X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=58abdc3926c1bf1badddf8e83e4b0724c06b30da;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=662240eea4e86ff19a944392efa99d4fd5abd4a6;hpb=1c0091b73c98691dc70cfd8f2fc0cd8e3b1afd03;p=jalview.git diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java index 662240e..58abdc3 100644 --- a/src/jalview/util/MapList.java +++ b/src/jalview/util/MapList.java @@ -41,12 +41,12 @@ public class MapList /* * Subregions (base 1) described as { [start1, end1], [start2, end2], ...} */ - private List fromShifts = new ArrayList(); + private List fromShifts; /* * Same format as fromShifts, for the 'mapped to' sequence */ - private List toShifts = new ArrayList(); + private List toShifts; /* * number of steps in fromShifts to one toRatio unit @@ -73,14 +73,21 @@ public class MapList private int toHighest; /** + * Constructor + */ + public MapList() + { + fromShifts = new ArrayList(); + toShifts = new ArrayList(); + } + + /** * Two MapList objects are equal if they are the same object, or they both * have populated shift ranges and all values are the same. */ @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; @@ -103,6 +110,19 @@ public class MapList } /** + * 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; + } + + /** * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...} * * @return @@ -180,7 +200,9 @@ public class MapList } /** - * Constructor. + * 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. * * @param from * contiguous regions as [start1, end1, start2, end2, ...] @@ -193,27 +215,51 @@ public class MapList */ public MapList(int from[], int to[], int fromRatio, int toRatio) { + this(); this.fromRatio = fromRatio; this.toRatio = toRatio; - fromLowest = from[0]; - fromHighest = from[1]; + fromLowest = Integer.MAX_VALUE; + fromHighest = Integer.MIN_VALUE; + int added = 0; + for (int i = 0; i < from.length; i += 2) { - fromLowest = Math.min(fromLowest, from[i]); - fromHighest = Math.max(fromHighest, from[i + 1]); - - fromShifts.add(new int[] - { from[i], from[i + 1] }); + /* + * note lowest and highest values - bearing in mind the + * direction may be reversed + */ + 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++; + } } - toLowest = to[0]; - toHighest = to[1]; + toLowest = Integer.MAX_VALUE; + toHighest = Integer.MIN_VALUE; + added = 0; for (int i = 0; i < to.length; i += 2) { - toLowest = Math.min(toLowest, to[i]); - toHighest = Math.max(toHighest, to[i + 1]); - toShifts.add(new int[] - { to[i], to[i + 1] }); + 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++; + } } } @@ -224,6 +270,7 @@ public class MapList */ public MapList(MapList map) { + this(); // TODO not used - remove? this.fromLowest = map.fromLowest; this.fromHighest = map.fromHighest; @@ -236,53 +283,134 @@ public class MapList { for (int[] r : map.fromShifts) { - fromShifts.add(new int[] - { r[0], r[1] }); + fromShifts.add(new int[] { r[0], r[1] }); } } if (map.toShifts != null) { for (int[] r : map.toShifts) { - toShifts.add(new int[] - { r[0], r[1] }); + toShifts.add(new int[] { r[0], r[1] }); } } } /** - * Constructor given ranges as lists of [start, end] positions + * Constructor given ranges as lists of [start, end] positions. There is no + * validation check that the ranges do not overlap each other. * * @param fromRange * @param toRange * @param fromRatio * @param toRatio */ - public MapList(List fromRange, List toRange, - int fromRatio, int toRatio) + public MapList(List fromRange, List toRange, int fromRatio, + int toRatio) { + this(); + fromRange = coalesceRanges(fromRange); + toRange = coalesceRanges(toRange); this.fromShifts = fromRange; this.toShifts = toRange; this.fromRatio = fromRatio; this.toRatio = toRatio; fromLowest = Integer.MAX_VALUE; - fromHighest = 0; - for (int[] range : fromRange) { - fromLowest = Math.min(fromLowest, range[0]); - fromHighest = Math.max(fromHighest, range[1]); + fromHighest = Integer.MIN_VALUE; + for (int[] range : fromRange) + { + fromLowest = Math.min(fromLowest, Math.min(range[0], range[1])); + fromHighest = Math.max(fromHighest, Math.max(range[0], range[1])); } toLowest = Integer.MAX_VALUE; - toHighest = 0; + toHighest = Integer.MIN_VALUE; for (int[] range : toRange) { - toLowest = Math.min(toLowest, range[0]); - toHighest = Math.max(toHighest, range[1]); + toLowest = Math.min(toLowest, Math.min(range[0], range[1])); + toHighest = Math.max(toHighest, Math.max(range[0], range[1])); } } /** + * 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). + * + * @param ranges + * @return the same list (if unchanged), else a new merged list, leaving the + * input list unchanged + */ + public static List coalesceRanges(final List ranges) + { + if (ranges == null || ranges.size() < 2) + { + return ranges; + } + + boolean changed = false; + 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) + { + 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; + + /* + * 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 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)) + { + lastRange[1] = range[1]; + changed = true; + } + else + { + lastRange = new int[] { range[0], range[1] }; + merged.add(lastRange); + // careful: merging [5, 5] after [7, 6] should keep negative direction + lastDirection = (range[1] == range[0]) ? lastDirection : direction; + } + } + + return changed ? merged : ranges; + } + + /** * get all mapped positions from 'from' to 