--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * A simple way of bijectively mapping a non-contiguous linear range to another
+ * non-contiguous linear range.
+ *
+ * Use at your own risk!
+ *
+ * TODO: efficient implementation of private posMap method
+ *
+ * TODO: test/ensure that sense of from and to ratio start position is conserved
+ * (codon start position recovery)
+ */
+public class MapList
+{
+
+ public static final int POS = 0;
+ public static final int POS_FROM = 1; // for countPos
+ public static final int DIR_FROM = 2; // for countPos
+ public static final int POS_TO = 3; // for countToPos
+ public static final int DIR_TO = 4; // for countToPos
+ private static final int FROM_REMAINDER = 5;
+ public static final int LEN = 6;
+/*
+ * Subregions (base 1) described as { [start1, end1], [start2, end2], ...}
+ */
+ private List<int[]> fromShifts;
+
+ /*
+ * Same format as fromShifts, for the 'mapped to' sequence
+ */
+ private List<int[]> toShifts;
+
+ /*
+ * number of steps in fromShifts to one toRatio unit
+ */
+ private int fromRatio;
+
+ /*
+ * number of steps in toShifts to one fromRatio
+ */
+ private int toRatio;
+
+ /*
+ * lowest and highest value in the from Map
+ */
+ private int fromLowest;
+
+ private int fromHighest;
+
+ /*
+ * lowest and highest value in the to Map
+ */
+ private int toLowest;
+
+ 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)
+ {
+ if (o == null || !(o instanceof MapList))
+ {
+ return false;
+ }
+
+ MapList obj = (MapList) o;
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj.fromRatio != fromRatio || obj.toRatio != toRatio
+ || obj.fromShifts == null || obj.toShifts == null)
+ {
+ return false;
+ }
+ 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;
+ for (int[] shift : fromShifts)
+ {
+ hashCode = 31 * hashCode + shift[0];
+ hashCode = 31 * hashCode + shift[1];
+ }
+ for (int[] shift : toShifts)
+ {
+ hashCode = 31 * hashCode + shift[0];
+ hashCode = 31 * hashCode + shift[1];
+ }
+
+ return hashCode;
+ }
+
+ /**
+ * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List<int[]> getFromRanges()
+ {
+ return fromShifts;
+ }
+
+ /**
+ * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List<int[]> getToRanges()
+ {
+ return toShifts;
+ }
+
+ /**
+ * Flattens a list of [start, end] into a single [start1, end1, start2,
+ * end2,...] array.
+ *
+ * @param shifts
+ * @return
+ */
+ protected static int[] getRanges(List<int[]> shifts)
+ {
+ int[] rnges = new int[2 * shifts.size()];
+ int i = 0;
+ for (int[] r : shifts)
+ {
+ rnges[i++] = r[0];
+ rnges[i++] = r[1];
+ }
+ return rnges;
+ }
+
+ /**
+ *
+ * @return length of mapped phrase in from
+ */
+ public int getFromRatio()
+ {
+ return fromRatio;
+ }
+
+ /**
+ *
+ * @return length of mapped phrase in to
+ */
+ public int getToRatio()
+ {
+ return toRatio;
+ }
+
+ public int getFromLowest()
+ {
+ return fromLowest;
+ }
+
+ public int getFromHighest()
+ {
+ return fromHighest;
+ }
+
+ public int getToLowest()
+ {
+ return toLowest;
+ }
+
+ public int getToHighest()
+ {
+ return toHighest;
+ }
+
+ /**
+ * 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, ...]
+ * @param to
+ * same format as 'from'
+ * @param fromRatio
+ * phrase length in 'from' (e.g. 3 for dna)
+ * @param toRatio
+ * phrase length in 'to' (e.g. 1 for protein)
+ */
+ public MapList(int from[], int to[], int fromRatio, int toRatio)
+ {
+ this();
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
+ fromLowest = Integer.MAX_VALUE;
+ fromHighest = Integer.MIN_VALUE;
+ int added = 0;
+
+ for (int i = 0; i < from.length; i += 2)
+ {
+ /*
+ * 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 = 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++;
+ }
+ }
+ }
+
+ /**
+ * Copy constructor. Creates an identical mapping.
+ *
+ * @param map
+ */
+ public MapList(MapList map)
+ {
+ this();
+ // TODO not used - remove?
