@Override
public void runDiscovery(MotifFactory factory) {
System.err.println("run ab discovery");
ArrayList<Sequence> revSequences = BaseSequence.generateReverseComplements(sequences);
// add sentinels and replace non ACGT chars with sentinel
// not necessary to repeat this for every position + no deep copy of seqs!
// long start = System.nanoTime();
ArrayList<Sequence> sequencesPreprocessed =
GeneralizedSuffixTree.preprocessSequences(sequences, false);
ArrayList<Sequence> revSequencesPreprocessed =
GeneralizedSuffixTree.preprocessSequences(revSequences, false);
// System.err.println("Seq preprocessing: "+(System.nanoTime()-start)/1000000);
// start = System.nanoTime();
ArrayList<IndexStructure> forwardIndexes = generateIndexes(sequencesPreprocessed);
ArrayList<IndexStructure> reverseIndexes = generateIndexes(revSequencesPreprocessed);
// System.err.println("Index building: "+(System.nanoTime()-start)/1000000);
if (extractor != null) {
SortedSet<String> prefixes = generateAllPrefixes();
// int counter=0;
// start = System.nanoTime();
prefixLoop:
for (String prefix : prefixes) {
// counter++;
extractor.reset(); // flushes motif map before new prefix is procesed
// System.out.println("p: "+prefix);
if (countNumberOfDegs(prefix) > motifSearchSpace.getMaxNumberOfDegeneratePositions()) {
continue prefixLoop;
}
for (int i = 0; i < sequences.get(0).length(); i++) {
launchDiscoveryForPosition(
i, factory, prefix, sequencesPreprocessed, forwardIndexes.get(i));
}
for (int i = 0; i < revSequences.get(0).length(); i++) {
launchDiscoveryForPosition(
i, factory, prefix, revSequencesPreprocessed, reverseIndexes.get(i));
}
/*if (counter%100==0){
System.err.println("Prefix: " + counter + " "+(System.nanoTime()-start)/1000000);
start = System.nanoTime();
}*/
}
}
}