'to' * * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int @@ -313,8 +441,7 @@ public class MapList * returning mapped position */ private int[][] posMap(List shiftTo, int ratio, - List shiftFrom, - int toRatio) + List shiftFrom, int toRatio) { // TODO not used - remove?? int iv = 0, ivSize = shiftTo.size(); @@ -374,9 +501,8 @@ public class MapList } mp[i] = m; } - int[][] map = new int[][] - { new int[] - { from, to, tF, tT }, new int[to - from + 2] }; + int[][] map = new int[][] { new int[] { from, to, tF, tT }, + new int[to - from + 2] }; map[0][2] = tF; map[0][3] = tT; @@ -461,8 +587,7 @@ public class MapList return null; // throw new Error("Bad Mapping!"); } // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount); - return new int[] - { toPos[0], fromRemainder, toPos[1] }; + return new int[] { toPos[0], fromRemainder, toPos[1] }; } /** @@ -482,8 +607,7 @@ public class MapList { if (pos >= intv[0] && pos <= intv[1]) { - return new int[] - { count + pos - intv[0] + 1, +1 }; + return new int[] { count + pos - intv[0] + 1, +1 }; } else { @@ -494,8 +618,7 @@ public class MapList { if (pos >= intv[1] && pos <= intv[0]) { - return new int[] - { count + intv[0] - pos + 1, -1 }; + return new int[] { count + intv[0] - pos + 1, -1 }; } else { @@ -516,8 +639,7 @@ public class MapList protected static int[] countToPos(List shiftFrom, int pos) { int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size(); - int[] intv = - { 0, 0 }; + int[] intv = { 0, 0 }; while (iv < ivSize) { intv = shiftFrom.get(iv++); @@ -526,8 +648,7 @@ public class MapList { if (pos <= count + 1 + diff) { - return new int[] - { pos - count - 1 + intv[0], +1 }; + return new int[] { pos - count - 1 + intv[0], +1 }; } else { @@ -538,8 +659,7 @@ public class MapList { if (pos <= count + 1 - diff) { - return new int[] - { intv[0] - (pos - count - 1), -1 }; + return new int[] { intv[0] - (pos - count - 1), -1 }; } else { @@ -597,8 +717,7 @@ public class MapList * region to final position of ending region inclusive */ protected static int[] getIntervals(List shiftFrom, - int[] fromStart, - int[] fromEnd, int fromRatio2) + int[] fromStart, int[] fromEnd, int fromRatio2) { if (fromStart == null || fromEnd == null) { @@ -688,8 +807,7 @@ public class MapList i = fs; // truncate initial interval iv = shiftFrom.get(intv++); - iv = new int[] - { iv[0], iv[1] };// clone + iv = new int[] { iv[0], iv[1] };// clone if (i == fs) { iv[0] = startpos; @@ -698,8 +816,7 @@ public class MapList { ranges.add(iv); // add initial range iv = shiftFrom.get(intv++); // get next interval - iv = new int[] - { iv[0], iv[1] };// clone + iv = new int[] { iv[0], iv[1] };// clone i++; } if (i == fe) @@ -717,8 +834,7 @@ public class MapList i--; } iv = shiftFrom.get(i); - iv = new int[] - { iv[1], iv[0] };// reverse and clone + iv = new int[] { iv[1], iv[0] };// reverse and clone // truncate initial interval if (i == fs) { @@ -728,8 +844,7 @@ public class MapList { // fix apparent logic bug when fe==-1 ranges.add(iv); // add (truncated) reversed interval iv = shiftFrom.get(i); - iv = new int[] - { iv[1], iv[0] }; // reverse and clone + iv = new int[] { iv[1], iv[0] }; // reverse and clone } if (i == fe) { @@ -788,8 +903,7 @@ public class MapList int[] mp = shiftTo(mpos); if (mp != null) { - return new int[] - { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) }; + return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) }; } return null; } @@ -818,8 +932,7 @@ public class MapList int[] mp = shiftFrom(pos); if (mp != null) { - return new int[] - { mp[0], mp[0] + mp[2] * (getToRatio() - 1) }; + return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) }; } return null; } @@ -867,13 +980,14 @@ public class MapList public String toString() { StringBuilder sb = new StringBuilder(64); - sb.append("From (").append(fromRatio).append(":").append(toRatio) - .append(") ["); + sb.append("["); for (int[] shift : fromShifts) { sb.append(" ").append(Arrays.toString(shift)); } - sb.append(" ] To ["); + sb.append(" ] "); + sb.append(fromRatio).append(":").append(toRatio); + sb.append(" to ["); for (int[] shift : toShifts) { sb.append(" ").append(Arrays.toString(shift)); @@ -881,4 +995,124 @@ public class MapList sb.append(" ]"); return sb.toString(); } + + /** + * Extend this map list by adding the given map's ranges. There is no + * validation check that the ranges do not overlap existing ranges (or each + * other), but contiguous ranges are merged. + * + * @param map + */ + 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); + this.toHighest = Math.max(toHighest, map.toHighest); + + for (int[] range : map.getFromRanges()) + { + addRange(range, fromShifts); + } + for (int[] range : map.getToRanges()) + { + 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. + * + * @param range + * @param addTo + */ + static void addRange(int[] range, List addTo) + { + /* + * 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; + } + + /* + * just add the new range + */ + addTo.add(range); + } + + /** + * 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. + * + * @return + */ + public boolean isFromForwardStrand() + { + boolean forwardStrand = true; + for (int[] range : getFromRanges()) + { + if (range[1] > range[0]) + { + break; // forward strand confirmed + } + else if (range[1] < range[0]) + { + forwardStrand = false; + break; // reverse strand confirmed + } + } + 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); + } + }