[Biojava-dev] [Bug 2741] New: oboFileParser - findUnescaped

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2741

           Summary: oboFileParser - findUnescaped
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: ontology
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: alex.gawronski at gmail.com


When the oboFileParser parser checks for quotes using findUnescaped, it never
starts reading again. If there is a quote character then it ignores all the
characters until it sees another quote character. The problem is that it never
started reading again after it sees the second quote character. This caused the
method to miss the escape character. I added "inQuotes = false;" to the
findUnescaped method and it works fine.

public static int findUnescaped(String str, char toChar, int startindex,
                        int endindex, boolean honorQuotes) {
                boolean inQuotes = false;
                char quoteChar = '\0';
                for (int i = startindex; i < endindex; i++) {
                        char c = str.charAt(i);
                        if (c == '\\') {
                                i++;
                                continue;
                        } else if (inQuotes) {
                                if (c == quoteChar)
                                        inQuotes = false;
                                        continue;
                        } else if (c == toChar) {
                                return i;
                        } else if (honorQuotes && isQuote(c)) {
                                inQuotes = true;
                                quoteChar = c;
                        }
                }
                return -1;
        }


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