import java.util.BitSet;
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.
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- System.err.println("Invalid format for fromRange "
+ Cache.log.error("Invalid format for fromRange "
+ Arrays.toString(range) + " may cause errors");
}
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- System.err.println("Invalid format for toRange "
+ Cache.log.error("Invalid format for toRange "
+ Arrays.toString(range) + " may cause errors");
}
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
int mp[][] = new int[to - from + 2][];
for (int i = 0; i < mp.length; i++)
{
- int[] m = shift(i + from, shiftTo, sourceRatio, shiftFrom, targetRatio);
+ int[] m = shift(i + from, shiftTo, sourceRatio, shiftFrom,
+ targetRatio);
if (m != null)
{
if (i == 0)
}
/**
- * 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.
+ * <<<<<<< HEAD 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
*/
public int[] locateInFrom(int start, int end)
{
- return mapPositions(start, end, toShifts, fromShifts,
- toRatio, fromRatio);
+ return mapPositions(start, end, toShifts, fromShifts, toRatio,
+ fromRatio);
}
/**
*/
public int[] locateInTo(int start, int end)
{
- return mapPositions(start, end, fromShifts, toShifts,
- fromRatio, toRatio);
+ return mapPositions(start, end, fromShifts, toShifts, fromRatio,
+ toRatio);
}
/**
* @return
*/
protected final static BitSet getMappedOffsetsForPositions(int start,
- int end, List<int[]> sourceRange, int sourceWordLength, int targetWordLength)
+ int end, List<int[]> sourceRange, int sourceWordLength,
+ int targetWordLength)
{
BitSet overlaps = new BitSet();
int offset = 0;
return added;
}
+
+ /*
+ * 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]);
+ }
}
* no overlap
*/
assertNull(ml.locateInFrom(0, 0));
-
+
}
/**
assertEquals("[10, 10, 12, 12, 14, 14]",
Arrays.toString(ml.locateInFrom(3, 3)));
assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
-
+
/*
* codons at 11-16, 21-26, 31-36 mapped to peptide positions 1, 3-4, 6-8
*/
}
/**
+ * Tests for method that locates the overlap of the ranges in the 'from' map
+ * for given range in the 'to' map
+ */
+ @Test(groups = { "Functional" })
+ public void testGetOverlapsInFrom_withIntrons()
+ {
+ /*
+ * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
+ * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
+ */
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+ int[] protein = { 11, 14 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+
+ assertEquals("[2, 3, 5, 5]",
+ Arrays.toString(ml.getOverlapsInFrom(11, 11)));
+ assertEquals("[2, 3, 5, 7, 9, 9]",
+ Arrays.toString(ml.getOverlapsInFrom(11, 12)));
+ // out of range 5' :
+ assertEquals("[2, 3, 5, 7, 9, 9]",
+ Arrays.toString(ml.getOverlapsInFrom(8, 12)));
+ // out of range 3' :
+ assertEquals("[10, 10, 12, 12, 14, 14, 16, 18]",
+ Arrays.toString(ml.getOverlapsInFrom(13, 16)));
+ // out of range both :
+ assertEquals("[2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18]",
+ Arrays.toString(ml.getOverlapsInFrom(1, 16)));
+ // no overlap:
+ assertNull(ml.getOverlapsInFrom(20, 25));
+ }
+
+ /**
+ * Tests for method that locates the overlap of the ranges in the 'to' map for
+ * given range in the 'from' map
+ */
+ @Test(groups = { "Functional" })
+ public void testGetOverlapsInTo_withIntrons()
+ {
+ /*
+ * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [17, 18, 19] i.e.
+ * 2-3, 5-7, 9-10, 12-12, 14-14, 17-19
+ */
+ int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 17, 19 };
+ /*
+ * Mapped proteins at positions 1, 3, 4, 6 in the sequence
+ */
+ int[] protein = { 1, 1, 3, 4, 6, 6 };
+ MapList ml = new MapList(codons, protein, 3, 1);
+
+ /*
+ * Can't map from an unmapped position
+ */
+ assertNull(ml.getOverlapsInTo(1, 1));
+ assertNull(ml.getOverlapsInTo(4, 4));
+ assertNull(ml.getOverlapsInTo(15, 16));
+
+ /*
+ * nor from a range that includes no mapped position (exon)
+ */
+ assertNull(ml.getOverlapsInTo(15, 16));
+
+ // end of codon 1 maps to first peptide
+ assertEquals("[1, 1]", Arrays.toString(ml.getOverlapsInTo(2, 2)));
+ // end of codon 1 and start of codon 2 maps to first 2 peptides
+ assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(3, 7)));
+
+ // range overlaps 5' end of dna:
+ assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 6)));
+ assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 8)));
+
+ // range overlaps 3' end of dna:
+ assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(17, 24)));
+ assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(16, 24)));
+
+ // dna positions 8, 11 are intron but include end of exon 2 and start of
+ // exon 3
+ assertEquals("[3, 4]", Arrays.toString(ml.getOverlapsInTo(8, 11)));
+ }
+
+ /**
* Tests for method that locates ranges in the 'to' map for given range in the
* 'from' map.
