/* * 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 . * 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 fromShifts; /* * Same format as fromShifts, for the 'mapped to' sequence */ private List 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 getFromRanges() { return fromShifts; } /** * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...} * * @return */ public List 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 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 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 = 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 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 // * [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 shiftTo, int ratio, // List 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 shiftTo, int fromRatio, List 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 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 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 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 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 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 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. *

* 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<>(); List 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); } }