Method cutHairPinLoop

src/rnabloom/util/SeqUtils.java:1154–1238

(final String seq, final int seedSize, final float minPercentIdentity)

    }
    
    public static final String cutHairPinLoop(final String seq, final int seedSize, final float minPercentIdentity) {
        int seqLen = seq.length();
        int halfLen = seqLen/2;
        
        final int maxSeedSearchDepth = Math.min(halfLen, 200);
        final int maxLoopLength = Math.max(200, halfLen);
        final int maxLoopDiameter = maxLoopLength/2;
        
        int lastSeedIndex = maxSeedSearchDepth - seedSize;
        
        for (int i=0; i<lastSeedIndex; i+=seedSize) {
            String seed = seq.substring(i, i+seedSize);
            int seedRevCompIndex = seq.indexOf(reverseComplement(seed), i+seedSize);

            if (seedRevCompIndex >= 0) {
                int endIndex = seedRevCompIndex + seedSize;
                int halfIndex = (i + endIndex)/2;

                if (i+seedSize >= seedRevCompIndex-maxLoopLength) {
                   if (halfIndex < halfLen) {
                        return seq.substring(halfIndex);
                    }
                    else {
                        return seq.substring(0, halfIndex);
                    }
                }
                else {
                    String left = seq.substring(i, halfIndex-maxLoopDiameter);
                    String right = seq.substring(halfIndex+maxLoopDiameter, endIndex);

                    float pid = getPercentIdentity(left, reverseComplement(right));
                    
                    if (pid >= minPercentIdentity) {
                        if (halfIndex < halfLen) {
                            return seq.substring(halfIndex);
                        }
                        else {
                            return seq.substring(0, halfIndex);
                        }
                    }
                }
                
                break;
            }
        }
        
        lastSeedIndex = seqLen-maxSeedSearchDepth;
        
        for (int i=seqLen-seedSize; i>=lastSeedIndex; i-=seedSize) {
            String seed = seq.substring(i, i+seedSize);
            int seedRevCompIndex = seq.lastIndexOf(reverseComplement(seed));

            if (seedRevCompIndex >= 0 && seedRevCompIndex < i-seedSize) {
                int halfIndex = (seedRevCompIndex + i + seedSize)/2;
                
                if (seedRevCompIndex+seedSize >= i-maxLoopLength) {
                    if (halfIndex < halfLen) {
                        return seq.substring(halfIndex);