Swap letters in a string

Question

I need to swap letters in a string with the following rules:

• A is replaced by T
• T is replaced by A
• C is replaced by G
• G is replaced

Answer 1

DNA has a small alphabet. You can use a lookup table, replacing some statements with a simple array indexing.

This approach:

• Traverses the sequence only once.
• Eliminates the conditional statements.
• Can be stable in terms of letter case, which is sometimes used to communicate information in DNA sequences.
• Can handle IUPAC ambiguity codes.
• Can handle gaps.
• Can easily provide a reverse complement.

First, you need a lookup table.

private static final String COMPLEMENT_TABLE 
  // 0123456789ABCDEF0123456789ABCDEF
  = "                                " // 0-31
  + "             -                  " // 32-63
  + " TVGH  CD  M KN   YSAABWXR      " // 64-95
  + " tvgh  cd  m kn   ysaabwxr      "; // 96-127
  //  ABCDEFGHIJKLMNOPQRSTUVWXYZ

private static final byte[] COMPLEMENT_TABLE_BYTES 
  = COMPLEMENT_TABLE.getBytes( StandardCharsets.US_ASCII );

Then, you can find the complement's bases by a simple table lookup.

public static byte[] complement( byte[] sequence ) {
    int length = sequence.length;
    byte[] result = new byte[ length ];

    for ( int i = 0; i < length; ++i ) {
        result[i] = COMPLEMENT_TABLE_BYTES[ sequence[i] ];
    }

    return result;
}

If desired for convenience with small sequences, you can provide a method that accepts and returns a String.

public static String complement( String sequence ) {
    byte[] complementBytes = complement( 
      sequence.getBytes( StandardCharsets.US_ASCII ));
    return new String( complementBytes, StandardCharsets.US_ASCII );
}

The reverse complement can be computed in the same loop.

public static byte[] reverseComplement( byte[] sequence ) {
    int length = sequence.length;
    byte[] result = new byte[ length ];

    for ( int i = 0; i < length; ++i ) {
        result[ (length - i) - 1] = COMPLEMENT_TABLE_BYTES[ sequence[i] ];
    }

    return result;
}

public static String reverseComplement( String sequence ) {
    byte[] complementBytes = reverseComplement( 
      sequence.getBytes( StandardCharsets.US_ASCII ));
    return new String( complementBytes, StandardCharsets.US_ASCII );
}

Using your example sequence:

public static void main(String[] args) {
    String sequence = "ACGTA";

    String complementSequence = complement( sequence );
    System.out.println( String.format( 
       "complement(%s) = %s", sequence, complementSequence ));

    String reverseComplementSequence = reverseComplement( sequence );
    System.out.println( String.format( 
      "reverseComplement(%s) = %s", sequence, reverseComplementSequence ));
}

We get this output:

complement(ACGTA) = TGCAT
reverseComplement(ACGTA) = TACGT