+ this.fromLowest = map.fromLowest;
+ this.fromHighest = map.fromHighest;
+ this.toLowest = map.toLowest;
+ this.toHighest = map.toHighest;
+
+ this.fromRatio = map.fromRatio;
+ this.toRatio = map.toRatio;
+ if (map.fromShifts != null)
+ {
+ for (int[] r : map.fromShifts)
+ {
+ 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] });
+ }
+ }
+ }
+
+ /**
+ * 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<int[]> fromRange, List<int[]> 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 = Integer.MIN_VALUE;
+ for (int[] range : fromRange)
+ {
+ if (range.length != 2)
+ {
+ // throw new IllegalArgumentException(range);
+ System.err.println(
+ "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]));
+ }
+
+ toLowest = Integer.MAX_VALUE;
+ toHighest = Integer.MIN_VALUE;
+ for (int[] range : toRange)
+ {
+ if (range.length != 2)
+ {
+ // throw new IllegalArgumentException(range);
+ System.err.println("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]));
+ }
+ }
+
+ /**
+ * 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<int[]> coalesceRanges(final List<int[]> ranges)
+ {
+ if (ranges == null || ranges.size() < 2)
+ {
+ return ranges;
+ }
+
+ boolean changed = false;
+ List<int[]> 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
+// * [fromFinish-fromStart+2] { toStart..toFinish mappings}}
+// */
+// protected int[][] makeFromMap()
+// {
+// // TODO not used - remove??
+// return posMap(fromShifts, fromRatio, toShifts, toRatio);
+// }
+//
+// /**
+// * get all mapped positions from 'to' to 'from'
+// *
+// * @return int[to position]=position mapped in from
+// */
+// protected int[][] makeToMap()
+// {
+// // TODO not used - remove??
+// return posMap(toShifts, toRatio, fromShifts, fromRatio);
+// }
+
+// /**
+// * construct an int map for intervals in intVals
+// *
+// * @param shiftTo
+// * @return int[] { from, to pos in range }, int[range.to-range.from+1]
+// * returning mapped position
+// */
+// private int[][] posMap(List<int[]> shiftTo, int ratio,
+// List<int[]> shiftFrom, int toRatio)
+// {
+// // TODO not used - remove??
+//
+// int[] reg = new int[LEN];
+//
+// int iv = 0, ivSize = shiftTo.size();
+// if (iv >= ivSize)
+// {
+// return null;
+// }
+// int[] intv = shiftTo.get(iv++);
+// int from = intv[0], to = intv[1];
+// if (from > to)
+// {
+// from = intv[1];
+// to = intv[0];
+// }
+// while (iv < ivSize)
+// {
+// intv = shiftTo.get(iv++);
+// if (intv[0] < from)
+// {
+// from = intv[0];
+// }
+// if (intv[1] < from)
+// {
+// from = intv[1];
+// }
+// if (intv[0] > to)
+// {
+// to = intv[0];
+// }
+// if (intv[1] > to)
+// {
+// to = intv[1];
+// }
+// }
+// int tF = 0, tT = 0;
+// int mp[][] = new int[to - from + 2][];
+// for (int i = 0; i < mp.length; i++)
+// {
+// reg[POS] = i + from;
+// int[] m = shift(reg, shiftTo, ratio, shiftFrom, toRatio);
+// if (m != null)
+// {
+// if (i == 0)
+// {
+// tF = tT = m[0];
+// }
+// else
+// {
+// if (m[0] < tF)
+// {
+// tF = m[0];
+// }
+// if (m[0] > tT)
+// {
+// tT = m[0];
+// }
+// }
+// }
+// mp[i] = m;
+// }
+// int[][] map = new int[][] { new int[] { from, to, tF, tT },
+// new int[to - from + 2] };
+//
+// map[0][2] = tF;
+// map[0][3] = tT;
+//
+// for (int i = 0; i < mp.length; i++)
+// {
+// if (mp[i] != null)
+// {
+// map[1][i] = mp[i][0] - tF;
+// }
+// else
+// {
+// map[1][i] = -1; // indicates an out of range mapping
+// }
+// }
+// return map;
+// }
+
+ /**
+ * addShift
+ *
+ * @param pos
+ * start position for shift (in original reference frame)
