checkProjectDependencies(filelist, projectDir, bQuiet)

function [fileDepends] = checkProjectDependencies(filelist, projectDir, bQuiet)
    %CHECKPROJECTDEPENDENCIES check project files for dependency functions
    %
    %Usage: fileDepends = checkProjectDependencies(filelist, projectDir)
    %
    %fileDepends:   list of files missing from the main project
    %filelist:      list of project files
    %projectDir:    root folder of the project
    %bQuiet:        report whether there are non-matlab dependencies
    
    %default as empty
    fileDepends = [];
    %check inputs
    if nargin < 2
        return;
    elseif nargin == 2
        bQuiet = true;
    end
    
    %select only the m-files for depndency check
    funFiles = ~cellfun('isempty', regexpi(filelist, '\.m$', 'once'));
    funFiles = filelist(funFiles);
    %check dependencies for each file
    for f = 1:numel(funFiles)
        %get the function file
        funFile      = funFiles{f};
        
        %check possible dependencies on java functions
        extdep  = mlint('-calls', funFile);
        extdep  = {extdep.message};
        extfltr = ~cellfun('isempty', regexp(extdep, '(javaaddpath)|(import)', 'once'));
        if any(extfltr)
            %external java dependencies are used
            bExtraDepends(f) = true;
            extraDepends(f)  = {funFile};
        else
            bExtraDepends(f) = false;
            extraDepends(f)  = {''};
        end
        list = depfun(funFile, '-toponly', '-quiet');
        %remove matlab toolbox functions
        toolpath = fullfile(matlabroot, 'toolbox');
        if ispc()
            toolpath_ = regexprep(toolpath, '\\','/');
            list_     = regexprep(list, '\\', '/');
            toolfltr  = cellfun('isempty', regexpi(list_, ['^' toolpath_], 'once'));
        else
            toolfltr = cellfun('isempty', regexpi(list, ['^' toolpath], 'once'));
        end
        newlist  = list(toolfltr);
        %remove the current function under investigation
        if ispc()
            newlist_ = regexprep(newlist, '\\', '/');
            funFile_ = regexprep(funFile, '\\', '/');
            selffltr = cellfun('isempty', regexpi(newlist_, [funFile_ '$'], 'once'));
        else
            selffltr = cellfun('isempty', regexpi(newlist, [funFile '$'], 'once'));
        end
        newlist  = newlist(selffltr);
        %remove files from the project folder
        if ispc()
            newlist_ = regexprep(newlist, '\\', '/');
            projectDir_ = regexprep(projectDir, '\\', '/');
            rootfltr = cellfun('isempty', regexpi(newlist_, ['^' projectDir_], 'once'));
        else
            rootfltr = cellfun('isempty', regexpi(newlist, ['^' projectDir], 'once'));
        end
        newlist  = newlist(rootfltr);
        if isempty(newlist)
            %no dependencies in the form of matlab functions
            continue;
        end
        
        if isempty(fileDepends)
            fileDepends = newlist';
        else
            %check if items on the new list already exist in fileDepends
            doublefltr = cellfun(@(c) strcmpi(newlist, c), fileDepends, 'UniformOutput', false);
            doublefltr = cellfun(@any, doublefltr);
            if sum(doublefltr) == numel(newlist)
                continue;
            end
            fileDepends = [fileDepends, newlist'];
        end
    end
    
    %check if there are any extra dependencies not found by depfun
    if ~bQuiet && any(bExtraDepends)
        msg = {'the following functions had extra dependencies that need to be manually resolved:'};
        
        %check which files have extra dependencies
        fltr = ~cellfun('isempty', extraDepends);
        extraDepends = extraDepends(fltr);
        msg = [msg; extraDepends'];
        helpdlg(msg, 'Unresolved dependencies');
    end
end