Method overlapMaximally

src/rnabloom/util/SeqUtils.java:1335–1379

(String left, String right, int minOverlap)

    }
    
    public static String overlapMaximally(String left, String right, int minOverlap) {
        String prefix = right.substring(0, minOverlap);
        int leftLength = left.length();
        int rightLength = right.length();
        
        int lowerL = 0;
        int maxLi = leftLength - minOverlap;
        
        while (lowerL >= 0 && lowerL <= maxLi) {
            lowerL = left.indexOf(prefix, lowerL);
            
            if (lowerL >= 0) {
                int upperL = lowerL+rightLength;
                if (upperL < leftLength) {
                    // could `right` be contained in `left`?
                    String leftTail = left.substring(lowerL+minOverlap, upperL);
                    String rightTail = right.substring(minOverlap);
                    if (leftTail.equals(rightTail)) {
                        // overlap: rightLength
                        return left;
                    }
                }
                else {
                    upperL = leftLength;
                    String leftTail = left.substring(lowerL+minOverlap, upperL);
                    String rightTail = right.substring(minOverlap, upperL-lowerL);
                    if (leftTail.equals(rightTail)) {
                        // overlap: leftLength - lowerL
                        return left + right.substring(upperL-lowerL);
                    }
                }
                ++lowerL;
            }
        }

        if (leftLength >= rightLength && left.contains(right)) {
            return left;
        }
        
        if (leftLength < rightLength && right.contains(left)) {
            return right;
        }
        
        return null;
    }
        
    public static String overlapMinimally(String left, String right, int minOverlap) {
        int li = left.length() - minOverlap;