*/
*/
assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 13)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 2)));
-
+
/*
* no overlap
*/
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 4)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 4)));
-
+
/*
* no overlap
*/
toRanges = compound.getToRanges();
assertEquals(2, toRanges.size());
assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0));
- assertArrayEquals(new int[] { 600, 582}, toRanges.get(1));
+ assertArrayEquals(new int[] { 600, 582 }, toRanges.get(1));
/*
* 1:1 plus 1:3 should result in 1:3
* no overlap
*/
assertNull(ml.locateInTo(0, 0));
-
+
/*
* partial overlap
*/
ml = new MapList(gene, cds, 1, 1);
assertEquals("[13203, 13204]",
Arrays.toString(ml.locateInTo(13468, 13468)));
-
+
/*
* gene to protein
* the base at 13468 is in the codon for 4401N and also 4402R
public void testAddOffsetPositions()
{
List<int[]> mapped = new ArrayList<>();
- int[] range = new int[] {10, 20};
+ int[] range = new int[] { 10, 20 };
BitSet offsets = new BitSet();
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertArrayEquals(new int[] { 14, 13 }, mapped.get(1));
assertArrayEquals(new int[] { 10, 10 }, mapped.get(2));
}
-
+
@Test(groups = { "Functional" })
public void testGetPositionsForOffsets()
{
BitSet offsets = new BitSet();
List<int[]> mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertTrue(mapped.isEmpty()); // no ranges and no offsets!
-
+
offsets.set(5, 1000);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertTrue(mapped.isEmpty()); // no ranges
-
+
/*
* one range with overlap of offsets
*/
- ranges.add(new int[] {15, 25});
+ ranges.add(new int[] { 15, 25 });
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(1, mapped.size());
- assertArrayEquals(new int[] {20, 25}, mapped.get(0));
-
+ assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
+
/*
* two ranges
*/
- ranges.add(new int[] {300, 320});
+ ranges.add(new int[] { 300, 320 });
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
- assertArrayEquals(new int[] {20, 25}, mapped.get(0));
- assertArrayEquals(new int[] {300, 320}, mapped.get(1));
-
+ assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
+ assertArrayEquals(new int[] { 300, 320 }, mapped.get(1));
+
/*
* boundary case - right end of first range overlaps
*/
offsets.set(10);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(1, mapped.size());
- assertArrayEquals(new int[] {25, 25}, mapped.get(0));
-
+ assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
+
/*
* boundary case - left end of second range overlaps
*/
offsets.set(11);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
- assertArrayEquals(new int[] {25, 25}, mapped.get(0));
- assertArrayEquals(new int[] {300, 300}, mapped.get(1));
-
+ assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
+ assertArrayEquals(new int[] { 300, 300 }, mapped.get(1));
+
/*
* offsets into a circular range are reported in
* the order in which they are traversed
*/
ranges.clear();
- ranges.add(new int[] {100, 150});
- ranges.add(new int[] {60, 80});
+ ranges.add(new int[] { 100, 150 });
+ ranges.add(new int[] { 60, 80 });
offsets.clear();
offsets.set(45, 55); // sets bits 45 to 54
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
- assertArrayEquals(new int[] {145, 150}, mapped.get(0)); // offsets 45-50
- assertArrayEquals(new int[] {60, 63}, mapped.get(1)); // offsets 51-54
+ assertArrayEquals(new int[] { 145, 150 }, mapped.get(0)); // offsets 45-50
+ assertArrayEquals(new int[] { 60, 63 }, mapped.get(1)); // offsets 51-54
/*
* reverse range overlap is reported with start < end
*/
ranges.clear();
- ranges.add(new int[] {4321, 4000});
+ ranges.add(new int[] { 4321, 4000 });
offsets.clear();
offsets.set(20, 22); // sets bits 20 and 21
offsets.set(30);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
- assertArrayEquals(new int[] {4301, 4300}, mapped.get(0));
- assertArrayEquals(new int[] {4291, 4291}, mapped.get(1));
+ assertArrayEquals(new int[] { 4301, 4300 }, mapped.get(0));
+ assertArrayEquals(new int[] { 4291, 4291 }, mapped.get(1));
}
-
+
@Test(groups = { "Functional" })
public void testGetMappedOffsetsForPositions()
{
* start by verifying the examples in the method's Javadoc!
