X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=58abdc3926c1bf1badddf8e83e4b0724c06b30da;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=4a59f88aa50066da55870f06ec3651a68fb968db;hpb=539bd323123b239afdac5ef7b7706d6ccfc6a41d;p=jalview.git

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 4a59f88..58abdc3 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,222 +1,508 @@
 /*
- * 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;
 
 /**
- * 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
 {
-  /* (non-Javadoc)
-   * @see java.lang.Object#clone()
+
+  /*
+   * 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
    */
-  protected Object clone() throws CloneNotSupportedException {
-    // TODO Auto-generated method stub
-    return super.clone();
+  private int toLowest;
+
+  private int toHighest;
+
+  /**
+   * Constructor
+   */
+  public MapList()
+  {
+    fromShifts = new ArrayList<int[]>();
+    toShifts = new ArrayList<int[]>();
   }
-  /* (non-Javadoc)
-   * @see java.lang.Object#equals(java.lang.Object)
+
+  /**
+   * Two MapList objects are equal if they are the same object, or they both
+   * have populated shift ranges and all values are the same.
    */
-  public boolean equals(MapList obj) {
-    if (obj==this)
-      return true;
-    if (obj!=null && obj.fromRatio==fromRatio && obj.toRatio==toRatio
-        && obj.fromShifts!=null && obj.toShifts!=null) {
-      int i,iSize=fromShifts.size(),j,jSize=obj.fromShifts.size();
-      if (iSize!=jSize)
-        return false;
-      for (i=0,iSize=fromShifts.size(),j=0, jSize=obj.fromShifts.size(); i<iSize;) {
-        int[] mi=(int[]) fromShifts.elementAt(i++);
-        int[] mj=(int[]) obj.fromShifts.elementAt(j++);
-        if (mi[0]!=mj[0] || mi[1]!=mj[1])
-          return false;
-      }
-      iSize=toShifts.size();
-      jSize=obj.toShifts.size();
-      if (iSize!=jSize)
-        return false;
-      for (i=0,j=0; i<iSize;) {
-        int[] mi=(int[]) toShifts.elementAt(i++);
-        int[] mj=(int[]) obj.toShifts.elementAt(j++);
-        if (mi[0]!=mj[0] || mi[1]!=mj[1])
-          return false;
-      }
+  @Override
+  public boolean equals(Object o)
+  {
+    if (o == null || !(o instanceof MapList))
+    {
+      return false;
+    }
+
+    MapList obj = (MapList) o;
+    if (obj == this)
+    {
       return true;
     }
-    return false;
+    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());
   }
-  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
+
   /**
-   * lowest and highest value in the from Map
+   * Returns a hashcode made from the fromRatio, toRatio, and from/to ranges
    */
-  int[] fromRange=null;
+  @Override
+  public int hashCode()
+  {
+    int hashCode = 31 * fromRatio;
+    hashCode = 31 * hashCode + toRatio;
+    hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
+    hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+    return hashCode;
+  }
+
   /**
-   * lowest and highest value in the to Map
+   * 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
    */
-  int[] toRange=null;
   public int getFromRatio()
   {
     return fromRatio;
   }
+
+  /**
+   * 
+   * @return length of mapped phrase in to
+   */
   public int getToRatio()
   {
     return toRatio;
   }
-  public int getFromLowest() {
-    return fromRange[0];
-  }
-  public int getFromHighest() {
-    return fromRange[1];
+
+  public int getFromLowest()
+  {
+    return fromLowest;
   }
-  public int getToLowest() {
-    return toRange[0];
+
+  public int getFromHighest()
+  {
+    return fromHighest;
   }
-  public int getToHighest() {
-    return toRange[1];
+
+  public int getToLowest()
+  {
+    return toLowest;
   }
-  private void ensureRange(int[] limits, int pos) {
-    if (limits[0]>pos)
-      limits[0]=pos;
-    if (limits[1]<pos)
-      limits[1]=pos;
+
+  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)
   {
-    fromRange=new int[] { from[0],from[1] };
-    toRange=new int[] { to[0],to[1] };
+    this();
+    this.fromRatio = fromRatio;
+    this.toRatio = toRatio;
+    fromLowest = Integer.MAX_VALUE;
+    fromHighest = Integer.MIN_VALUE;
+    int added = 0;
 
-    fromShifts = new Vector();
-    for (int i=0;i<from.length; i+=2)
+    for (int i = 0; i < from.length; i += 2)
     {
-      ensureRange(fromRange, from[i]);
-      ensureRange(fromRange, 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]));
+      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++;
+      }
+    }
 
