+ SequenceI sequence;
+
+ /**
+ * Start position of match in sequence (base 1)
+ */
+ int start;
+
+ /**
+ * End position (inclusive) (base 1)
+ */
+ int end;
+
+ /**
+ * Constructor
+ *
+ * @param seq
+ * a sequence
+ * @param start
+ * start position of matched range (base 1)
+ * @param end
+ * end of matched range (inclusive, base 1)
+ */
+ public Match(SequenceI seq, int start, int end)
+ {
+ sequence = seq;
+
+ /*
+ * always hold in forwards order, even if given in reverse order
+ * (such as from a mapping to a reverse strand); this avoids
+ * trouble for routines that highlight search results etc
+ */
+ if (start <= end)
+ {
+ this.start = start;
+ this.end = end;
+ }
+ else
+ {
+ this.start = end;
+ this.end = start;
+ }
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public int getStart()
+ {
+ return start;
+ }
+
+ public int getEnd()