X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2FMapList.java;fp=unused%2FMapList.java;h=a5aa8fd23549c7b0a00032207c4b8f1deedbdca6;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=0000000000000000000000000000000000000000;hpb=9dabc02511e3a334a5749a504f57f69d6c9017bd;p=jalview.git

diff --git a/unused/MapList.java b/unused/MapList.java
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+/*
+ * 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);
+  }
+
+}