-      fromShifts.addElement(new int[]
-                             {from[i], from[i + 1]});
+    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++;
+      }
     }
-    toShifts = new Vector();
-    for (int i=0;i<to.length; i+=2)
+  }
+
+  /**
+   * 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)
+    {
+      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)
+    {
+      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)
     {
-      ensureRange(toRange, to[i]);
-      ensureRange(toRange, to[i+1]);
-      toShifts.addElement(new int[]
-                           {to[i], to[i + 1]});
+      return ranges;
+    }
+
+    boolean changed = false;
+    List<int[]> merged = new ArrayList<int[]>();
+    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;
+      }
     }
-    this.fromRatio=fromRatio;
-    this.toRatio=toRatio;
+
+    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()
   {
-    return posMap(toShifts,toRatio, fromShifts, fromRatio);
+    // 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)
   {
-    int iv=0,ivSize = intVals.size();
-    if (iv>=ivSize)
+    // TODO not used - remove??
+    int iv = 0, ivSize = shiftTo.size();
+    if (iv >= ivSize)
     {
       return null;
     }
-    int[] intv=(int[]) intVals.elementAt(iv++);
-    int from=intv[0],to=intv[1];
+    int[] intv = shiftTo.get(iv++);
+    int from = intv[0], to = intv[1];
     if (from > to)
     {
       from = intv[1];
-      to=intv[0];
+      to = intv[0];
     }
-    while (iv<ivSize)
+    while (iv < ivSize)
     {
-      intv = (int[]) intVals.elementAt(iv++);
-      if (intv[0]<from)
+      intv = shiftTo.get(iv++);
+      if (intv[0] < from)
       {
-        from=intv[0];
+        from = intv[0];
       }
-      if (intv[1]<from)
+      if (intv[1] < from)
       {
-        from=intv[1];
+        from = intv[1];
       }
-      if (intv[0]>to)
+      if (intv[0] > to)
       {
-        to=intv[0];
+        to = intv[0];
       }
-      if (intv[1]>to)
+      if (intv[1] > to)
       {
-        to=intv[1];
+        to = intv[1];
       }
     }
-    int tF=0,tT=0;
-    int mp[][] = new int[to-from+2][];
+    int tF = 0, tT = 0;
+    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)
         {
-          tF=tT=m[0];
+          tF = tT = m[0];
         }
         else
         {
           if (m[0] < tF)
           {
-            tF=m[0];
+            tF = m[0];
           }
           if (m[0] > tT)
           {
-            tT=m[0];
+            tT = m[0];
           }
         }
       }
       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;
@@ -225,7 +511,7 @@ public class MapList
     {
       if (mp[i] != null)
       {
-        map[1][i] = mp[i][0]-tF;
+        map[1][i] = mp[i][0] - tF;
       }
       else
       {
@@ -234,28 +520,29 @@ public class MapList
     }
     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;
-  }
+   * 
+   * @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, direction of mapped symbol in To
+   * 
+   * @param pos
+   *          int
+   * @return int shifted position in To, frameshift in From, direction of mapped
+   *         symbol in To
    */
   public int[] shiftFrom(int pos)
   {
@@ -264,429 +551,568 @@ 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, direction of mapped symbol in From
+   * 
+   * @param pos
+   *          (in To)
+   * @return shifted position in From, frameshift in To, direction of mapped
+   *         symbol in From
    */
   public int[] shiftTo(int pos)
   {
     return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
   }
+
   /**
-   *
-   * @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, pos);
-    if (fromCount==null)
+    // 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, toCount);
-    if (toPos==null)
+    int fromRemainder = (fromCount[0] - 1) % fromRatio;
+    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, toPos[1]};
+    // 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(Vector intVals, int pos)
+  protected static int[] countPos(List<int[]> shiftTo, int pos)
   {
-    int count=0,intv[],iv=0,ivSize=intVals.size();
-    while (iv<ivSize)
+    int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
+    while (iv < ivSize)
     {
-      intv = (int[])intVals.elementAt(iv++);
+      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
         {
-          count+=intv[1]-intv[0]+1;
+          count += intv[1] - intv[0] + 1;
         }
       }
       else
       {
         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
         {
-          count+=intv[0]-intv[1]+1;
+          count += intv[0] - intv[1] + 1;
         }
       }
     }
     return null;
   }
+
   /**
    * 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(Vector intVals, int pos)
+  protected static int[] countToPos(List<int[]> shiftFrom, int pos)
   {
-    int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
-    {
-        0, 0};
-    while (iv<ivSize)
+    int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+    int[] intv = { 0, 0 };
+    while (iv < ivSize)
     {
-      intv = (int[])intVals.elementAt(iv++);
-      diff = intv[1]-intv[0];
+      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
         {
-          count+=1+diff;
+          count += 1 + diff;
         }
       }
       else
       {
         if (pos <= count + 1 - diff)
         {
-          return new int[]
-                         {
-              intv[0] - (pos - count - 1), -1};
+          return new int[] { intv[0] - (pos - count - 1), -1 };
         }
         else
         {
-          count+=1-diff;
+          count += 1 - diff;
         }
       }
     }
-    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 in to map
-   * @param end position in to map
-   * @return series of ranges in 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) {
+  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);
-    if (fromStart==null || fromEnd==null)
-      return null;
-    int iv[] = getIntervals(fromShifts, fromStart, fromEnd,fromRatio);
-    return iv;
+
+    return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
   }
 
