X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=c94434541eb39ff4a4206be1cfc0ef69a9c08e4f;hb=0a680b4ff1aaad7580d3b10941233307e2190be4;hp=ab811a93d6659d3e758535690a8790dc91ffd501;hpb=9c39e96af6b84257604da448101505361dced686;p=jalview.git diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java index ab811a9..c944345 100644 --- a/src/jalview/util/MapList.java +++ b/src/jalview/util/MapList.java @@ -77,8 +77,8 @@ public class MapList */ public MapList() { - fromShifts = new ArrayList(); - toShifts = new ArrayList(); + fromShifts = new ArrayList<>(); + toShifts = new ArrayList<>(); } /** @@ -88,8 +88,6 @@ public class MapList @Override public boolean equals(Object o) { - // TODO should also override hashCode to ensure equal objects have equal - // hashcodes if (o == null || !(o instanceof MapList)) { return false; @@ -105,10 +103,22 @@ public class MapList { return false; } - return Arrays - .deepEquals(fromShifts.toArray(), obj.fromShifts.toArray()) - && Arrays - .deepEquals(toShifts.toArray(), obj.toShifts.toArray()); + return Arrays.deepEquals(fromShifts.toArray(), obj.fromShifts.toArray()) + && Arrays.deepEquals(toShifts.toArray(), + obj.toShifts.toArray()); + } + + /** + * Returns a hashcode made from the fromRatio, toRatio, and from/to ranges + */ + @Override + public int hashCode() + { + int hashCode = 31 * fromRatio; + hashCode = 31 * hashCode + toRatio; + hashCode = 31 * hashCode + fromShifts.toArray().hashCode(); + hashCode = 31 * hashCode + toShifts.toArray().hashCode(); + return hashCode; } /** @@ -331,18 +341,19 @@ public class MapList */ public static List coalesceRanges(final List ranges) { - if (ranges == null || ranges.size() < 2) { + if (ranges == null || ranges.size() < 2) + { return ranges; } boolean changed = false; - List merged = new ArrayList(); + List merged = new ArrayList<>(); int[] lastRange = ranges.get(0); int lastDirection = lastRange[1] >= lastRange[0] ? 1 : -1; lastRange = new int[] { lastRange[0], lastRange[1] }; merged.add(lastRange); boolean first = true; - + for (final int[] range : ranges) { if (first) @@ -361,10 +372,12 @@ public class MapList * 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]) + && 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])) + && range[1] <= lastRange[0] + && range[1] >= lastRange[1])) { changed = true; continue; @@ -376,10 +389,13 @@ public class MapList * if next range is in the same direction as last and contiguous, * just update the end position of the last range */ - boolean sameDirection = range[1] == range[0] || direction == lastDirection; + 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]); + 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)) { lastRange[1] = range[1]; @@ -393,7 +409,7 @@ public class MapList lastDirection = (range[1] == range[0]) ? lastDirection : direction; } } - + return changed ? merged : ranges; } @@ -787,7 +803,7 @@ public class MapList { return null; } - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); if (fs <= fe) { intv = fs; @@ -948,15 +964,17 @@ public class MapList // TODO not used - remove? if (local) { - return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map - .getFromHighest()) || (getFromLowest() <= map.getFromLowest() && getFromHighest() >= map - .getFromHighest())); + return ((getFromLowest() >= map.getFromLowest() + && getFromHighest() <= map.getFromHighest()) + || (getFromLowest() <= map.getFromLowest() + && getFromHighest() >= map.getFromHighest())); } else { - return ((getToLowest() >= map.getToLowest() && getToHighest() <= map - .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map - .getToHighest())); + return ((getToLowest() >= map.getToLowest() + && getToHighest() <= map.getToHighest()) + || (getToLowest() <= map.getToLowest() + && getToHighest() >= map.getToHighest())); } } @@ -992,6 +1010,10 @@ public class MapList */ public void addMapList(MapList map) { + if (this.equals(map)) + { + return; + } this.fromLowest = Math.min(fromLowest, map.fromLowest); this.toLowest = Math.min(toLowest, map.toLowest); this.fromHighest = Math.max(fromHighest, map.fromHighest); @@ -1072,8 +1094,33 @@ public class MapList */ public boolean isFromForwardStrand() { + return isForwardStrand(getFromRanges()); + } + + /** + * 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()); + } + + /** + * 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 + */ + private boolean isForwardStrand(List ranges) + { boolean forwardStrand = true; - for (int[] range : getFromRanges()) + for (int[] range : ranges) { if (range[1] > range[0]) { @@ -1087,4 +1134,74 @@ public class MapList } return forwardStrand; } + + /** + * + * @return true if from, or to is a three to 1 mapping + */ + public boolean isTripletMap() + { + return (toRatio == 3 && fromRatio == 1) + || (fromRatio == 3 && toRatio == 1); + } + + /** + * Returns a map which is the composite of this one and the input map. That + * is, the output map has the fromRanges of this map, and its toRanges are the + * toRanges of this map as transformed by the input map. + *

+ * Returns null if the mappings cannot be traversed (not all toRanges of this + * map correspond to fromRanges of the input), or if this.toRatio does not + * match map.fromRatio. + * + * 

+   * Example 1:
+   *    this:   from [1-100] to [501-600]
+   *    input:  from [10-40] to [60-90]
+   *    output: from [10-40] to [560-590]
+   * Example 2 ('reverse strand exons'):
+   *    this:   from [1-100] to [2000-1951], [1000-951] // transcript to loci
+   *    input:  from [1-50]  to [41-90] // CDS to transcript
+   *    output: from [10-40] to [1960-1951], [1000-971] // CDS to gene loci
+   *
+ * + * @param map + * @return + */ + public MapList traverse(MapList map) + { + if (map == null) + { + return null; + } + + /* + * compound the ratios by this rule: + * A:B with M:N gives A*M:B*N + * reduced by greatest common divisor + * so 1:3 with 3:3 is 3:9 or 1:3 + * 1:3 with 3:1 is 3:3 or 1:1 + * 1:3 with 1:3 is 1:9 + * 2:5 with 3:7 is 6:35 + */ + int outFromRatio = getFromRatio() * map.getFromRatio(); + int outToRatio = getToRatio() * map.getToRatio(); + int gcd = MathUtils.gcd(outFromRatio, outToRatio); + outFromRatio /= gcd; + outToRatio /= gcd; + + List toRanges = new ArrayList<>(); + for (int[] range : getToRanges()) + { + int[] transferred = map.locateInTo(range[0], range[1]); + if (transferred == null) + { + return null; + } + toRanges.add(transferred); + } + + return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio); + } + }