From 7c8aa60802a7711a3d6b1df511ec56263ae5ffd7 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 20 Nov 2020 11:58:42 +0000 Subject: [PATCH] JAL-3761 debugged and working (but not tidied) locateInFrom2/To2 --- src/jalview/util/MapList.java | 131 ++++++++---- test/jalview/util/MapListTest.java | 383 ++++++++++++++++++++++++++---------- 2 files changed, 379 insertions(+), 135 deletions(-) diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java index 2e673e0..0d71bb4 100644 --- a/src/jalview/util/MapList.java +++ b/src/jalview/util/MapList.java @@ -703,12 +703,13 @@ public class MapList */ public int[] locateInFrom(int start, int end) { + return locateInFrom2(start, end); + // inefficient implementation - int fromStart[] = shiftTo(start); + // int fromStart[] = shiftTo(start); // needs to be inclusive of end of symbol position - int fromEnd[] = shiftTo(end); - System.out.println("locateInFrom"); - return getIntervals(fromShifts, fromStart, fromEnd, fromRatio); + // int fromEnd[] = shiftTo(end); + // return getIntervals(fromShifts, fromStart, fromEnd, fromRatio); } /** @@ -722,9 +723,11 @@ public class MapList */ public int[] locateInTo(int start, int end) { - int toStart[] = shiftFrom(start); - int toEnd[] = shiftFrom(end); - return getIntervals(toShifts, toStart, toEnd, toRatio); + return locateInTo2(start, end); + + // int toStart[] = shiftFrom(start); + // int toEnd[] = shiftFrom(end); + // return getIntervals(toShifts, toStart, toEnd, toRatio); } /** @@ -1212,6 +1215,7 @@ public class MapList List toRanges = new ArrayList<>(); for (int[] range : getToRanges()) { + int fromLength = Math.abs(range[1] - range[0]) + 1; int[] transferred = map.locateInTo(range[0], range[1]); if (transferred == null || transferred.length % 2 != 0) { @@ -1222,11 +1226,21 @@ public class MapList * convert [start1, end1, start2, end2, ...] * to [[start1, end1], [start2, end2], ...] */ + int toLength = 0; for (int i = 0; i < transferred.length;) { toRanges.add(new int[] { transferred[i], transferred[i + 1] }); + toLength += Math.abs(transferred[i + 1] - transferred[i]) + 1; i += 2; } + + /* + * check we mapped the full range - if not, abort + */ + if (fromLength * map.getToRatio() != toLength * map.getFromRatio()) + { + return null; + } } return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio); @@ -1245,8 +1259,8 @@ public class MapList /** * Returns the [start, end, start, end, ...] ranges in the 'from' range that - * map to the given start-end in the 'to' range. Returns null if either - * {@code start} or {@code end} is not a mapped 'to' range position. + * map to positions between {@code start} and {@code end} in the 'to' range. + * Returns null if no mapped positions are found in start-end. * * @param start * @param end @@ -1295,6 +1309,13 @@ public class MapList List ranges1, List ranges2, int wordLength1, int wordLength2) { + if (end < start) + { + int tmp = end; + end = start; + start = tmp; + } + /* * first traverse ranges1 and record count of mapped positions * to any that overlap start-end @@ -1306,7 +1327,7 @@ public class MapList } /* - * convert positions to equivalent 'word' positions in ranges + * convert positions to equivalent 'word' positions in ranges2 */ mapWords(overlaps, wordLength1, wordLength2); @@ -1317,24 +1338,52 @@ public class MapList List mapped = new ArrayList<>(); final int s1 = overlaps.size(); final int s2 = ranges2.size(); - int rangeIndex = 0; - int rangeOffset = 0; - int mappedCount = 0; + int ranges2Index = 0; - for (int i = 0 ; i < s1 ; i++) + /* + * count of mapped positions preceding ranges2[ranges2Index] + */ + int traversed = 0; + + /* + * for each [from-to] range in overlaps: + * - walk (what remains of) ranges2 + * - record the values at offsets [from-to] + * - stop when past 'to' positions (or at end of ranges2) + */ + for (int i = 0; i < s1; i++) { - /* - * for each range in overlaps, walk ranges2 and record the values - * at the offsets, advancing rangeIndex / Offset - */ - int [] mappedRange = ranges2.get(rangeIndex); - int [] overlap = overlaps.get(s1); - while (mappedCount < overlap[1]) + int[] overlap = overlaps.get(i); + final int toAdd = overlap[1] - overlap[0] + 1; + int added = 0; // how much of overlap has been 'found' + for (; added < toAdd && ranges2Index < s2; ranges2Index++) { - + int[] range2 = ranges2.get(ranges2Index); + int rangeStart = range2[0]; + int rangeEnd = range2[1]; + boolean reverseStrand = range2[1] < range2[0]; + int rangeLength = Math.abs(rangeEnd - rangeStart) + 1; + if (traversed + rangeLength <= overlap[0]) + { + /* + * precedes overlap - keep looking + */ + traversed += rangeLength; + continue; + } + int overlapStart = overlap[0] - traversed; + int overlapEnd = Math.min(overlapStart + toAdd - added - 1, + rangeLength - 1); + int mappedFrom = range2[0] + (reverseStrand ? - overlapStart : overlapStart); + int mappedTo = range2[0] + (reverseStrand ? - overlapEnd : overlapEnd); + mapped.add(new int[] { mappedFrom, mappedTo }); + int found = overlapEnd - overlapStart + 1; + added += found; + overlap[0] += found; + traversed += rangeLength; } } - + return mapped; } @@ -1389,10 +1438,10 @@ public class MapList /** * Helper method that returns a (possibly empty) list of offsets in - * {@code ranges} to subranges that overlap {@code start-end}. The list - * returned holds counts of the number of positions traversed (inclusive) to - * reach the overlapping positions, not the overlapping values. Returns null - * if there are no overlaps. + * {@code ranges} to subranges that overlap {@code start-end} (where start <= + * end}. The list returned holds counts of the number of positions traversed + * (exclusive) to reach the overlapping positions, not the overlapping values. + * Returns null if there are no overlaps. * * @param ranges * @param start @@ -1416,8 +1465,8 @@ public class MapList /** * A helper method that checks whether {@code range} overlaps - * {@code start-end}, and if so adds the positional offset of the overlap to - * {@code positions}. + * {@code start-end}, and if so adds the offset of the overlap in + * {@code range}, plus {@code pos}, to {@code positions}. * * @param positions * a list of map offsets to add to @@ -1445,10 +1494,25 @@ public class MapList * overlap */ int overlapStart = Math.max(start, range[0]); + int overlapStartOffset = pos + overlapStart - range[0]; int overlapEnd = Math.min(end, range[1]); - positions - .add(new int[] - { 1 + overlapStart - range[0], 1 + overlapEnd - range[0] }); + int overlapEndOffset = pos + overlapEnd - range[0]; + int[] lastOverlap = positions.isEmpty() ? null + : positions.get(positions.size() - 1); + if (lastOverlap != null && overlapStartOffset == lastOverlap[1] + 1) + { + /* + * just extending the last overlap range + */ + lastOverlap[1] = overlapEndOffset; + } + else + { + /* + * add a new (discontiguous) overlap range + */ + positions.add(new int[] { overlapStartOffset, overlapEndOffset }); + } } } else @@ -1465,7 +1529,8 @@ public class MapList int overlapEnd = Math.min(end, range[0]); positions .add(new int[] - { 1 + range[0] - overlapStart, 1 + range[0] - overlapEnd }); + { pos + range[0] - overlapEnd, + pos + range[0] - overlapStart }); } } } diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index 07da78f..fd34902 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -53,7 +53,7 @@ public class MapListTest JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - @Test(groups = { "Functional" }) + @Test(groups = { "Functional" }, enabled = false) public void testSomething() { MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, @@ -271,17 +271,24 @@ public class MapListTest assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4))); assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2))); assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3))); + // reversed range treated as if forwards: + assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(3, 1))); assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4))); assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3))); assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4))); assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4))); assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4))); - // reversing the range reverses the result: - assertEquals("[12, 7]", Arrays.toString(ml.locateInFrom(4, 3))); // fails with [10, 9] ! + /* + * partial overlap + */ + assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 5))); + assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1))); + + /* + * no overlap + */ assertNull(ml.locateInFrom(0, 0)); - assertNull(ml.locateInFrom(1, 5)); - assertNull(ml.locateInFrom(-1, 1)); } /** @@ -314,8 +321,8 @@ public class MapListTest assertEquals("[12, 10]", Arrays.toString(ml.locateInFrom(1, 1))); assertEquals("[9, 4]", Arrays.toString(ml.locateInFrom(2, 3))); } - - /** + + /** * Tests for method that locates ranges in the 'to' map for given range in the * 'from' map. */ @@ -337,8 +344,8 @@ public class MapListTest assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12))); assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6))); assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12))); - // reversing the 'from' range reverses the result - assertEquals("[4, 2]", Arrays.toString(ml.locateInTo(12, 4))); + // reverse range treated as if forwards: + assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(12, 4))); /* * A part codon is treated as if a whole one. @@ -350,9 +357,16 @@ public class MapListTest assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11))); assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11))); + /* + * partial overlap + */ + assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 13))); + assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 2))); + + /* + * no overlap + */ assertNull(ml.locateInTo(0, 0)); - assertNull(ml.locateInTo(1, 13)); - assertNull(ml.locateInTo(-1, 1)); } /** @@ -374,14 +388,6 @@ public class MapListTest MapList ml = new MapList(codons, protein, 3, 1); /* - * Can't map from an unmapped position - */ - assertNull(ml.locateInTo(1, 2)); - assertNull(ml.locateInTo(1, 4)); - assertNull(ml.locateInTo(2, 4)); - assertNull(ml.locateInTo(4, 4)); - - /* * Valid range or subrange of codon1 maps to protein1 */ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2))); @@ -395,6 +401,18 @@ public class MapListTest // codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6 assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17))); + + /* + * partial 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 + */ + assertNull(ml.locateInTo(4, 4)); } /** @@ -941,10 +959,10 @@ public class MapListTest assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1)); /* - * method returns null if not all regions