/** * //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); }