = ceil(randNum*(numRes-j+1));
        thisRes = ResCount(thisResPos);
      
        oldRes = SA(i).Residue(j);
        newRes = SA(i).Residue(thisRes);
        
        ScrambledSA(i).Residue(j) = newRes;

        ResSA = Residues(oldRes).SA/AAsurf(Residues(oldRes).ResType);
        newResSArea = round(ResSA*AAsurf(Residues(newRes).ResType));

        ScrambledStruct(oldRes).ScrambledResType = Residues(newRes).ResType;
        ScrambledStruct(oldRes).ResType = Residues(oldRes).ResType;
        ScrambledStruct(oldRes).Align = Residues(newRes).Align;
        ScrambledStruct(oldRes).SA = newResSArea;
       
        ResCount = [ResCount(1:thisResPos-1) ResCount(thisResPos+1:length(ResCount))];
    end
end

ExProStruct = ScrambledStruct;

function ValAligns = IdentifyValidAligns(AlignID,MinIDcut)
%Function to find out which aligns fullfills the threshold
ValAligns = [];
j = 1;
for i = 1:length(AlignID),
    if AlignID(i) >= MinIDcut,
        ValAligns(j) = i;
        j = j + 1;
    end
end



function SA = SaBin(CombiChain,AcMin,AcMax,AcRes,UseComulative)
%Function to grup residues into shells from their SA

SaSteps = (AcMax-AcMin)/AcRes;

for i = 1:(SaSteps+2),
    SA(i).Residue(1) = 0;
end

for i = 1:size(CombiChain,2),
    ResSa = CombiChain(i).SA/AAsurf(CombiChain(i).ResType);
    ThisSa = ResSa - AcMin;
    if ResSa <= AcMin,
        ThisSaStep = 1;
    elseif ResSa >= AcMax,
        ThisSaStep = SaSteps + 2;
    else
        ThisSaStep = ceil(ThisSa/AcRes) + 1;
    end
    if UseComulative,
        for j = 1:ThisSaStep,
            if SA(j).Residue(1) == 0,
                ThisResidue = 1;
            else
                ThisResidue = size(SA(j).Residue,2)+1;
            end
            SA(j).Residue(ThisResidue) = i;
        end
    else
        if SA(ThisSaStep).Residue(1) == 0,
            ThisResidue = 1;
        else
            ThisResidue = size(SA(ThisSaStep).Residue,2)+1;
        end
        SA(ThisSaStep).Residue(ThisResidue) = i;
    end
end

function ThisCLStep = CLBin(ChainLength,CLMin,CLMax,CLRes)
%Function to find the shell number of the current chainlength

CLSteps = (CLMax-CLMin)/CLRes;

ThisCL = ChainLength - CLMin;
if ChainLength <= CLMin,
    ThisCLStep = 1;
elseif ChainLength >= CLMax,
    ThisCLStep = CLSteps + 2;
else
    ThisCLStep = ceil(ThisCL/CLRes) + 1;
end


function Dist = CalcDist(Res1,Res2,DistMin,DistMax,DistRes,DistMode)
%Function to calculate distance between residues. Mode 1 - closest distance,
%mode 2 - geometrical midpoints, mode 3 - CAs, mode 4 - functional groups

Res1Type = Res1.ResType;
Res2Type = Res2.ResType;

Atom1 = Res1.Atom;
Atom2 = Res2.Atom;

switch DistMode,
    case 1 %Shortest distance
        Dist = 1000000;
        for i = 1:size(Atom1,2),
            for j = 1:size(Atom2,2),
                x = (Atom1(i).X - Atom2(j).X)^2;
                y = (Atom1(i).Y - Atom2(j).Y)^2;
                z = (Atom1(i).Z - Atom2(j).Z)^2;
                
                ThisDist = sqrt(x+y+z);
                
                if ThisDist < Dist,
                    Dist = ThisDist;
                end
            end
        end
    case 2%Geometrical midpoints
        %GM of first residue (x1,y1,z1)
        xr1 = 0;
        yr1 = 0;
        zr1 = 0;
        for i = 1:size(Atom1,2),
            xr1 = xr1 + Atom1(i).X;
            yr1 = yr1 + Atom1(i).Y;
            zr1 = zr1 + Atom1(i).Z;
        end
        x1 = xr1 / size(Atom1,2);
        y1 = xr1 / size(Atom1,2);
        z1 = xr1 / size(Atom1,2);
        %GM of second residue (x2,y2,z2)