are mapped through + * if not all regions are mapped through, returns what is */ ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1); - ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 3); + ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 1); compound = ml1.traverse(ml2); assertNull(compound); } @@ -1000,19 +1018,29 @@ public class MapListTest assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3))); assertEquals("[7, 12, 12, 17]", Arrays.toString(ml.locateInFrom(3, 6))); + /* + * partial overlap of range + */ + assertEquals("[4, 12, 12, 17]", Arrays.toString(ml.locateInFrom(2, 7))); + assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1))); + + /* + * no overlap in range + */ assertNull(ml.locateInFrom(0, 0)); - assertNull(ml.locateInFrom(1, 7)); - assertNull(ml.locateInFrom(-1, 1)); /* * gene to CDS...from EMBL:MN908947 */ - int [] gene = new int[] { 266, 13468, 13468, 21555 }; - int [] cds = new int[] { 1, 21291 }; + int[] gene = new int[] { 266, 13468, 13468, 21555 }; + int[] cds = new int[] { 1, 21291 }; ml = new MapList(gene, cds, 1, 1); - assertEquals("[13468, 13468]", Arrays.toString(ml.locateInFrom(13203, 13203))); - assertEquals("[13468, 13468]", Arrays.toString(ml.locateInFrom(13204, 13204))); - assertEquals("[13468, 13468]", Arrays.toString(ml.locateInFrom(13203, 13204))); + assertEquals("[13468, 13468]", + Arrays.toString(ml.locateInFrom(13203, 13203))); + assertEquals("[13468, 13468]", + Arrays.toString(ml.locateInFrom(13204, 13204))); + assertEquals("[13468, 13468, 13468, 13468]", + Arrays.toString(ml.locateInFrom(13203, 13204))); } /** @@ -1038,17 +1066,36 @@ public class MapListTest assertEquals("[4, 6]", Arrays.toString(ml.locateInTo(11, 15))); assertEquals("[6, 6]", Arrays.toString(ml.locateInTo(15, 17))); + /* + * no overlap + */ assertNull(ml.locateInTo(0, 0)); - assertNull(ml.locateInTo(1, 18)); - assertNull(ml.locateInTo(-1, 1)); + + /* + * partial overlap + */ + assertEquals("[1, 6]", Arrays.toString(ml.locateInTo(1, 18))); + assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 1))); /* * gene to CDS...from EMBL:MN908947 + * the base at 13468 is used twice in transcription */ - int [] gene = new int[] { 266, 13468, 13468, 21555 }; - int [] cds = new int[] { 1, 21291 }; + int[] gene = new int[] { 266, 13468, 13468, 21555 }; + int[] cds = new int[] { 1, 21291 }; ml = new MapList(gene, cds, 1, 1); - assertEquals("[13203, 13204]", Arrays.toString(ml.locateInTo(13468, 13468))); + 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 + */ + gene = new int[] { 266, 13468, 13468, 21552 }; // stop codon excluded + protein = new int[] { 1, 7096 }; + ml = new MapList(gene, protein, 3, 1); + assertEquals("[4401, 4402]", + Arrays.toString(ml.locateInTo(13468, 13468))); } @Test(groups = { "Functional" }) @@ -1074,121 +1121,253 @@ public class MapListTest } List intervals = new ArrayList<>(); - assertNull(MapList.countPositions(intervals, 1)); - + assertNull(MapList.countPositions(intervals, 1)); + /* * forward strand */ - intervals.add(new int[] {10, 20}); - assertNull(MapList.countPositions(intervals, 9)); - assertNull(MapList.countPositions(intervals, 21)); - assertArrayEquals(new int[] {1, 1}, MapList.countPositions(intervals, 10)); - assertArrayEquals(new int[] {6, 1}, MapList.countPositions(intervals, 15)); - assertArrayEquals(new int[] {11, 1}, MapList.countPositions(intervals, 20)); - - intervals.add(new int[] {25, 25}); - assertArrayEquals(new int[] {12, 1}, MapList.countPositions(intervals, 25)); - - // next interval repeats position 25 - which should be counted twice if traversed - intervals.add(new int[] {25, 26}); - assertArrayEquals(new int[] {12, 1}, MapList.countPositions(intervals, 25)); - assertArrayEquals(new int[] {14, 1}, MapList.countPositions(intervals, 26)); - + intervals.add(new int[] { 10, 20 }); + assertNull(MapList.countPositions(intervals, 9)); + assertNull(MapList.countPositions(intervals, 21)); + assertArrayEquals(new int[] { 1, 1 }, + MapList.countPositions(intervals, 10)); + assertArrayEquals(new int[] { 6, 1 }, + MapList.countPositions(intervals, 15)); + assertArrayEquals(new int[] { 11, 1 }, + MapList.countPositions(intervals, 20)); + + intervals.add(new int[] { 25, 25 }); + assertArrayEquals(new int[] { 12, 1 }, + MapList.countPositions(intervals, 25)); + + // next interval repeats position 25 - which should be counted twice if + // traversed + intervals.add(new int[] { 25, 26 }); + assertArrayEquals(new int[] { 12, 1 }, + MapList.countPositions(intervals, 25)); + assertArrayEquals(new int[] { 14, 1 }, + MapList.countPositions(intervals, 26)); + /* * reverse strand */ intervals.clear(); - intervals.add(new int[] {5, -5}); - assertNull(MapList.countPositions(intervals, 6)); - assertNull(MapList.countPositions(intervals, -6)); - assertArrayEquals(new int[] {1, -1}, MapList.countPositions(intervals, 5)); - assertArrayEquals(new int[] {7, -1}, MapList.countPositions(intervals, -1)); - assertArrayEquals(new int[] {11, -1}, MapList.countPositions(intervals, -5)); - + intervals.add(new int[] { 5, -5 }); + assertNull(MapList.countPositions(intervals, 6)); + assertNull(MapList.countPositions(intervals, -6)); + assertArrayEquals(new int[] { 1, -1 }, + MapList.countPositions(intervals, 5)); + assertArrayEquals(new int[] { 7, -1 }, + MapList.countPositions(intervals, -1)); + assertArrayEquals(new int[] { 11, -1 }, + MapList.countPositions(intervals, -5)); + /* * reverse then forward */ - intervals.add(new int[] {5, 10}); - assertArrayEquals(new int[] {13, 1}, MapList.countPositions(intervals, 6)); - + intervals.add(new int[] { 5, 10 }); + assertArrayEquals(new int[] { 13, 1 }, + MapList.countPositions(intervals, 6)); + /* * reverse then forward then reverse */ - intervals.add(new int[] {-10, -20}); - assertArrayEquals(new int[] {20, -1}, MapList.countPositions(intervals, -12)); - + intervals.add(new int[] { -10, -20 }); + assertArrayEquals(new int[] { 20, -1 }, + MapList.countPositions(intervals, -12)); + /* * an interval [x, x] is treated as forward */ - intervals.add(new int[] {30, 30}); - assertArrayEquals(new int[] {29, 1}, MapList.countPositions(intervals, 30)); - + intervals.add(new int[] { 30, 30 }); + assertArrayEquals(new int[] { 29, 1 }, + MapList.countPositions(intervals, 30)); + /* * it is the first matched occurrence that is returned */ intervals.clear(); - intervals.add(new int[] {1, 2}); - intervals.add(new int[] {2, 3}); - assertArrayEquals(new int[] {2, 1}, MapList.countPositions(intervals, 2)); - intervals.add(new int[] {-1, -2}); - intervals.add(new int[] {-2, -3}); - assertArrayEquals(new int[] {6, -1}, MapList.countPositions(intervals, -2)); + intervals.add(new int[] { 1, 2 }); + intervals.add(new int[] { 2, 3 }); + assertArrayEquals(new int[] { 2, 1 }, + MapList.countPositions(intervals, 2)); + intervals.add(new int[] { -1, -2 }); + intervals.add(new int[] { -2, -3 }); + assertArrayEquals(new int[] { 6, -1 }, + MapList.countPositions(intervals, -2)); + } + + /** + * Tests for helper method that adds any overlap (plus offset) to a list of + * overlaps + */ + @Test(groups = { "Functional" }) + public void testAddOverlap() + { + List overlaps = new ArrayList<>(); + int[] candidate = new int[] { 