*/
List<int[]> ranges = new ArrayList<>();
- ranges.add(new int[] {10, 20});
- ranges.add(new int[] {31, 40});
- BitSet overlaps = MapList.getMappedOffsetsForPositions(1, 9, ranges, 1, 1);
+ ranges.add(new int[] { 10, 20 });
+ ranges.add(new int[] { 31, 40 });
+ BitSet overlaps = MapList.getMappedOffsetsForPositions(1, 9, ranges, 1,
+ 1);
assertTrue(overlaps.isEmpty());
overlaps = MapList.getMappedOffsetsForPositions(1, 11, ranges, 1, 1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(1));
overlaps = MapList.getMappedOffsetsForPositions(15, 35, ranges, 1, 1);
assertEquals(11, overlaps.cardinality());
- for (int i = 5 ; i <= 11 ; i++)
+ for (int i = 5; i <= 11; i++)
{
assertTrue(overlaps.get(i));
}
-
+
ranges.clear();
- ranges.add(new int[] {1, 200});
+ ranges.add(new int[] { 1, 200 });
overlaps = MapList.getMappedOffsetsForPositions(9, 9, ranges, 1, 3);
assertEquals(3, overlaps.cardinality());
assertTrue(overlaps.get(24));
assertTrue(overlaps.get(25));
assertTrue(overlaps.get(26));
-
+
ranges.clear();
- ranges.add(new int[] {101, 150});
- ranges.add(new int[] {171, 180});
+ ranges.add(new int[] { 101, 150 });
+ ranges.add(new int[] { 171, 180 });
overlaps = MapList.getMappedOffsetsForPositions(101, 102, ranges, 3, 1);
assertEquals(1, overlaps.cardinality());
assertTrue(overlaps.get(0));
overlaps = MapList.getMappedOffsetsForPositions(150, 171, ranges, 3, 1);
assertEquals(1, overlaps.cardinality());
assertTrue(overlaps.get(16));
-
+
ranges.clear();
- ranges.add(new int[] {101, 150});
- ranges.add(new int[] {21, 30});
+ ranges.add(new int[] { 101, 150 });
+ ranges.add(new int[] { 21, 30 });
overlaps = MapList.getMappedOffsetsForPositions(24, 40, ranges, 3, 1);
assertEquals(3, overlaps.cardinality());
assertTrue(overlaps.get(17));
assertTrue(overlaps.get(18));
assertTrue(overlaps.get(19));
-
+
/*
* reverse range 1:1 (e.g. reverse strand gene to transcript)
*/
ranges.clear();
- ranges.add(new int[] {20, 10});
+ ranges.add(new int[] { 20, 10 });
overlaps = MapList.getMappedOffsetsForPositions(12, 13, ranges, 1, 1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(7));
assertTrue(overlaps.get(8));
-
+
/*
* reverse range 3:1 (e.g. reverse strand gene to peptide)
* from EMBL:J03321 to P0CE20
*/
ranges.clear();
- ranges.add(new int[] {1480, 488});
- overlaps = MapList.getMappedOffsetsForPositions(1460, 1460, ranges, 3, 1);
+ ranges.add(new int[] { 1480, 488 });
+ overlaps = MapList.getMappedOffsetsForPositions(1460, 1460, ranges, 3,
+ 1);
// 1460 is the end of the 7th codon
assertEquals(1, overlaps.cardinality());
assertTrue(overlaps.get(6));
// add one base (part codon)
- overlaps = MapList.getMappedOffsetsForPositions(1459, 1460, ranges, 3, 1);
+ overlaps = MapList.getMappedOffsetsForPositions(1459, 1460, ranges, 3,
+ 1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
// add second base (part codon)
- overlaps = MapList.getMappedOffsetsForPositions(1458, 1460, ranges, 3, 1);
+ overlaps = MapList.getMappedOffsetsForPositions(1458, 1460, ranges, 3,
+ 1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
// add third base (whole codon)
- overlaps = MapList.getMappedOffsetsForPositions(1457, 1460, ranges, 3, 1);
+ overlaps = MapList.getMappedOffsetsForPositions(1457, 1460, ranges, 3,
+ 1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
// add one more base (part codon)
- overlaps = MapList.getMappedOffsetsForPositions(1456, 1460, ranges, 3, 1);
+ overlaps = MapList.getMappedOffsetsForPositions(1456, 1460, ranges, 3,
+ 1);
assertEquals(3, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
git://source.jalview.org / jalview.git / commitdiff