cdgea.m

function [pw1, pw0] = cdgea(isconfirmed)
%CDGEA - Change working directory to the scGEAToolbox folder

if nargin < 1
    isconfirmed = true;
end

pw0 = pwd; % Get current directory
pw1 = fileparts(mfilename('fullpath')); % Get directory of this file

% Check if current directory differs from scGEAToolbox directory
if ~strcmp(pw0, pw1) && ~isconfirmed
    % Ask the user for confirmation before changing directory
    selectedButton = uigetpref('scgeatoolbox', ... % Group
        'cdgea_ask', ... % Preference
        'Changing Working Directory', ... % Window title
        {'Do you want to change current working directory to scGEApp directory?'}, ...
        {'always', 'never'; 'Yes', 'No'}, ... % Values and button strings
        'ExtraOptions', 'Cancel', ... % Additional button
        'DefaultButton', 'Yes');
    
    switch selectedButton
        case {'always', 'Yes'}
            cd(pw1); % Change directory to scGEAToolbox folder
        case {'never', 'No', 'Cancel'}
            % Do nothing
    end
else
    cd(pw1); % Automatically change directory without confirmation
end

% Only run the following if not compiled or deployed
if ~(ismcc || isdeployed)
    % Check if required directories exist, else download them
    if ~exist(fullfile(pw1, 'example_data/'), 'dir') || ...
       ~exist(fullfile(pw1, 'resources/'), 'dir') || ...
       ~exist(fullfile(pw1, '+run', 'external/'), 'dir')
   
        f = waitbar(0.33, 'Initializing SCGEATOOL on the first run...');
        
        % Download example_data if missing
        if ~exist(fullfile(pw1, 'example_data/'), 'dir')
            try
                unzip('https://github.com/jamesjcai/jamesjcai.github.io/raw/master/data/example_data.zip');
            catch ME
                warndlg(ME.message);
                warning(ME.message);
            end
        end
        
        waitbar(0.66, f, 'Initializing SCGEATOOL on the first run...');
        
        % Download resources if missing
        if ~exist(fullfile(pw1, 'resources/'), 'dir')
            try
                unzip('https://github.com/jamesjcai/jamesjcai.github.io/raw/master/data/resources.zip');
            catch ME
                warndlg(ME.message);
                warning(ME.message);
            end
        end
        
        waitbar(0.85, f, 'Initializing SCGEATOOL on the first run...');
        
        % Download external tools if missing
        if ~exist(fullfile(pw1, '+run', 'external/'), 'dir')
            try
                a = unzip('https://github.com/jamesjcai/jamesjcai.github.io/raw/master/data/external.zip');
            catch ME
                warndlg(ME.message);
                warning(ME.message);
            end
            
            if ~iscell(a)
                errordlg('SCGEATOOL could not download the supporting file.\nPlease check network connection and try again.');
                return;
            end
            
            try
                movefile(fullfile(pw1, 'external/'), fullfile(pw1, '+run', 'external/'));
            catch ME
                warndlg(ME.message);
                warning(ME.message);
            end
        end
        
        pause(0.5);
        waitbar(1, f, 'Finishing');
        pause(1);
        
        if isvalid(f)
            close(f); % Close waitbar when finished
        end
    end
end

end