10, 19 }; + MapList.addOverlap(overlaps, 5, candidate, 20, 30); // doesn't overlap + assertTrue(overlaps.isEmpty()); + MapList.addOverlap(overlaps, 5, candidate, 31, 40); // doesn't overlap + assertTrue(overlaps.isEmpty()); + + /* + * 10-19 overlaps 15-25 at 15-19, which is offset 5-9 in 10-19 + * + 5 initial offset + */ + MapList.addOverlap(overlaps, 5, candidate, 15, 25); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 10, 14 }, overlaps.get(0)); + + /* + * reverse range overlap: + * 300-20 overlaps 15-25 at 25-20, which is offset 275-280 in 300-20 + * + 8 initial offset + */ + overlaps.clear(); + candidate = new int[] { 300, 20 }; + MapList.addOverlap(overlaps, 8, candidate, 15, 25); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 283, 288 }, overlaps.get(0)); } @Test(groups = { "Functional" }) public void testFindOverlapPositions() { List ranges = new ArrayList<>(); - List overlaps = MapList.findOverlapPositions(ranges, 20, 30); + List overlaps = MapList.findOverlapPositions(ranges, 20, 30); + assertTrue(overlaps.isEmpty()); // nothing to overlap + + ranges.add(new int[] { 15, 25 }); + overlaps = MapList.findOverlapPositions(ranges, 5, 10); + assertTrue(overlaps.isEmpty()); // no overlap + + overlaps = MapList.findOverlapPositions(ranges, 20, 20); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 5, 5 }, overlaps.get(0)); + + overlaps = MapList.findOverlapPositions(ranges, 5, 19); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 0, 4 }, overlaps.get(0)); + + ranges.add(new int[] { 35, 45 }); + overlaps = MapList.findOverlapPositions(ranges, 26, 34); assertTrue(overlaps.isEmpty()); - ranges.add(new int[] {15, 25}); - overlaps = MapList.findOverlapPositions(ranges, 20, 30); + + /* + * 24-37 overlaps the end of 15-25 and the start of 35-45 + * - offset positions are contiguous in the map so merged + */ + overlaps = MapList.findOverlapPositions(ranges, 24, 37); assertEquals(1, overlaps.size()); - assertArrayEquals(new int[] {6, 11}, overlaps.get(0)); + assertArrayEquals(new int[] { 9, 13 }, overlaps.get(0)); + + /* + * EMBL:MN908947 https://www.ebi.ac.uk/ena/browser/api/embl/MN908947 + * (Covid-SARS-2) CDS mapping with 'slippage' + * (base 13468 is used twice in transcription) + */ + ranges.clear(); + ranges.add(new int[] { 266, 13468 }); + ranges.add(new int[] { 13468, 21555 }); + + // 13468 occupies two offsets in the range list + overlaps = MapList.findOverlapPositions(ranges, 13468, 13468); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 13202, 13203 }, overlaps.get(0)); + overlaps = MapList.findOverlapPositions(ranges, 13469, 13470); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 13204, 13205 }, overlaps.get(0)); + + /* + * EMBL:J03321 https://www.ebi.ac.uk/ena/browser/api/embl/J03321 + * circular dna: CDS at [7022-7502, 1-437] + * = 481 + 437 = 918 bases = 305 aa's + stop codon + */ + ranges.clear(); + ranges.add(new int[] { 7022, 7502 }); + ranges.add(new int[] { 1, 437 }); + + overlaps = MapList.findOverlapPositions(ranges, 438, 7021); + assertTrue(overlaps.isEmpty()); + + // overlap first exon only: + overlaps = MapList.findOverlapPositions(ranges, 7000, 7100); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 0, 78 }, overlaps.get(0)); + + // overlap second exon only: offset to mapping includes first exon + overlaps = MapList.findOverlapPositions(ranges, 400, 500); + assertEquals(1, overlaps.size()); + assertArrayEquals(new int[] { 880, 917 }, overlaps.get(0)); + + // overlap both exons: first exon overlap precedes second exon overlap + // offsets of overlaps are not contiguous + overlaps = MapList.findOverlapPositions(ranges, 200, 7500); + assertEquals(2, overlaps.size()); + // first overlap is offsets of 7022-7500 in exon 1 (7022-7502): + assertArrayEquals(new int[] { 0, 478 }, overlaps.get(0)); + // second overlap offsets is (first exon length = 481) + (200-437) + assertArrayEquals(new int[] { 680, 917 }, overlaps.get(1)); } @Test(groups = { "Functional" }) public void testMapWords() { List ranges = new ArrayList<>(); - + /* * 1:1 (trivial) case */ - ranges.add(new int[] {2, 4}); - ranges.add(new int[] {6, 9}); - MapList.mapWords(ranges, 1, 1); + ranges.add(new int[] { 2, 4 }); + ranges.add(new int[] { 6, 9 }); + MapList.mapWords(ranges, 1, 1); assertEquals(ranges.size(), 2); - assertArrayEquals(new int[] {2, 4}, ranges.get(0)); - assertArrayEquals(new int[] {6, 9}, ranges.get(1)); - + assertArrayEquals(new int[] { 2, 4 }, ranges.get(0)); + assertArrayEquals(new int[] { 6, 9 }, ranges.get(1)); + /* * 1:3 case (peptide to codon ranges) */ - MapList.mapWords(ranges, 1, 3); + MapList.mapWords(ranges, 1, 3); assertEquals(ranges.size(), 2); - assertArrayEquals(new int[] {6, 14}, ranges.get(0)); - assertArrayEquals(new int[] {18, 29}, ranges.get(1)); - + assertArrayEquals(new int[] { 6, 14 }, ranges.get(0)); + assertArrayEquals(new int[] { 18, 29 }, ranges.get(1)); + /* * 3:1 case (codon or part codon to peptide) */ ranges.clear(); - ranges.add(new int[] {0, 5}); // 2 whole codons - ranges.add(new int[] {7, 11}); // part + whole codon - ranges.add(new int[] {15, 19}); // whole + part codon - ranges.add(new int[] {23, 27}); // part + part codon - ranges.add(new int[] {30, 30}); // first base of codon - ranges.add(new int[] {31, 31}); // second base of codon - ranges.add(new int[] {32, 32}); // third base of codon - MapList.mapWords(ranges, 3, 1); + ranges.add(new int[] { 0, 5 }); // 2 whole codons + ranges.add(new int[] { 7, 11 }); // part + whole codon + ranges.add(new int[] { 15, 19 }); // whole + part codon + ranges.add(new int[] { 23, 27 }); // part + part codon + ranges.add(new int[] { 30, 30 }); // first base of codon + ranges.add(new int[] { 31, 31 }); // second base of codon + ranges.add(new int[] { 32, 32 }); // third base of codon + MapList.mapWords(ranges, 3, 1); assertEquals(ranges.size(), 7); - assertArrayEquals(new int[] {0, 1}, ranges.get(0)); - assertArrayEquals(new int[] {2, 3}, ranges.get(1)); - assertArrayEquals(new int[] {5, 6}, ranges.get(2)); - assertArrayEquals(new int[] {7, 9}, ranges.get(3)); - assertArrayEquals(new int[] {10, 10}, ranges.get(4)); - assertArrayEquals(new int[] {10, 10}, ranges.get(5)); - assertArrayEquals(new int[] {10, 10}, ranges.get(6)); + assertArrayEquals(new int[] { 0, 1 }, ranges.get(0)); + assertArrayEquals(new int[] { 2, 3 }, ranges.get(1)); + assertArrayEquals(new int[] { 5, 6 }, ranges.get(2)); + assertArrayEquals(new int[] { 7, 9 }, ranges.get(3)); + assertArrayEquals(new int[] { 10, 10 }, ranges.get(4)); + assertArrayEquals(new int[] { 10, 10 }, ranges.get(5)); + assertArrayEquals(new int[] { 10, 10 }, ranges.get(6)); + } + + @Test(groups = { "Functional" }) + public void testLocateInFrom2() + { + /* + * codons at 11-16, 21-26, 31-36 mapped to peptide positions 1, 3-4, 6-8 + */ + MapList ml = new MapList(new int[] { 11, 16, 21, 26, 31, 36 }, + new int[] + { 1, 1, 3, 4, 6, 8 }, 3, 1); + assertArrayEquals(new int[] { 11, 13 }, ml.locateInFrom2(1, 1)); + assertArrayEquals(new int[] { 11, 16 }, ml.locateInFrom2(1, 3)); + assertArrayEquals(new int[] { 11, 16, 21, 23 }, ml.locateInFrom2(1, 4)); + assertArrayEquals(new int[] { 14, 16, 21, 23 }, ml.locateInFrom2(3, 4)); } } -- 1.7.10.2