X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2FMapList.java;fp=unused%2FMapList.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=a5aa8fd23549c7b0a00032207c4b8f1deedbdca6;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/unused/MapList.java b/unused/MapList.java
deleted file mode 100644
index a5aa8fd..0000000
--- a/unused/MapList.java
+++ /dev/null
@@ -1,1286 +0,0 @@
-/*
- * 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);
-  }
-
-}