+ * @param shift
+ * length of shift
+ *
+ * public void addShift(int pos, int shift) { int sidx = 0; int[]
+ * rshift=null; while (sidx<shifts.size() && (rshift=(int[])
+ * shifts.elementAt(sidx))[0]<pos) sidx++; if (sidx==shifts.size())
+ * shifts.insertElementAt(new int[] { pos, shift}, sidx); else
+ * rshift[1]+=shift; }
+ */
+
+ /**
+ * shift from pos to To(pos)
+ *
+ * @param reg[POS]
+ *
+ * @return int[] reg[POS_TO:shifted position in To,
+ * FROM_REMAINDER: frameshift in From,
+ * DIR_TO: direction of mapped symbol in To]
+ */
+ public int[] shiftFrom(int[] reg)
+ {
+ return shift(reg, fromShifts, fromRatio, toShifts, toRatio);
+ }
+
+ /**
+ * inverse of shiftFrom - maps pos in To to a position in From
+ *
+ * @param pos
+ * (in To)
+ * @return shifted position in From, frameshift in To, direction of mapped
+ * symbol in From
+ */
+ public int[] shiftTo(int[] reg)
+ {
+ return shift(reg, toShifts, toRatio, fromShifts, fromRatio);
+ }
+
+ /**
+ *
+ * @param reg[POS]
+ * @param shiftTo
+ * @param fromRatio
+ * @param shiftFrom
+ * @param toRatio
+ * @return reg[COUNT_TO, FROM_REMAINDER, DIR_TO]
+ */
+ protected static int[] shift(int[] reg, List<int[]> shiftTo, int fromRatio,
+ List<int[]> shiftFrom, int toRatio)
+ {
+ // TODO: javadoc; tests
+ reg = countPos(shiftTo, reg);
+ if (reg == null)
+ {
+ return null;
+ }
+ reg[FROM_REMAINDER] = (reg[POS_FROM] - 1) % fromRatio;
+ reg[POS] = 1 + (((reg[POS_FROM] - 1) / fromRatio) * toRatio); // toCount
+ reg = countToPos(shiftFrom, reg);
+ if (reg == null)
+ {
+ return null; // throw new Error("Bad Mapping!");
+ }
+ // reg is now filled
+ // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
+// ret3[0] = toPos[0];
+// ret3[1] = fromRemainder;
+// ret3[2] = toPos[1];
+ return reg;
+ }
+
+ /**
+ * count how many positions pos is along the series of intervals.
+ *
+ * @param shiftTo
+ * @param pos
+ * @return number of positions or null if pos is not within intervals
+ */
+ protected static int[] countPos(List<int[]> shiftTo, int[] reg)
+ {
+ int pos = reg[POS];
+ int count = 0, iv = 0, ivSize = shiftTo.size();
+ while (iv < ivSize)
+ {
+ int[] intv = shiftTo.get(iv++);
+ if (intv[0] <= intv[1])
+ {
+ if (pos >= intv[0] && pos <= intv[1])
+ {
+ reg[POS_FROM] = count + pos - intv[0] + 1;
+ reg[DIR_FROM] = 1;
+ return reg;
+ }
+ else
+ {
+ count += intv[1] - intv[0] + 1;
+ }
+ }
+ else
+ {
+ if (pos >= intv[1] && pos <= intv[0])
+ {
+ reg[POS_FROM] = count - pos + intv[0] + 1;
+ reg[DIR_FROM] = -1;
+ return reg;
+ }
+ else
+ {
+ count += intv[0] - intv[1] + 1;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * count out pos positions into a series of intervals and return the position
+ *
+ * @param shiftFrom
+ * @param pos
+ * @return position pos in interval set
+ */
+ protected static int[] countToPos(List<int[]> shiftFrom, int[] reg)
+ {
+ int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+ int pos = reg[POS];
+ while (iv < ivSize)
+ {
+ int[] intv = shiftFrom.get(iv++);
+ diff = intv[1] - intv[0];
+ if (diff >= 0)
+ {
+ if (pos <= count + 1 + diff)
+ {
+ reg[POS_TO] = intv[0] + pos - count - 1;
+ reg[DIR_TO] = 1;
+ return reg;
+ }
+ else
+ {
+ count += 1 + diff;
+ }
+ }
+ else
+ {
+ if (pos <= count + 1 - diff)
+ {
+ reg[POS_TO] = intv[0] - (pos - count - 1);
+ reg[DIR_TO] = -1;
+ return reg;
+ }
+ else
+ {
+ count += 1 - diff;
+ }
+ }
+ }
+ return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);
+ }
+
+ /**
+ * find series of intervals mapping from start-end in the From map.
