code: public static void getAlign(AFPChain afpChain,Atom[] ca1,Atom[] ca2) {
  		getAlign(afpChain, ca1, ca2, false);
  	}
docs: Extract the alignment output
  <p>eg<pre>
  STWNTWACTWHLKQP--WSTILILA
  111111111111     22222222
  SQNNTYACSWKLKSWNNNSTILILG
  </pre>
  Those position pairs labeled by 1 and 2 are equivalent positions, belongs to
  two blocks 1 and 2. The residues between labeled residues are non-equivalent,
  with '-' filling in their resulting gaps.
  <p>
  The three lines can be accessed using
  {@link AFPChain#getAlnseq1()}, {@link AFPChain#getAlnsymb()},
  and {@link AFPChain#getAlnseq2()}.