+
+ return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
+ }
+
+ /**
+ * Answers true if the mapping is from one contiguous range to another, else
+ * false
+ *
+ * @return
+ */
+ public boolean isContiguous()
+ {
+ return fromShifts.size() == 1 && toShifts.size() == 1;
+ }
+
+ /**
+ * Returns the [start1, end1, start2, end2, ...] positions in the 'from' range
+ * that map to positions between {@code start} and {@code end} in the 'to'
+ * range. Note that for a reverse strand mapping this will return ranges with
+ * end < start. Returns null if no mapped positions are found in start-end.
+ *
+ * @param start
+ * @param end
+ * @return
+ */
+ public int[] locateInFrom(int start, int end)
+ {
+ return mapPositions(start, end, toShifts, fromShifts,
+ toRatio, fromRatio);
+ }
+
+ /**
+ * Returns the [start1, end1, start2, end2, ...] positions in the 'to' range
+ * that map to positions between {@code start} and {@code end} in the 'from'
+ * range. Note that for a reverse strand mapping this will return ranges with
+ * end < start. Returns null if no mapped positions are found in start-end.
+ *
+ * @param start
+ * @param end
+ * @return
+ */
+ public int[] locateInTo(int start, int end)
+ {
+ return mapPositions(start, end, fromShifts, toShifts,
+ fromRatio, toRatio);
+ }
+
+ /**
+ * Helper method that returns the [start1, end1, start2, end2, ...] positions
+ * in {@code targetRange} that map to positions between {@code start} and
+ * {@code end} in {@code sourceRange}. Note that for a reverse strand mapping
+ * this will return ranges with end < start. Returns null if no mapped
+ * positions are found in start-end.
+ *
+ * @param start
+ * @param end
+ * @param sourceRange
+ * @param targetRange
+ * @param sourceWordLength
+ * @param targetWordLength
+ * @return
+ */
+ final static int[] mapPositions(int start, int end,
+ List<int[]> sourceRange, List<int[]> targetRange,
+ int sourceWordLength, int targetWordLength)
+ {
+ if (end < start)