private void printSequenceAlignmentWeb(StringBuilder s, int counter, String idFormat, int start, int end) {
		S as = sequences.get(counter - 1), seq1 = sequences.get(0), seq2 = sequences.get(1);

		if (idFormat != null) {
			s.append(String.format(idFormat, as.getAccession()));
		}

		String mySeq = as.getSubSequence(start, end).getSequenceAsString();
		String s1 = seq1.getSubSequence(start, end).getSequenceAsString();
		String s2 = seq2.getSubSequence(start, end).getSequenceAsString();
		CompoundSet<C> cs = getCompoundSet();

		for (int i = 0; i < s1.length(); i++) {
			if (i >= s2.length() || i >= mySeq.length())
				break;
			char c1 = s1.charAt(i);
			char c2 = s2.charAt(i);
			char c = mySeq.charAt(i);
			s.append(IOUtils.getPDBCharacter(true, c1, c2, cs.compoundsEquivalent(seq1.getCompoundAt(i),
					seq2.getCompoundAt(i)), c));
		}

		s.append(String.format("%n"));
	}
private void printSequenceAlignmentWeb ( StringBuilder s , int counter , String idFormat , int start , int end ) { S as = sequences . get ( counter - 1 ) , seq1 = sequences . get ( 0 ) , seq2 = sequences . get ( 1 ) ; if ( idFormat != null ) { s . append ( String . format ( idFormat , as . getAccession ( ) ) ) ; } String mySeq = as . getSubSequence ( start , end ) . getSequenceAsString ( ) ; String s1 = seq1 . getSubSequence ( start , end ) . getSequenceAsString ( ) ; String s2 = seq2 . getSubSequence ( start , end ) . getSequenceAsString ( ) ; CompoundSet < C > cs = getCompoundSet ( ) ; for ( int i = 0 ; i < s1 . length ( ) ; i ++ ) { if ( i >= s2 . length ( ) || i >= mySeq . length ( ) ) break ; char c1 = s1 . charAt ( i ) ; char c2 = s2 . charAt ( i ) ; char c = mySeq . charAt ( i ) ; s . append ( IOUtils . getPDBCharacter ( true , c1 , c2 , cs . compoundsEquivalent ( seq1 . getCompoundAt ( i ) , seq2 . getCompoundAt ( i ) ) , c ) ) ; } s . append ( String . format ( "%n" ) ) ; }
@param s
@param counter
@param idFormat
@param start
@param end