source: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java @ 1667

package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;

import java.util.ArrayList;
import java.util.logging.Level;

import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm;
import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory;
import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
import de.ugoe.cs.util.console.Console;

public class PairwiseAlignmentGenerator {

        public static PairwiseAlignmentStorage generate(
                        ArrayList<NumberSequence> numberseqs,
                        ObjectDistanceSubstitionMatrix submat, 
                        int threshold) {
                PairwiseAlignmentStorage alignments = new PairwiseAlignmentStorage(
                                numberseqs.size(), numberseqs.size());
                int smithWatermanThreshold = threshold;

                for (int i = 0; i < numberseqs.size(); i++) {
                        NumberSequence ns1 = numberseqs.get(i);
                        for (int j = 0; j < numberseqs.size(); j++) {
                                NumberSequence ns2 = numberseqs.get(j);

                                if (i != j) {
                                        Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j);
                                
                                        AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
                                        aa.align(ns1, ns2, submat,
                                                        smithWatermanThreshold);
                                        alignments.set(i, j, aa);
                                }
                        }
                }
                return alignments;
        }
}