X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;fp=src%2Fjalview%2Futil%2FMapList.java;h=c5654fbee62fd697f85c53ebb55e44302eb28b29;hb=39b4859e1a1b011af5d06058461db4d075acb578;hp=731e976ecb1686b62ef2037c60fc3b9e0328360b;hpb=f3dcb2f8f602117ac390799b1f310dcaa9918592;p=jalview.git
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 731e976..c5654fb 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -24,6 +24,8 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import jalview.bin.Cache;
+
/**
* A simple way of bijectively mapping a non-contiguous linear range to another
* non-contiguous linear range.
@@ -209,8 +211,7 @@ public class MapList
/**
* Constructor given from and to ranges as [start1, end1, start2, end2,...].
- * If any end is equal to the next start, the ranges will be merged. There is
- * no validation check that the ranges do not overlap each other.
+ * There is no validation check that the ranges do not overlap each other.
*
* @param from
* contiguous regions as [start1, end1, start2, end2, ...]
@@ -228,7 +229,6 @@ public class MapList
this.toRatio = toRatio;
fromLowest = Integer.MAX_VALUE;
fromHighest = Integer.MIN_VALUE;
- int added = 0;
for (int i = 0; i < from.length; i += 2)
{
@@ -238,36 +238,16 @@ public class MapList
*/
fromLowest = Math.min(fromLowest, Math.min(from[i], from[i + 1]));
fromHighest = Math.max(fromHighest, Math.max(from[i], from[i + 1]));
- if (added > 0 && from[i] == fromShifts.get(added - 1)[1])
- {
- /*
- * this range starts where the last ended - just extend it
- */
- fromShifts.get(added - 1)[1] = from[i + 1];
- }
- else
- {
- fromShifts.add(new int[] { from[i], from[i + 1] });
- added++;
- }
+ fromShifts.add(new int[] { from[i], from[i + 1] });
}
toLowest = Integer.MAX_VALUE;
toHighest = Integer.MIN_VALUE;
- added = 0;
for (int i = 0; i < to.length; i += 2)
{
toLowest = Math.min(toLowest, Math.min(to[i], to[i + 1]));
toHighest = Math.max(toHighest, Math.max(to[i], to[i + 1]));
- if (added > 0 && to[i] == toShifts.get(added - 1)[1])
- {
- toShifts.get(added - 1)[1] = to[i + 1];
- }
- else
- {
- toShifts.add(new int[] { to[i], to[i + 1] });
- added++;
- }
+ toShifts.add(new int[] { to[i], to[i + 1] });
}
}
@@ -330,9 +310,8 @@ public class MapList
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- System.err.println(
- "Invalid format for fromRange " + Arrays.toString(range)
- + " may cause errors");
+ Cache.log.error("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]));
@@ -345,9 +324,8 @@ public class MapList
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- System.err.println("Invalid format for toRange "
- + Arrays.toString(range)
- + " may cause errors");
+ Cache.log.error("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]));
@@ -357,6 +335,16 @@ public class MapList
/**
* Consolidates a list of ranges so that any contiguous ranges are merged.
* This assumes the ranges are already in start order (does not sort them).
+ *
+ * The main use case for this method is when mapping cDNA sequence to its
+ * protein product, based on CDS feature ranges which derive from spliced
+ * exons, but are contiguous on the cDNA sequence. For example
+ *
+ * CDS 1-20 // from exon1
+ * CDS 21-35 // from exon2
+ * CDS 36-71 // from exon3
+ * 'coalesce' to range 1-71
+ *
*
* @param ranges
* @return the same list (if unchanged), else a new merged list, leaving the
@@ -384,27 +372,6 @@ public class MapList
first = false;
continue;
}
- if (range[0] == lastRange[0] && range[1] == lastRange[1])
- {
- // drop duplicate range
- changed = true;
- continue;
- }
-
- /*
- * drop this range if it lies within the last range
- */
- if ((lastDirection == 1 && range[0] >= lastRange[0]
- && range[0] <= lastRange[1] && range[1] >= lastRange[0]
- && range[1] <= lastRange[1])
- || (lastDirection == -1 && range[0] <= lastRange[0]
- && range[0] >= lastRange[1]
- && range[1] <= lastRange[0]
- && range[1] >= lastRange[1]))
- {
- changed = true;
- continue;
- }
int direction = range[1] >= range[0] ? 1 : -1;
@@ -415,11 +382,7 @@ public class MapList
boolean sameDirection = range[1] == range[0]
|| direction == lastDirection;
boolean extending = range[0] == lastRange[1] + lastDirection;
- boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0]
- && range[0] <= lastRange[1])
- || (lastDirection == -1 && range[0] <= lastRange[0]
- && range[0] >= lastRange[1]);
- if (sameDirection && (overlapping || extending))
+ if (sameDirection && extending)
{
lastRange[1] = range[1];
changed = true;
@@ -1134,8 +1097,8 @@ public class MapList
}
/**
- * 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.
+ * 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
@@ -1246,4 +1209,36 @@ public class MapList
{
return fromShifts.size() == 1 && toShifts.size() == 1;
}
+
+ /**
+ * Returns the [start, end...] positions in the range mapped from, that are
+ * mapped to by part or all of the given begin-end of the range mapped to.
+ * Returns null if begin-end does not overlap any position mapped to.
+ *
+ * @param begin
+ * @param end
+ * @return
+ */
+ public int[] getOverlapsInFrom(final int begin, final int end)
+ {
+ int[] overlaps = MappingUtils.findOverlap(toShifts, begin, end);
+
+ return overlaps == null ? null : locateInFrom(overlaps[0], overlaps[1]);
+ }
+
+ /**
+ * Returns the [start, end...] positions in the range mapped to, that are
+ * mapped to by part or all of the given begin-end of the range mapped from.
+ * Returns null if begin-end does not overlap any position mapped from.
+ *
+ * @param begin
+ * @param end
+ * @return
+ */
+ public int[] getOverlapsInTo(final int begin, final int end)
+ {
+ int[] overlaps = MappingUtils.findOverlap(fromShifts, begin, end);
+
+ return overlaps == null ? null : locateInTo(overlaps[0], overlaps[1]);
+ }
}