Split a string on commas not contained within double-quotes with a twist

A home-grown parser is easily written.

For example, this ANTLR grammar takes care of your example input without much trouble:

parse
  :  line*
  ;

line
  :  Quoted ( ',' Quoted )* ( '\r'? '\n' | EOF )
  ;

Quoted
  :  '"' ( Atom )* '"'
  ;

fragment
Atom
  :  Parentheses
  |  ~( '"' | '\r' | '\n' | '(' | ')' )
  ;

fragment
Parentheses
  :  '(' ~( '(' | ')' | '\r' | '\n' )* ')'
  ;

Space
  :  ( ' ' | '\t' ) {skip();}
  ;

and it would be easy to extend this to take escaped quotes or parenthesis into account.

When feeding the parser generated by that grammar to following two lines of input:

"Thanks,", "in advance,", "for("the", "help")"
"and(,some,more)","data , here"

it gets parsed like this:

If you consider to use ANTLR for this, I can post a little HOW-TO to get a parser from that grammar I posted, if you want.

Sometimes it is easier to match what you want instead of what you don't want:

String s = "\"Thanks,\", \"in advance,\", \"for(\"the\", \"help\")\"";
String regex = "\"(\\([^)]*\\)|[^\"])*\"";
Pattern p = Pattern.compile(regex);
Matcher m = p.matcher(s);
while(m.find()) {
    System.out.println(s.substring(m.start(),m.end()));
}

Output:

"Thanks,"
"in advance,"
"for("the", "help")"

If you also need it to ignore closing brackets inside the quotes sections that are inside the brackets, then you need this:

 String regex = "\"(\\((\"[^\"]*\"|[^)])*\\)|[^\"])*\"";

An example of a string which needs this second, more complex version is:

 "foo","bar","baz(":-)",":-o")"

Output:

"foo"
"bar"
"baz(":-)",":-o")"

However, I'd advise you to change your data format if at all possible. This would be a lot easier if you used a standard format like XML to store your tokens.