+ /**
+ * fraction of seq2 matched in the alignment
+ * @return NaN or [0..1]
+ */
+ public double getS2Coverage()
+ {
+ if (match>=0)
+ {
+ return ((double)match)/((double)s2.getEnd()-s2.getStart()+1);
+ }
+ return Double.NaN;
+ }
+ /**
+ * fraction of seq1 matched in the alignment
+ * @return NaN or [0..1]
+ */
+ public double getS1Coverage()
+ {
+ if (match>=0)
+ {
+ return ((double)match)/((double)s1.getEnd()-s1.getStart()+1);
+ }
+ return Double.NaN;
+ }