private int[][] generateInstanceSimilarityMatrix(int maxPermutationCount,
			IndexPermutator permutator) {
		maxPermutationCount = Math.min(permutator.getPermutationCount(),
				maxPermutationCount);
		int[][] permSimilarities = new int[maxPermutationCount][instances.length];
		for (int i = 0; i < maxPermutationCount; ++i) {
			int[] permIdx = permutator.next();
			generatePermutationSimilarityVector(permSimilarities[i], permIdx);
			// System.out.println(Arrays.toString(permIdx) + ": "
			// + Arrays.toString(permSimilarities[i]));
		}
		return permSimilarities;
	}