+ *
+ * @param start
+ * position mapped 'to'
+ * @param end
+ * position mapped 'to'
+ * @return series of [start, end] ranges in sequence mapped 'from'
+ */
+ public int[] locateInFrom(int start, int end)
+ {
+ int[] reg = new int[LEN];
+ // inefficient implementation
+ reg[POS] = start;
+ reg = shiftTo(reg);
+ if (reg == null)
+ return null;
+ // needs to be inclusive of end of symbol position
+ start = reg[POS_TO];
+ reg[POS] = end;
+ reg = shiftTo(reg);
+ if (reg == null)
+ return null;
+ end = reg[POS_TO];
+ return getIntervals(fromShifts, start, end, fromRatio);
+ }
+
+ /**
+ * find series of intervals mapping from start-end in the to map.
+ *
+ * @param start
+ * position mapped 'from'
+ * @param end
+ * position mapped 'from'
+ * @return series of [start, end] ranges in sequence mapped 'to'
+ */
+ public int[] locateInTo(int start, int end)
+ {
+ int[] reg = new int[LEN];
+ reg[POS] = start;
+ reg = shiftFrom(reg);
+ if (reg == null)
+ return null;
+ start = reg[POS_FROM];
+ reg[POS] = end;
+ reg = shiftFrom(reg);
+ if (reg == null)
+ return null;
+ end = reg[POS_FROM];
+ return getIntervals(toShifts, start, end, toRatio);
+ }
+
+ /**
+ * like shift - except returns the intervals in the given vector of shifts
+ * which were spanned in traversing fromStart to fromEnd
+ *
+ * @param shiftFrom
+ * @param fromStart
+ * @param fromEnd
+ * @param fromRatio2
+ * @return series of from,to intervals from from first position of starting
+ * region to final position of ending region inclusive
+ */
+ protected static int[] getIntervals(List<int[]> shiftFrom,
+ int startpos, int endpos, int fromRatio2)
+ {
+// if (fromStart == null || fromEnd == null)
+// {
+// return null;
+// }
+// int startpos, endpos;
+// startpos = fromStart[0]; // first position in fromStart
+// endpos = fromEnd[0]; // last position in fromEnd
+ int endindx = (fromRatio2 - 1); // additional positions to get to last
+ // position from endpos
+ int intv = 0, intvSize = shiftFrom.size();
+ int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
+ // search intervals to locate ones containing startpos and count endindx
+ // positions on from endpos
+ while (intv < intvSize && (fs == -1 || fe == -1))
+ {
+ iv = shiftFrom.get(intv++);
+ if (fe_s > -1)
+ {
+ endpos = iv[0]; // start counting from beginning of interval
+ endindx--; // inclusive of endpos
+ }
+ if (iv[0] <= iv[1])
+ {
+ if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
+ {
+ fs = i;
+ }
+ if (endpos >= iv[0] && endpos <= iv[1])
+ {
+ if (fe_s == -1)
+ {
+ fe_s = i;
+ }
+ if (fe_s != -1)
+ {
+ if (endpos + endindx <= iv[1])
+ {
+ fe = i;
+ endpos = endpos + endindx; // end of end token is within this
+ // interval
+ }
+ else
+ {
+ endindx -= iv[1] - endpos; // skip all this interval too
+ }
+ }
+ }
+ }
+ else
+ {
+ if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
+ {
+ fs = i;
+ }
+ if (endpos <= iv[0] && endpos >= iv[1])
+ {
+ if (fe_s == -1)
+ {
+ fe_s = i;
+ }
+ if (fe_s != -1)
+ {
+ if (endpos - endindx >= iv[1])
+ {
+ fe = i;
+ endpos = endpos - endindx; // end of end token is within this
+ // interval
+ }
+ else
+ {
+ endindx -= endpos - iv[1]; // skip all this interval too
+ }
+ }
+ }
+ }
+ i++;
+ }
+ if (fs == fe && fe == -1)
+ {
+ return null;
+ }
+ List<int[]> ranges = new ArrayList<>();
+ if (fs <= fe)
+ {
+ intv = fs;
+ i = fs;
+ // truncate initial interval
+ iv = shiftFrom.get(intv++);
+ iv = new int[] { iv[0], iv[1] };// clone
+ if (i == fs)
+ {
+ iv[0] = startpos;
+ }
+ while (i != fe)
+ {
+ ranges.add(iv); // add initial range
+ iv = shiftFrom.get(intv++); // get next interval
+ iv = new int[] { iv[0], iv[1] };// clone
+ i++;
+ }
+ if (i == fe)
+ {
+ iv[1] = endpos;
+ }
+ ranges.add(iv); // add only - or final range
+ }
+ else
+ {
+ // walk from end of interval.
