Classes for searching for oligonucleotides within nucleic acid sequences.

For example:
// Create search object.
Search search = SearchFactory.createMismatchSearch(getAllowedMismatches());
// Run search.
try {search.run(oligo, sequence);}
catch(NonIUBCharacterException nce) {
JOptionPane.showMessageDialog(
this,
"One or more illegal base characters present.",
"Non IUB Character Exception",
JOptionPane.ERROR_MESSAGE
);
}

// Display results.
SearchOutcomeCollection collection = search.getSearchOutcomeCollection();

SearchOutcome outcome = null;
StringBuffer buffer = new StringBuffer();
for (int i = 0; i < collection.getSize(); i++) {
outcome = collection.getSearchOutcome(i);

System.out.println(
outcome.getStartPosition() + "," +
outcome.getEndPosition() + ", " +
outcome.getSearchResult().toString()
);
}