code: 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;
  
  	}
docs: filter 2 for AFP extration: the context
  @param p1b
  @param p1e
  @param p2b
  @param p2e
  @return