@reducedProtein = initializeStructure   ##some operations(\@residueArray,\@secondaryStructureArray);

if ($ERRORCHECK ==1)          #if global errorcheck is 1
{$response = confirmExit(@ERRORTYPE);} #call error function

if($response==1){		
simulate(@reducedProtein);} #if not, go to calculations etc

##</code><code>##

sub confirmExit
 {
 *create a window*

 my @ERRORTYPE=@_;

 *write something on the window according to errortype values*

 *create button exit, which exits the program when pressed*

 *create button ignore, which sets the value of $response to 0 if pressed*

 return $reponse;