/**
* //extract the alignment output // eg // STWNTWACTWHLKQP--WSTILILA // 111111111111 22222222 //
* SQNNTYACSWKLKSWNNNSTILILG // 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
*/
public static void getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2) {
boolean showSeq = false;
getAlign(afpChain, ca1, ca2, showSeq);
}
