Method reverseComplement

src/rnabloom/util/SeqUtils.java:1120–1152

(String seq)

    }
        
    public static final String reverseComplement(String seq) {
        int seqLen = seq.length();
        char[] rc = new char[seqLen];
        
        PrimitiveIterator.OfInt itr = seq.chars().iterator();
        int i = seqLen;
        int c;
        
        while (itr.hasNext()) {
            c = itr.nextInt();
            switch(c) {
                case CHAR_A_INT:
                    rc[--i] = 'T';
                    break;
                case CHAR_C_INT:
                    rc[--i] = 'G';
                    break;
                case CHAR_G_INT:
                    rc[--i] = 'C';
                    break;
                case CHAR_T_INT:
                    rc[--i] = 'A';
                    break;
                case CHAR_U_INT:
                    rc[--i] = 'A';
                    break;
                default:
                    rc[--i] = 'N';
            }
        }
        
        return new String(rc);
    }
    
    public static final String cutHairPinLoop(final String seq, final int seedSize, final float minPercentIdentity) {
        int seqLen = seq.length();