I have created a Lucene index with the following analyzer.

public class DocSpecAnalyzer extends Analyzer {
   private static CharArraySet stopSet;// = new HashSet<String>(Arrays.asList());//STOP_WORDS_SET;
   static {
     stopSet = new CharArraySet(FDConstants.stopwords, true);
// uncommenting this displays all the stop words
//      for (String s: FDConstants.stopwords) {
//          System.out.println(s);
//      }
    }

  /**
   * Specifies whether deprecated acronyms should be replaced with HOST type.
   * See {@linkplain https://issues.apache.org/jira/browse/LUCENE-1068}
   */
  private final boolean enableStopPositionIncrements;

  private final Version matchVersion;

  public DocSpecAnalyzer(Version matchVersion) {
    this.matchVersion = matchVersion;
    enableStopPositionIncrements =         
    StopFilter.getEnablePositionIncrementsVersionDefault(matchVersion);
  }


  public TokenStream tokenStream(String fieldName, Reader reader) {

     StandardTokenizer tokenStream = new StandardTokenizer(matchVersion, reader);
     tokenStream.setMaxTokenLength(DEFAULT_MAX_TOKEN_LENGTH);
     TokenStream result = new StandardFilter(tokenStream);

     result = new LowerCaseFilter(result);
     result = new StopFilter(enableStopPositionIncrements, result, stopSet);
     result = new PorterStemFilter(result);

     return result;
   }

   /** Default maximum allowed token length */
       public static final int DEFAULT_MAX_TOKEN_LENGTH = 255;

}

Now when I search for documents for a query containing stop words, i get hits for stop words also. As I post this problem, I found the bug. It is because of http://lucene.apache.org/java/2_9_2/api/contrib-misc/org/apache/lucene/queryParser/analyzing/AnalyzingQueryParser.html not handling stop words. Is there a substitute?

Update: forgot to mention that I need to do a fuzzy search. that is why i am using an AnalyzingQueryParser.