X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=c5654fbee62fd697f85c53ebb55e44302eb28b29;hp=215ece943af8f0e10fa792732c5233c30e5fa88b;hb=c17981672620e0b780a2338bd0c74e55cf9ddec2;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 215ece9..c5654fb 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,98 +1,453 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import jalview.bin.Cache;
 
 /**
- * MapList
- * Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range
+ * 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)
- * TODO: optimize to use int[][] arrays rather than vectors.
+ * 
+ * TODO: test/ensure that sense of from and to ratio start position is conserved
+ * (codon start position recovery)
  */
 public class MapList
 {
-  public Vector fromShifts;
-  public Vector toShifts;
-  int fromRatio; // number of steps in fromShifts to one toRatio unit
-  int toRatio; // number of steps in toShifts to one fromRatio
+
+  /*
+   * 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,...].
+   * 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)
   {
-    fromShifts = new Vector();
+    this();
+    this.fromRatio = fromRatio;
+    this.toRatio = toRatio;
+    fromLowest = Integer.MAX_VALUE;
+    fromHighest = Integer.MIN_VALUE;
+
     for (int i = 0; i < from.length; i += 2)
     {
-      fromShifts.add(new int[]
-                     {from[i], from[i + 1]});
+      /*
+       * note lowest and highest values - bearing in mind the
+       * direction may be reversed
+       */
+      fromLowest = Math.min(fromLowest, Math.min(from[i], from[i + 1]));
+      fromHighest = Math.max(fromHighest, Math.max(from[i], from[i + 1]));
+      fromShifts.add(new int[] { from[i], from[i + 1] });
     }
-    toShifts = new Vector();
+
+    toLowest = Integer.MAX_VALUE;
+    toHighest = Integer.MIN_VALUE;
     for (int i = 0; i < to.length; i += 2)
     {
-      toShifts.add(new int[]
-                   {to[i], to[i + 1]});
+      toLowest = Math.min(toLowest, Math.min(to[i], to[i + 1]));
+      toHighest = Math.max(toHighest, Math.max(to[i], to[i + 1]));
+      toShifts.add(new int[] { to[i], to[i + 1] });
     }
+  }
+
+  /**
+   * 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);
+        Cache.log.error("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);
+        Cache.log.error("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).
+   * <p>
+   * The main use case for this method is when mapping cDNA sequence to its
+   * protein product, based on CDS feature ranges which derive from spliced
+   * exons, but are contiguous on the cDNA sequence. For example 
+   * <pre>
+   *   CDS 1-20  // from exon1
+   *   CDS 21-35 // from exon2
+   *   CDS 36-71 // from exon3
+   * 'coalesce' to range 1-71
+   * </pre>
+   * 
+   * @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;
+      }
+
+      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;
+      if (sameDirection && 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}}
+   * 
+   * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int
+   *         [fromFinish-fromStart+2] { toStart..toFinish mappings}}
    */
-  public int[][] makeFromMap()
+  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
    */
-  public int[][] makeToMap()
+  protected int[][] makeToMap()
   {
+    // TODO not used - remove??
     return posMap(toShifts, toRatio, fromShifts, fromRatio);
   }
 
