private static final  boolean filterTerminal(Atom[] ca1, Atom[] ca2, int p1b, int p1e, int p2b, int p2e, int fragLen, int minLen)
	{
		int     d1 = (p1b < p2b)?p1b:p2b;
		int     d2 = (ca1.length - p1e) < (ca2.length - p2e)?(ca1.length - p1e):(ca2.length - p2e);
		int     d3 = d1 + d2 + fragLen; //maximum alignment length from current AFP


		/// DO NOT DO Math.round() this will give different results to FATCAT....
		int     d4 = (int)(0.3 * minLen);

		return d3 < d4;

	}
private static final boolean filterTerminal ( Atom [ ] ca1 , Atom [ ] ca2 , int p1b , int p1e , int p2b , int p2e , int fragLen , int minLen ) { int d1 = ( p1b < p2b ) ? p1b : p2b ; int d2 = ( ca1 . length - p1e ) < ( ca2 . length - p2e ) ? ( ca1 . length - p1e ) : ( ca2 . length - p2e ) ; int d3 = d1 + d2 + fragLen ; int d4 = ( int ) ( 0.3 * minLen ) ; return d3 < d4 ; }
filter 2 for AFP extration: the context
@param p1b
@param p1e
@param p2b
@param p2e
@return