        xr2 = 0;
        yr2 = 0;
        zr2 = 0;
        for i = 1:size(Atom2,2),
            xr2 = xr2 + Atom2(i).X;
            yr2 = yr2 + Atom2(i).Y;
            zr2 = zr2 + Atom2(i).Z;
        end
        x2 = xr2 / size(Atom2,2);
        y2 = xr2 / size(Atom2,2);
        z2 = xr2 / size(Atom2,2);
        %Find Dist
        x = (x1-x2)^2;
        y = (y1-y2)^2;
        z = (z1-z2)^2;
        Dist = sqrt(x+y+z);
    case 3
        %CA of first residue (x1,y1,z1)
        for i = 1:size(Atom1,2),
            if strcmp(Atom1(i).ID,'CA')
                x1 = Atom1(i).X;
                y1 = Atom1(i).Y;
                z1 = Atom1(i).Z;
            end
        end
        %CA of second residue (x2,y2,z2)
        for i = 1:size(Atom2,2),
            if strcmp(Atom2(i).ID,'CA'),
                x2 = Atom2(i).X;
                y2 = Atom2(i).Y;
                z2 = Atom2(i).Z;
            end
        end
        %Find Dist
        x = (x1-x2)^2;
        y = (y1-y2)^2;
        z = (z1-z2)^2;
        Dist = sqrt(x+y+z);
    case 4
        FAtom1 = FunctAtom(Res1Type);
        FAtom2 = FunctAtom(Res2Type);

        Dist = 1000000;
        
        %FR of first residue (x1,y1,z1)
        for r = 1:length(FAtom1),
            for t = 1:length(FAtom2),
                for i = 1:size(Atom1,2),
                    if strcmp(Atom1(i).ID,FAtom1(r)),
                        x1 = Atom1(i).X;
                        y1 = Atom1(i).Y;
                        z1 = Atom1(i).Z;
                    end
                end
                %FR of second residue (x2,y2,z2)
                for i = 1:size(Atom2,2),
                    if strcmp(Atom2(i).ID,FAtom2(t)),
                        x2 = Atom2(i).X;
                        y2 = Atom2(i).Y;
                        z2 = Atom2(i).Z;
                    end
                end
                %Find Dist

                x = (x1-x2)^2;
                y = (y1-y2)^2;
                z = (z1-z2)^2;
                ThisDist = sqrt(x+y+z);
                if ThisDist < Dist,
                    Dist = ThisDist;
                end
            end
        end
end


function ThisDistStep = DistBin(Dist,DistMin,DistMax,DistRes)
%Function to find distance shell number of current shell

DistSteps = (DistMax-DistMin)/DistRes;

ThisDist = Dist - DistMin;
if Dist <= DistMin,
    ThisDistStep = 1;
elseif Dist == DistMax,
    ThisDistStep = DistSteps + 1;
else
    ThisDistStep = ceil(ThisDist/DistRes) + 1;
end

function LogPath = ErrorLogging(ErrorType,ErrorMsg)
%Function to log errors to logfiles

global ErrorCount

switch ErrorType
    case 1
        LogPath = 'HSSPlog.txt';
    case 2
        LogPath = 'PDBlog.txt';
    case 3
        LogPath = 'ExProStructlog.txt';
end

if ErrorCount(ErrorType) == 0,
    mode = 'w';
    ErrorCount(ErrorType) = 1;
    ErrorMsg = ['Errors encountered during executing at : ' datestr(now) '\n' ErrorMsg '\n'];
else
    mode = 'a';
    ErrorMsg = [ErrorMsg '\n'];
end

ErrorLog = fopen(LogPath,mode);
fprintf(ErrorLog,ErrorMsg);
fclose(ErrorLog);

function thetime = sec2time(sec)
%Function to concert seconds into h:m:s
min = floor(sec/60);
hr = floor(min/60);
thetime = [num2str(hr) ' hours, ' num2str(min-60*hr) ' minutes and ' num2str(round(sec-60*min)) ' seconds'];

function FAtom = FunctAtom(ResType)
%Function that defines functional groups of residues
switch ResType
    case 1
        FAtom{1} = 'CB';
    case 2 %ARG
        FAtom{1} = 'NH1';
        FAtom{2} = 'NH2';
        FAtom{3} = 'NE';
    case 3 %ASN
        FAtom{1} = 'ND2';
        FAtom{2} = 'OD1';
    case 4 %ASP
        FAtom{1} = 'OD1';
        FAtom{2} = 'OD2';
    case 5 %CYS
        FAtom{1} = 'SG';
    case 6 %GLN
        FAtom{1} = 'NE2';
        FAtom{2} = 'OE1';
    case 7 %GLU
        FAtom{1} = 'OE1';
        FAtom{2} = 'OE2';
    case 8
        FAtom{1} = 'CA';
    case 9 %HIS
        FAtom{1} = 'ND1';
        FAtom{2} = 'NE2';
    case 10 %ILE
        FAtom{1} = 'CG2';
        FAtom{2} = 'CD1';
    case 11 %LEU
        FAtom{1} = 'CD1';
        FAtom{2} = 'CD2';
    case 12 %LYS
        FAtom{1} = 'NZ';
    case 13 %MET
        FAtom{1} = 'SD';
        FAtom{2} = 'CE';
    case 14 %PHE
        FAtom{1} = 'CZ';
        FAtom{2} = 'CD1';
        FAtom{3} = 'CD2';
        FAtom{4} = 'CE1';
        FAtom{5} = 'CE2';
    case 15 %PRO
        FAtom{1} = 'CG';
        FAtom{2} = 'CD';
        FAtom{3} = 'CB';
    case 16 %SER
        FAtom{1} = 'OG';
    case 17 %THR
        FAtom{1} = 'OG1';
    case 18 %TRP
        FAtom{1} = 'NE1'; %??
    case 19 %TYR
        FAtom{1} = 'OH';
    case 20 %VAL
        FAtom{1} = 'CG1';
        FAtom{2} = 'CG2';
end


%%%%%%%%%%%%%USED WITH PROPACK PAPER%%%%%%%%%%%%%%%%%
%
%
% function FAtom = FunctAtom(ResType)
% %Function that defines functional groups of residues
% switch ResType
%     case 1
%         FAtom{1} = 'CB';
%     case 2
%         FAtom{1} = 'NH1';
%         FAtom{2} = 'NH2';
%     case 3
%         FAtom{1} = 'ND2';
%         FAtom{2} = 'OD1';
%     case 4
%         FAtom{1} = 'OD1';
%         FAtom{2} = 'OD2';
%     case 5
%         FAtom{1} = 'SG';
%     case 6
%         FAtom{1} = 'NE2';
%         FAtom{2} = 'OE1';
%     case 7
%         FAtom{1} = 'OE1';
%         FAtom{2} = 'OE2';
%     case 8
%         FAtom{1} = 'CA';
%     case 9
%         FAtom{1} = 'ND1';
%     case 10
%         FAtom{1} = 'CG1';
%         FAtom{2} = 'CG2';
%     case 11
%         FAtom{1} = 'CG';
%     case 12
%         FAtom{1} = 'NZ';
%     case 13
%         FAtom{1} = 'SD';
%     case 14
%         FAtom{1} = 'CZ';
%     case 15
%         FAtom{1} = 'CG';
%     case 16
%         FAtom{1} = 'OG';
%     case 17
%         FAtom{1} = 'OG1';
%     case 18
%         FAtom{1} = 'CE2';
%     case 19
%         FAtom{1} = 'OH';
%     case 20
%         FAtom{1} = 'CG1';
%         FAtom{2} = 'CG2';
% end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%







function AAint = AAsurf(AA)
%Function that defines surface area (Å^2) of residues
switch AA
  case {'v','V',20}
   AAint = 160;
  case {'l','L',11}
   AAint = 180;
  case {'i','I',10}
   AAint = 182;
  case {'m','M',13}
   AAint = 204;
  case {'f','F',14}
   AAint = 218;
  case {'w','W',18}
   AAint = 259;
  case {'y','Y',19}
   AAint = 229;
  case {'g','G',8}
   AAint = 85;
  case {'a','A',1}
   AAint = 113;
  case {'p','P',15}
   AAint = 143;
  case {'s','S',16}
   AAint = 122;
  case {'t','T',17}
   AAint = 146;
  case {'c','C',5}
   AAint = 140;
  case {'h','H',9}
   AAint = 194;
  case {'r','R',2}
   AAint = 241;
  case {'k','K',12}
   AAint = 211;
  case {'q','Q',6}
   AAint = 189;
  case {'e','E',7}
   AAint = 183;
  case {'n','N',3}
   AAint = 158;
  case {'d','D',4}
   AAint = 151;
  otherwise
   AAint = 100000;
end


function myint = aa2int(Subst)
switch Subst
    case 'A'
        myint = 1;
    case 'R'
        myint = 2;
    case 'N'
        myint = 3;
    case 'D'
        myint = 4;
    case 'C'
        myint = 5;
    case 'Q'
        myint = 6;
    case 'E'
        myint = 7;
    case 'G'
        myint = 8;
    case 'H'
        myint = 9;
    case 'I'
        myint = 10;
    case 'L'
        myint = 11;
    case 'K'
        myint = 12;
    case 'M'
        myint = 13;
    case 'F'
        myint = 14;
    case 'P'
        myint = 15;
    case 'S'
        myint = 16;
    case 'T'
        myint = 17;
    case 'W'
        myint = 18;
    case 'Y'
        myint = 19;
    case 'V'
        myint = 20;
    otherwise
        myint = 0;
end