   /**
    * construct an int map for intervals in intVals
-   * @param intVals
-   * @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position
+   * 
+   * @param shiftTo
+   * @return int[] { from, to pos in range }, int[range.to-range.from+1]
+   *         returning mapped position
    */
-  private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
-                         int toRatio)
+  private int[][] posMap(List<int[]> shiftTo, int ratio,
+          List<int[]> shiftFrom, int toRatio)
   {
-    Iterator iv = intVals.iterator();
-    if (!iv.hasNext())
+    // TODO not used - remove??
+    int iv = 0, ivSize = shiftTo.size();
+    if (iv >= ivSize)
     {
       return null;
     }
-    int[] intv = (int[]) iv.next();
+    int[] intv = shiftTo.get(iv++);
     int from = intv[0], to = intv[1];
     if (from > to)
     {
       from = intv[1];
       to = intv[0];
     }
-    while (iv.hasNext())
+    while (iv < ivSize)
     {
-      intv = (int[]) iv.next();
+      intv = shiftTo.get(iv++);
       if (intv[0] < from)
       {
         from = intv[0];
@@ -114,7 +469,7 @@ public class MapList
     int mp[][] = new int[to - from + 2][];
     for (int i = 0; i < mp.length; i++)
     {
-      int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
+      int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio);
       if (m != null)
       {
         if (i == 0)
@@ -135,11 +490,8 @@ public class MapList
       }
       mp[i] = m;
     }
-    int[][] map = new int[][]
-        {
-        new int[]
-        {
-        from, to, tF, tT}, new int[to - from + 2]};
+    int[][] map = new int[][] { new int[] { from, to, tF, tT },
+        new int[to - from + 2] };
 
     map[0][2] = tF;
     map[0][3] = tT;
@@ -160,26 +512,26 @@ public class MapList
 
   /**
    * 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;
-     }
+   * 
+   * @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 pos int
-   * @return int shifted position in To, frameshift in From
+   * 
+   * @param pos
+   *          int
+   * @return int shifted position in To, frameshift in From, direction of mapped
+   *         symbol in To
    */
   public int[] shiftFrom(int pos)
   {
@@ -188,8 +540,11 @@ public class MapList
 
   /**
    * inverse of shiftFrom - maps pos in To to a position in From
-   * @param pos (in To)
-   * @return shifted position in From, frameshift in To
+   * 
+   * @param pos
+   *          (in To)
+   * @return shifted position in From, frameshift in To, direction of mapped
+   *         symbol in From
    */
   public int[] shiftTo(int pos)
   {
@@ -197,53 +552,51 @@ public class MapList
   }
 
   /**
-   *
-   * @param fromShifts
+   * 
+   * @param shiftTo
    * @param fromRatio
-   * @param toShifts
+   * @param shiftFrom
    * @param toRatio
    * @return
    */
-  private int[] shift(int pos, Vector fromShifts, int fromRatio,
-                      Vector toShifts, int toRatio)
+  protected static int[] shift(int pos, List<int[]> shiftTo, int fromRatio,
+          List<int[]> shiftFrom, int toRatio)
   {
-    int[] fromCount = countPos(fromShifts.iterator(), pos);
+    // TODO: javadoc; tests
+    int[] fromCount = countPos(shiftTo, pos);
     if (fromCount == null)
     {
       return null;
     }
     int fromRemainder = (fromCount[0] - 1) % fromRatio;
-    int toCount = 1 + ( ( (fromCount[0] - 1) / fromRatio) * toRatio);
-    int[] toPos = countToPos(toShifts.iterator(), toCount);
+    int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
+    int[] toPos = countToPos(shiftFrom, toCount);
     if (toPos == null)
     {
       return null; // throw new Error("Bad Mapping!");
     }
-    //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
-    return new int[]
-        {
-        toPos[0], fromRemainder};
+    // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
+    return new int[] { toPos[0], fromRemainder, toPos[1] };
   }
 
   /**
    * count how many positions pos is along the series of intervals.
-   * @param intVals
+   * 
+   * @param shiftTo
    * @param pos
    * @return number of positions or null if pos is not within intervals
    */
-  private int[] countPos(Iterator intVals, int pos)
+  protected static int[] countPos(List<int[]> shiftTo, int pos)
   {
-    int count = 0, intv[];
-    while (intVals.hasNext())
+    int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
+    while (iv < ivSize)
     {
-      intv = (int[]) intVals.next();
+      intv = shiftTo.get(iv++);
       if (intv[0] <= intv[1])
       {
         if (pos >= intv[0] && pos <= intv[1])
         {
-          return new int[]
-              {
-              count + pos - intv[0] + 1, +1};
+          return new int[] { count + pos - intv[0] + 1, +1 };
         }
         else
         {
@@ -254,9 +607,7 @@ public class MapList
       {
         if (pos >= intv[1] && pos <= intv[0])
         {
-          return new int[]
-              {
-              count + intv[0] - pos + 1, -1};
+          return new int[] { count + intv[0] - pos + 1, -1 };
         }
         else
         {
@@ -269,26 +620,24 @@ public class MapList
 
   /**
    * count out pos positions into a series of intervals and return the position
-   * @param intVals
+   * 
+   * @param shiftFrom
    * @param pos
    * @return position pos in interval set
    */
-  private int[] countToPos(Iterator intVals, int pos)
+  protected static int[] countToPos(List<int[]> shiftFrom, int pos)
   {
-    int count = 0, diff = 0, intv[] =
-        {
-        0, 0};
-    while (intVals.hasNext())
+    int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+    int[] intv = { 0, 0 };
+    while (iv < ivSize)
     {
-      intv = (int[]) intVals.next();
+      intv = shiftFrom.get(iv++);
       diff = intv[1] - intv[0];
       if (diff >= 0)
       {
         if (pos <= count + 1 + diff)
         {
-          return new int[]
-              {
-              pos - count - 1 + intv[0], +1};
+          return new int[] { pos - count - 1 + intv[0], +1 };
         }
         else
         {
@@ -299,9 +648,7 @@ public class MapList
       {
         if (pos <= count + 1 - diff)
         {
-          return new int[]
-              {
-              intv[0] - (pos - count - 1), -1};
+          return new int[] { intv[0] - (pos - count - 1), -1 };
         }
         else
         {
@@ -309,87 +656,589 @@ public class MapList
         }
       }
     }
-    return null; //(diff<0) ? (intv[1]-1) : (intv[0]+1);
+    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)
+  {
+    // inefficient implementation
+    int fromStart[] = shiftTo(start);
+    // needs to be inclusive of end of symbol position
+    int fromEnd[] = shiftTo(end);
+
+    return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
   }
 
-  public static void testMap(MapList ml, int fromS, int fromE)
+  /**
+   * 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 toStart[] = shiftFrom(start);
+    int toEnd[] = shiftFrom(end);
+    return getIntervals(toShifts, toStart, toEnd, 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[] fromStart, int[] fromEnd, int fromRatio2)
   {
-    for (int from = 1; from <= 25; from++)
+    if (fromStart == null || fromEnd == null)
     {
-      int[] too = ml.shiftFrom(from);
-      System.out.print("ShiftFrom(" + from + ")==");
-      if (too == 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)
       {
-        System.out.print("NaN\n");
+        endpos = iv[0]; // start counting from beginning of interval
+        endindx--; // inclusive of endpos
       }
-      else
+      if (iv[0] <= iv[1])
       {
-        System.out.print(too[0] + " % " + too[1]);
-        System.out.print("\t+--+\t");
-        int[] toofrom = ml.shiftTo(too[0]);
-        if (toofrom != null)
+        if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
+        {
+          fs = i;
+        }
+        if (endpos >= iv[0] && endpos <= iv[1])
         {
-          if (toofrom[0] != from)
+          if (fe_s == -1)
           {
-            System.err.println("Mapping not reflexive:" + from + " " + too[0] +
-                               "->" + toofrom[0]);
+            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
+            }
           }
-          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
-                             toofrom[1]);
         }
-        else
+      }
+      else
+      {
+        if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
+        {
+          fs = i;
+        }
+        if (endpos <= iv[0] && endpos >= iv[1])
         {
-          System.out.println("ShiftTo(" + too[0] + ")==" +
-                             "NaN! - not Bijective Mapping!");
+          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;
     }
-    int mmap[][] = ml.makeFromMap();
-    System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
-                       mmap[0][2] + " " + mmap[0][3] + " ");
-    for (int i = 1; i <= mmap[1].length; i++)
+    List<int[]> ranges = new ArrayList<>();
+    if (fs <= fe)
     {
-      if (mmap[1][i - 1] == -1)
+      intv = fs;
+      i = fs;
+      // truncate initial interval
+      iv = shiftFrom.get(intv++);
+      iv = new int[] { iv[0], iv[1] };// clone
+      if (i == fs)
       {
-        System.out.print(i + "=XXX");
-
+        iv[0] = startpos;
       }
-      else
+      while (i != fe)
       {
-        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+        ranges.add(iv); // add initial range
+        iv = shiftFrom.get(intv++); // get next interval
+        iv = new int[] { iv[0], iv[1] };// clone
+        i++;
       }
-      if (i % 20 == 0)
+      if (i == fe)
       {
-        System.out.print("\n");
+        iv[1] = endpos;
       }
-      else
+      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 mpos)
+  {
+    // 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)
+  {
+    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 pos)
+  {
+    // TODO not used - remove??
+    int[] mp = shiftFrom(pos);
+    if (mp != null)
+    {
+      return mp[0];
+    }
+    return pos;
+  }
+
+  public int[] getMappedWord(int pos)
+  {
+    // TODO not used - remove??
+    int[] mp = shiftFrom(pos);
+    if (mp != 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])
       {
-        System.out.print(",");
+        forwardStrand = false;
+        break; // reverse strand confirmed
       }
     }
-    System.out.print("\n");
+    return forwardStrand;
   }
 
-  public static void main(String argv[])
+  /**
+   * 
+   * @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)
   {
-    MapList ml = new MapList(new int[]
-                             {1, 5, 10, 15, 25, 20},
-                             new int[]
-                             {51, 1}, 1, 3);
-    MapList ml1 = new MapList(new int[]
-                              {1, 3, 17, 4},
-                              new int[]
-                              {51, 1}, 1, 3);
+    if (map == null)
+    {
+      return null;
+    }
 
-    // test internal consistency
-    int to[] = new int[51];
-    MapList.testMap(ml, 1, 25);
     /*
-           for (int from=1; from<=51; from++) {
-        int[] too=ml.shiftTo(from);
-        int[] toofrom=ml.shiftFrom(too[0]);
-        System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
-           }*/
-    System.out.print("Success?\n"); // if we get here - something must be working!
+     * 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<>();
+    for (int[] range : getToRanges())
+    {
+      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; i < transferred.length;)
+      {
+        toRanges.add(new int[] { transferred[i], transferred[i + 1] });
+        i += 2;
+      }
+    }
+
+    return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
+  }
+
+  /**
+   * Answers true if the mapping is from one contiguous range to another, else
+   * false
+   * 
+   * @return
+   */
+  public boolean isContiguous()
+  {
+    return fromShifts.size() == 1 && toShifts.size() == 1;
+  }
+
+  /**
+   * Returns the [start, end...] positions in the range mapped from, that are
+   * mapped to by part or all of the given begin-end of the range mapped to.
+   * Returns null if begin-end does not overlap any position mapped to.
+   * 
+   * @param begin
+   * @param end
+   * @return
+   */
+  public int[] getOverlapsInFrom(final int begin, final int end)
+  {
+    int[] overlaps = MappingUtils.findOverlap(toShifts, begin, end);
+
+    return overlaps == null ? null : locateInFrom(overlaps[0], overlaps[1]);
+  }
+
+  /**
+   * Returns the [start, end...] positions in the range mapped to, that are
+   * mapped to by part or all of the given begin-end of the range mapped from.
+   * Returns null if begin-end does not overlap any position mapped from.
+   * 
+   * @param begin
+   * @param end
+   * @return
+   */
+  public int[] getOverlapsInTo(final int begin, final int end)
+  {
+    int[] overlaps = MappingUtils.findOverlap(fromShifts, begin, end);
+
+    return overlaps == null ? null : locateInTo(overlaps[0], overlaps[1]);
   }
 }