   /**
    * find series of intervals mapping from start-end in the to map.
-   * @param start position in from map
-   * @param end position in from map
-   * @return series of ranges in 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) {
-    // inefficient implementation
+  public int[] locateInTo(int start, int end)
+  {
     int toStart[] = shiftFrom(start);
     int toEnd[] = shiftFrom(end);
-    if (toStart==null || toEnd==null)
-      return null;
-    int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
-    return iv;
+    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 fromShifts2
+   * 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
+   * @return series of from,to intervals from from first position of starting
+   *         region to final position of ending region inclusive
    */
-  private int[] getIntervals(Vector fromShifts2, int[] fromStart, int[] fromEnd, int fromRatio2)
-  {
-    // correct for word direction for start and end
-    int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1);
-    int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1);
-    int intv=0,intvSize= fromShifts2.size();
-    int iv[],i=0,fs=-1,fe=-1; // containing intervals
-    while (intv<intvSize && (fs==-1 || fe==-1)) {
-      iv = (int[]) fromShifts2.elementAt(intv++);
-      if (iv[0]<=iv[1]) {
-        if (fs==-1 && startpos>=iv[0] && startpos<=iv[1]) {
+  protected static int[] getIntervals(List<int[]> shiftFrom,
+          int[] fromStart, int[] fromEnd, 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 (fe==-1 && endpos>=iv[0] && endpos<=iv[1]) {
-          fe = 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]) {
+      }
+      else
+      {
+        if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
+        {
           fs = i;
         }
-        if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
-          fe = 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)
+    if (fs == fe && fe == -1)
+    {
       return null;
-    Vector ranges=new Vector();
-    if (fs<=fe) {
+    }
+    List<int[]> ranges = new ArrayList<int[]>();
+    if (fs <= fe)
+    {
       intv = fs;
-      i=fs;
+      i = fs;
       // truncate initial interval
-      iv = (int[]) fromShifts2.elementAt(intv++);
-      iv = new int[] { iv[0], iv[1]};// clone
-      if (i==fs)
+      iv = shiftFrom.get(intv++);
+      iv = new int[] { iv[0], iv[1] };// clone
+      if (i == fs)
+      {
         iv[0] = startpos;
-      while (i!=fe) {
-        ranges.addElement(iv); // add initial range
-        iv = (int[]) fromShifts2.elementAt(intv++); // get next interval
-        iv = new int[] { iv[0], iv[1]};// clone
+      }
+      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)
+      if (i == fe)
+      {
         iv[1] = endpos;
-      ranges.addElement(iv); // add only - or final range
-    } else {
+      }
+      ranges.add(iv); // add only - or final range
+    }
+    else
+    {
       // walk from end of interval.
-      i=fromShifts2.size()-1;
-      while (i>fs) {
+      i = shiftFrom.size() - 1;
+      while (i > fs)
+      {
         i--;
       }
-      iv = (int[]) fromShifts2.elementAt(i);
-      iv = new int[] { iv[1], iv[0]};//  reverse and clone
+      iv = shiftFrom.get(i);
+      iv = new int[] { iv[1], iv[0] };// reverse and clone
       // truncate initial interval
-      if (i==fs)
+      if (i == fs)
       {
         iv[0] = startpos;
       }
-      while (i!=fe) {
-        ranges.addElement(iv); // add (truncated) reversed interval
-        iv = (int[]) fromShifts2.elementAt(--i);
+      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) {
+      if (i == fe)
+      {
         // interval is already reversed
         iv[1] = endpos;
       }
-      ranges.addElement(iv); // add only - or final range
+      ranges.add(iv); // add only - or final range
     }
     // create array of start end intervals.
     int[] range = null;
-    if (ranges!=null && ranges.size()>0)
+    if (ranges != null && ranges.size() > 0)
     {
-      range = new int[ranges.size()*2];
+      range = new int[ranges.size() * 2];
       intv = 0;
-      intvSize=ranges.size();
-      i=0;
-      while (intv<intvSize)
+      intvSize = ranges.size();
+      i = 0;
+      while (intv < intvSize)
       {
-        iv = (int[]) ranges.elementAt(intv);
+        iv = ranges.get(intv);
         range[i++] = iv[0];
         range[i++] = iv[1];
-        ranges.setElementAt(null, intv++); // remove
+        ranges.set(intv++, null); // remove
       }
     }
     return range;
   }
+
   /**
-   * test routine. not incremental.
-   * @param ml
-   * @param fromS
-   * @param fromE
+   * get the 'initial' position of mpos in To
+   * 
+   * @param mpos
+   *          position in from
+   * @return position of first word in to reference frame
    */
-  public static void testMap(MapList ml, int fromS, int fromE)
+  public int getToPosition(int mpos)
   {
-    for (int from = 1; from <= 25; from++)
+    // TODO not used - remove??
+    int[] mp = shiftTo(mpos);
+    if (mp != null)
     {
-      int[] too=ml.shiftFrom(from);
-      System.out.print("ShiftFrom("+from+")==");
-      if (too==null)
-      {
-        System.out.print("NaN\n");
-      }
-      else
-      {
-        System.out.print(too[0]+" % "+too[1]+" ("+too[2]+")");
-        System.out.print("\t+--+\t");
-        int[] toofrom=ml.shiftTo(too[0]);
-        if (toofrom != null)
-        {
-          if (toofrom[0]!=from)
-          {
-            System.err.println("Mapping not reflexive:" + from + " " + too[0] +
-                "->" + toofrom[0]);
-          }
-          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
-              toofrom[1]+" ("+toofrom[2]+")");
-        }
-        else
-        {
-          System.out.println("ShiftTo(" + too[0] + ")==" +
-          "NaN! - not Bijective Mapping!");
-        }
-      }
+      return mp[0];
     }
-    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++)
+    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)
     {
-      if (mmap[1][i - 1] == -1)
-      {
-        System.out.print(i+"=XXX");
+      return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
+    }
+    return null;
+  }
 