+ i = shiftFrom.size() - 1;
+ while (i > fs)
+ {
+ i--;
+ }
+ iv = shiftFrom.get(i);
+ iv = new int[] { iv[1], iv[0] };// reverse and clone
+ // truncate initial interval
+ if (i == fs)
+ {
+ iv[0] = startpos;
+ }
+ while (--i != fe)
+ { // 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
+ }
+ if (i == fe)
+ {
+ // interval is already reversed
+ iv[1] = endpos;
+ }
+ ranges.add(iv); // add only - or final range
+ }
+ // create array of start end intervals.
+ int[] range = null;
+ if (ranges != null && ranges.size() > 0)
+ {
+ range = new int[ranges.size() * 2];
+ intv = 0;
+ intvSize = ranges.size();
+ i = 0;
+ while (intv < intvSize)
+ {
+ iv = ranges.get(intv);
+ range[i++] = iv[0];
+ range[i++] = iv[1];
+ ranges.set(intv++, null); // remove
+ }
+ }
+ return range;
+ }
+
+// /**
+// * get the 'initial' position of mpos in To
+// *
+// * @param mpos
+// * position in from
+// * @return position of first word in to reference frame
+// */
+// public int getToPosition(int[])
+// {
+// // TODO not used - remove??
+// int[] mp = shiftTo(mpos);
+// if (mp != null)
+// {
+// return mp[0];
+// }
+// return mpos;
+// }
+//
+// /**
+// * get range of positions in To frame for the mpos word in From
+// *
+// * @param mpos
+// * position in From
+// * @return null or int[] first position in To for mpos, last position in to
+// * for Mpos
+// */
+// public int[] getToWord(int mpos)
+// {
+// // never called
+// int[] mp = shiftTo(mpos);
+// if (mp != null)
+// {
+// return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
+// }
+// return null;
+// }
+
+ /**
+ * get From position in the associated reference frame for position pos in the
+ * associated sequence.
+ *
+ * @param pos
+ * @return
+ */
+ public int getMappedPosition(int[] reg)
+ {
+ // TODO not used - remove??
+ int pos = reg[POS];
+ reg = shiftFrom(reg);
+ if (reg != null)
+ {
+ return reg[POS_TO];
+ }
+ return pos;
+ }
+
+// public int[] getMappedWord(int[] reg)
+// {
+// // TODO not used - remove??
+// reg = shiftFrom(reg);
+// if (reg != null)
+// {
+// return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
+// }
+// return null;
+// }
+
+ /**
+ *
+ * @return a MapList whose From range is this maplist's To Range, and vice
+ * versa
+ */
+ public MapList getInverse()
+ {
+ return new MapList(getToRanges(), getFromRanges(), getToRatio(),
+ getFromRatio());
+ }
+
+ /**
+ * test for containment rather than equivalence to another mapping
+ *
+ * @param map
+ * to be tested for containment
+ * @return true if local or mapped range map contains or is contained by this
+ * mapping
+ */
+ public boolean containsEither(boolean local, MapList map)
+ {
+ // TODO not used - remove?
+ if (local)
+ {
+ 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()));
+ }
+ }
+
+ /**
+ * String representation - for debugging, not guaranteed not to change
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder(64);
+ sb.append("[");
+ for (int[] shift : fromShifts)
+ {
+ sb.append(" ").append(Arrays.toString(shift));
+ }
+ sb.append(" ] ");
+ sb.append(fromRatio).append(":").append(toRatio);
+ sb.append(" to [");
+ for (int[] shift : toShifts)
+ {
+ sb.append(" ").append(Arrays.toString(shift));
+ }
+ 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<int[]> 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()
+ {
+ 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<int[]> ranges)
+ {
+ boolean forwardStrand = true;
+ for (int[] range : ranges)
+ {
+ 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);
+ }
+
+ /**
+ * 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.
+ * <p>
+ * 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.
+ *
+ * <pre>
+ * 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
+ * </pre>
+ *
+ * @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<int[]> toRanges = new ArrayList<>();
+ List<int[]> ranges = getToRanges();
+
+ for (int ir = 0, nr = ranges.size(); ir < nr; ir++)
+ {
+ int[] range = ranges.get(ir);
+ int[] transferred = map.locateInTo(range[0], range[1]);
+ if (transferred == null || transferred.length % 2 != 0)
+ {
+ return null;
+ }
+
+ /*
+ * convert [start1, end1, start2, end2, ...]
+ * to [[start1, end1], [start2, end2], ...]
+ */
+ for (int i = 0, n = transferred.length; i < n; i += 2)
+ {
+ toRanges.add(new int[] { transferred[i], transferred[i + 1] });
+ }
+ }
+
+ return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff