I have the following String and would like to extract the contents of rule i.e. My Rule Description Looks Like This:

rule "My Rule Description Looks Like This"      
        followed by some white space other characters such as quotes".

When i use the following I get a java.lang.StringIndexOutOfBoundsException: String index out of range: -2:

String ruleName = rule.substring(rule.indexOf("rule \"" + 7, rule.indexOf("\""));

and when i use lastIndexOf:

String ruleName = rule.substring(rule.indexOf("rule \"" + 7, rule.lastIndexOf("\""));

the code executes OK but the output looks like:

My Rule Description Looks Like This"        
        followed by some white space other characters and quotes

Any ideas why the first option throws an exception using indexOf?

For any sort of complex text extraction, you might want to consider using regular expressions. Here is a short script which can extract the rule, and it avoids nasty string manipulations, which, as you have seen, can be prone to error.

String line = "rule \"My Rule Description Looks Like This\"\n";
line += "followed by some white space other characters such as quotes\".";
String pattern = "rule\\s+\"(.*?)\".*";

Pattern r = Pattern.compile(pattern, Pattern.DOTALL);
Matcher m = r.matcher(line);
if (m.find()) {
   System.out.println("Found a rule: " + m.group(1) );
} else {
   System.out.println("Could not find a rule.");
}

Output:

My Rule Description Looks Like This

Demo here:

Rextester