-      }
-      else
-      {
-        System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
-      }
-      if (i % 20==0)
-      {
-        System.out.print("\n");
-      }
-      else
-      {
-        System.out.print(",");
-      }
+  /**
+   * 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];
     }
-    //test range function
-    System.out.print("\nTest locateInFrom\n");
+    return pos;
+  }
+
+  public int[] getMappedWord(int pos)
+  {
+    // TODO not used - remove??
+    int[] mp = shiftFrom(pos);
+    if (mp != null)
     {
-      int f=mmap[0][2],t=mmap[0][3];
-      while (f<t) {
-        System.out.println("Range "+f+" to "+t);
-        int rng[] = ml.locateInFrom(f,t);
-        if (rng!=null)
-        {
-          for (int i=0; i<rng.length; i++) {
-            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        System.out.print("\nReversed\n");
-        rng = ml.locateInFrom(t,f);
-        if (rng!=null)
-        {
-          for (int i=0; i<rng.length; i++) {
-            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        System.out.print("\n");
-        f++;t--;
-      }
+      return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
     }
-    System.out.print("\n");
-    mmap = ml.makeToMap();
-    System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
-        mmap[0][2] + " " + mmap[0][3] + " ");
-    for (int i = 1; i <= mmap[1].length; i++)
+    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)
     {
-      if (mmap[1][i - 1] == -1)
-      {
-        System.out.print(i+"=XXX");
+      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()));
+    }
+  }
 
-      }
-      else
-      {
-        System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
-      }
-      if (i % 20==0)
-      {
-        System.out.print("\n");
-      }
-      else
-      {
-        System.out.print(",");
-      }
+  /**
+   * 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));
     }
-    System.out.print("\n");
-    //test range function
-    System.out.print("\nTest locateInTo\n");
+    sb.append(" ] ");
+    sb.append(fromRatio).append(":").append(toRatio);
+    sb.append(" to [");
+    for (int[] shift : toShifts)
     {
-      int f=mmap[0][2],t=mmap[0][3];
-      while (f<t) {
-        System.out.println("Range "+f+" to "+t);
-        int rng[] = ml.locateInTo(f,t);
-        if (rng!=null) {
-          for (int i=0; i<rng.length; i++) {
-            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        System.out.print("\nReversed\n");
-        rng = ml.locateInTo(t,f);
-        if (rng!=null)
-        {
-          for (int i=0; i<rng.length; i++) {
-            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        f++; t--;
-        System.out.print("\n");
-      }
+      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);
+    }
   }
 
-  public static void main(String argv[])
+  /**
+   * 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)
   {
-    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);
-    MapList ml2 = new MapList(new int[] { 1, 60 },
-        new int[] { 1, 20 }, 3, 1);
-    // test internal consistency
-    int to[] = new int[51];
-    MapList.testMap(ml, 1, 60);
     /*
-      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!
+     * 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()
+  {
+    boolean forwardStrand = true;
+    for (int[] range : getFromRanges())
+    {
+      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);
+  }
+
 }