*/
public MapList()
{
- fromShifts = new ArrayList<int[]>();
- toShifts = new ArrayList<int[]>();
+ fromShifts = new ArrayList<>();
+ toShifts = new ArrayList<>();
}
/**
{
int hashCode = 31 * fromRatio;
hashCode = 31 * hashCode + toRatio;
- hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
- hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+ for (int[] shift : fromShifts)
+ {
+ hashCode = 31 * hashCode + shift[0];
+ hashCode = 31 * hashCode + shift[1];
+ }
+ for (int[] shift : toShifts)
+ {
+ hashCode = 31 * hashCode + shift[0];
+ hashCode = 31 * hashCode + shift[1];
+ }
+
return hashCode;
}
fromHighest = Integer.MIN_VALUE;
for (int[] range : fromRange)
{
+ if (range.length != 2)
+ {
+ // throw new IllegalArgumentException(range);
+ System.err.println(
+ "Invalid format for fromRange " + Arrays.toString(range)
+ + " may cause errors");
+ }
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
}
toHighest = Integer.MIN_VALUE;
for (int[] range : toRange)
{
+ if (range.length != 2)
+ {
+ // throw new IllegalArgumentException(range);
+ System.err.println("Invalid format for toRange "
+ + Arrays.toString(range)
+ + " may cause errors");
+ }
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
}
}
boolean changed = false;
- List<int[]> merged = new ArrayList<int[]>();
+ List<int[]> merged = new ArrayList<>();
int[] lastRange = ranges.get(0);
int lastDirection = lastRange[1] >= lastRange[0] ? 1 : -1;
lastRange = new int[] { lastRange[0], lastRange[1] };
{
return null;
}
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
if (fs <= fe)
{
intv = fs;
for (int[] range : map.getFromRanges())
{
- addRange(range, fromShifts);
+ MappingUtils.addRange(range, fromShifts);
}
for (int[] range : map.getToRanges())
{
- addRange(range, toShifts);
+ MappingUtils.addRange(range, toShifts);
}
}
/**
- * Adds the given range to a list of ranges. If the new range just extends
- * existing ranges, the current endpoint is updated instead.
+ * Returns true if mapping is from forward strand, false if from reverse
+ * strand. Result is just based on the first 'from' range that is not a single
+ * position. Default is true unless proven to be false. Behaviour is not well
+ * defined if the mapping has a mixture of forward and reverse ranges.
*
- * @param range
- * @param addTo
+ * @return
*/
- static void addRange(int[] range, List<int[]> addTo)
+ public boolean isFromForwardStrand()
{
- /*
- * list is empty - add to it!
- */
- if (addTo.size() == 0)
- {
- addTo.add(range);
- return;
- }
-
- int[] last = addTo.get(addTo.size() - 1);
- boolean lastForward = last[1] >= last[0];
- boolean newForward = range[1] >= range[0];
-
- /*
- * contiguous range in the same direction - just update endpoint
- */
- if (lastForward == newForward && last[1] == range[0])
- {
- last[1] = range[1];
- return;
- }
-
- /*
- * next range starts at +1 in forward sense - update endpoint
- */
- if (lastForward && newForward && range[0] == last[1] + 1)
- {
- last[1] = range[1];
- return;
- }
-
- /*
- * next range starts at -1 in reverse sense - update endpoint
- */
- if (!lastForward && !newForward && range[0] == last[1] - 1)
- {
- last[1] = range[1];
- return;
- }
+ return isForwardStrand(getFromRanges());
+ }
- /*
- * just add the new range
- */
- addTo.add(range);
+ /**
+ * Returns true if mapping is to forward strand, false if to reverse strand.
+ * Result is just based on the first 'to' range that is not a single position.
+ * Default is true unless proven to be false. Behaviour is not well defined if
+ * the mapping has a mixture of forward and reverse ranges.
+ *
+ * @return
+ */
+ public boolean isToForwardStrand()
+ {
+ return isForwardStrand(getToRanges());
}
/**
- * Returns true if mapping is from forward strand, false if from reverse
- * strand. Result is just based on the first 'from' range that is not a single
- * position. Default is true unless proven to be false. Behaviour is not well
- * defined if the mapping has a mixture of forward and reverse ranges.
+ * A helper method that returns true unless at least one range has start > end.
+ * Behaviour is undefined for a mixture of forward and reverse ranges.
*
+ * @param ranges
* @return
*/
- public boolean isFromForwardStrand()
+ private boolean isForwardStrand(List<int[]> ranges)
{
boolean forwardStrand = true;
- for (int[] range : getFromRanges())
+ for (int[] range : ranges)
{
if (range[1] > range[0])
{
for (int[] range : getToRanges())
{
int[] transferred = map.locateInTo(range[0], range[1]);
- if (transferred == null)
+ if (transferred == null || transferred.length % 2 != 0)
{
return null;
}
- toRanges.add(transferred);
+
+ /*
+ * convert [start1, end1, start2, end2, ...]
+ * to [[start1, end1], [start2, end2], ...]
+ */
+ for (int i = 0; i < transferred.length;)
+ {
+ toRanges.add(new int[] { transferred[i], transferred[i + 1] });
+ i += 2;
+ }
}
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff