From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 28 Jun 2007 19:56:17 +0000 (+0000)
Subject: imported utility classes for working with MapTypes from Jalview (v 2.3+ code)
X-Git-Tag: Release_0.2~100
X-Git-Url: http://source.jalview.org/gitweb/?p=vamsas.git;a=commitdiff_plain;h=ebf96b94c3df53770d7cb8585cb89edff3de075d

imported utility classes for working with MapTypes from Jalview (v 2.3+ code)

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@420 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/uk/ac/vamsas/objects/utils/MapList.java b/src/uk/ac/vamsas/objects/utils/MapList.java
new file mode 100644
index 0000000..5052c94
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/MapList.java
@@ -0,0 +1,810 @@
+/*
+ * This code was originated from
+ * 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
+ * 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.
+ *
+ * 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
+ */
+package uk.ac.vamsas.objects.utils;
+
+import java.util.*;
+
+/**
+ * MapList
+ * 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.
+ */
+public class MapList
+{
+  /* (non-Javadoc)
+   * @see java.lang.Object#equals(java.lang.Object)
+   */
+  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;
+      }
+      return true;
+    }
+    return false;
+  }
+  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
+  
+  /**
+   * 
+   * @return series of intervals mapped in from
+   */
+  public int[] getFromRanges()
+  {
+    return getRanges(fromShifts);
+  }
+  public int[] getToRanges()
+  {
+    return getRanges(toShifts);
+  }
+  
+  private int[] getRanges(Vector shifts)
+  {
+    int[] rnges = new int[2*shifts.size()];
+    Enumeration e = shifts.elements();
+    int i=0;
+    while (e.hasMoreElements())
+    {
+      int r[] = (int[]) e.nextElement();
+      rnges[i++] = r[0];
+      rnges[i++] = r[1];
+    }
+    return rnges;
+  }
+  /**
+   * lowest and highest value in the from Map
+   */
+  int[] fromRange=null;
+  /**
+   * lowest and highest value in the to Map
+   */
+  int[] toRange=null;
+  /**
+   * 
+   * @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 fromRange[0];
+  }
+  public int getFromHighest() {
+    return fromRange[1];
+  }
+  public int getToLowest() {
+    return toRange[0];
+  }
+  public int getToHighest() {
+    return toRange[1];
+  }
+  private void ensureRange(int[] limits, int pos) {
+    if (limits[0]>pos)
+      limits[0]=pos;
+    if (limits[1]<pos)
+      limits[1]=pos;
+  }
+  public MapList(int from[], int to[], int fromRatio, int toRatio)
+  {
+    fromRange=new int[] { from[0],from[1] };
+    toRange=new int[] { to[0],to[1] };
+
+    fromShifts = new Vector();
+    for (int i=0;i<from.length; i+=2)
+    {
+      ensureRange(fromRange, from[i]);
+      ensureRange(fromRange, from[i+1]);
+
+      fromShifts.addElement(new int[]
+                             {from[i], from[i + 1]});
+    }
+    toShifts = new Vector();
+    for (int i=0;i<to.length; i+=2)
+    {
+      ensureRange(toRange, to[i]);
+      ensureRange(toRange, to[i+1]);
+      toShifts.addElement(new int[]
+                           {to[i], to[i + 1]});
+    }
+    this.fromRatio=fromRatio;
+    this.toRatio=toRatio;
+  }
+  public MapList(MapList map)
+  {
+    this.fromRange = new int[]
+    { map.fromRange[0], map.fromRange[1] };
+    this.toRange = new int[]
+    { map.toRange[0], map.toRange[1] };
+    this.fromRatio = map.fromRatio;
+    this.toRatio = map.toRatio;
+    if (map.fromShifts != null)
+    {
+      this.fromShifts = new Vector();
+      Enumeration e = map.fromShifts.elements();
+      while (e.hasMoreElements())
+      {
+        int[] el = (int[]) e.nextElement();
+        fromShifts.addElement(new int[]
+        { el[0], el[1] });
+      }
+    }
+    if (map.toShifts != null)
+    {
+      this.toShifts = new Vector();
+      Enumeration e = map.toShifts.elements();
+      while (e.hasMoreElements())
+      {
+        int[] el = (int[]) e.nextElement();
+        toShifts.addElement(new int[]
+        { el[0], el[1] });
+      }
+    }
+  }
+  /**
+   * get all mapped positions from 'from' to 'to'
+   * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
+   */
+  public int[][] makeFromMap()
+  {
+    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()
+  {
+    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
+   */
+  private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
+      int toRatio)
+  {
+    int iv=0,ivSize = intVals.size();
+    if (iv>=ivSize)
+    {
+      return null;
+    }
+    int[] intv=(int[]) intVals.elementAt(iv++);
+    int from=intv[0],to=intv[1];
+    if (from > to)
+    {
+      from = intv[1];
+      to=intv[0];
+    }
+    while (iv<ivSize)
+    {
+      intv = (int[]) intVals.elementAt(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++)
+    {
+      int[] m = shift(i+from,intVals,ratio,toIntVals, 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 pos int
+   * @return int shifted position in To, frameshift in From, direction of mapped symbol in To
+   */
+  public int[] shiftFrom(int pos)
+  {
+    return shift(pos, 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 pos)
+  {
+    return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
+  }
+  /**
+   *
+   * @param fromShifts
+   * @param fromRatio
+   * @param toShifts
+   * @param toRatio
+   * @return
+   */
+  private int[] shift(int pos, Vector fromShifts, int fromRatio,
+      Vector toShifts, int toRatio)
+  {
+    int[] fromCount = countPos(fromShifts, 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)
+    {
+      return null; // throw new Error("Bad Mapping!");
+    }
+    //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 pos
+   * @return number of positions or null if pos is not within intervals
+   */
+  private int[] countPos(Vector intVals, int pos)
+  {
+    int count=0,intv[],iv=0,ivSize=intVals.size();
+    while (iv<ivSize)
+    {
+      intv = (int[])intVals.elementAt(iv++);
+      if (intv[0] <= intv[1])
+      {
+        if (pos >= intv[0] && pos <= intv[1])
+        {
+          return new int[]
+                         {
+              count + pos - intv[0] + 1, +1};
+        }
+        else
+        {
+          count+=intv[1]-intv[0]+1;
+        }
+      }
+      else
+      {
+        if (pos >= intv[1] && pos <= intv[0])
+        {
+          return new int[]
+                         {
+              count + intv[0] - pos + 1, -1};
+        }
+        else
+        {
+          count+=intv[0]-intv[1]+1;
+        }
+      }
+    }
+    return null;
+  }
+  /**
+   * count out pos positions into a series of intervals and return the position
+   * @param intVals
+   * @param pos
+   * @return position pos in interval set
+   */
+  private int[] countToPos(Vector intVals, int pos)
+  {
+    int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
+    {
+        0, 0};
+    while (iv<ivSize)
+    {
+      intv = (int[])intVals.elementAt(iv++);
+      diff = intv[1]-intv[0];
+      if (diff >= 0)
+      {
+        if (pos <= count + 1 + diff)
+        {
+          return new int[]
+                         {
+              pos - count - 1 + intv[0], +1};
+        }
+        else
+        {
+          count+=1+diff;
+        }
+      }
+      else
+      {
+        if (pos <= count + 1 - diff)
+        {
+          return new int[]
+                         {
+              intv[0] - (pos - count - 1), -1};
+        }
+        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 in to map
+   * @param end position in to map
+   * @return series of ranges in from map
+   */
+  public int[] locateInFrom(int start, int end) {
+    // inefficient implementation
+    int fromStart[] = shiftTo(start);
+    int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol position
+    if (fromStart==null || fromEnd==null)
+      return null;
+    int iv[] = getIntervals(fromShifts, fromStart, fromEnd,fromRatio);
+    return iv;
+  }
+
+  /**
+   * 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
+   */
+  public int[] locateInTo(int start, int end) {
+    // inefficient implementation
+    int toStart[] = shiftFrom(start);
+    int toEnd[] = shiftFrom(end);
+    if (toStart==null || toEnd==null)
+      return null;
+    int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
+    return iv;
+  }
+  /**
+   * like shift - except returns the intervals in the given vector of shifts which were spanned
+   * in traversing fromStart to fromEnd
+   * @param fromShifts2
+   * @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
+   */
+  private int[] getIntervals(Vector fromShifts2, int[] fromStart, int[] fromEnd, int fromRatio2)
+  {
+    int startpos,endpos;
+    startpos = fromStart[0]; // first position in fromStart 
+    endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1); // last position in fromEnd
+    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]) {
+          fs = i;
+        }
+        if (fe==-1 && endpos>=iv[0] && endpos<=iv[1]) {
+          fe = i;
+        }
+      } else {
+        if (fs==-1 && startpos<=iv[0] && startpos>=iv[1]) {
+          fs = i;
+        }
+        if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
+          fe = i;
+        }
+      }
+      i++;
+    }
+    if (fs==fe && fe==-1)
+      return null;
+    Vector ranges=new Vector();
+    if (fs<=fe) {
+      intv = fs;
+      i=fs;
+      // truncate initial interval
+      iv = (int[]) fromShifts2.elementAt(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
+        i++;
+      }
+      if (i==fe)
+        iv[1] = endpos;
+      ranges.addElement(iv); // add only - or final range
+    } else {
+      // walk from end of interval.
+      i=fromShifts2.size()-1;
+      while (i>fs) {
+        i--;
+      }
+      iv = (int[]) fromShifts2.elementAt(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.addElement(iv); // add (truncated) reversed interval
+        iv = (int[]) fromShifts2.elementAt(i);
+        iv = new int[] { iv[1], iv[0] }; // reverse and clone
+      }
+      if (i==fe) {
+        // interval is already reversed
+        iv[1] = endpos;
+      }
+      ranges.addElement(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 = (int[]) ranges.elementAt(intv);
+        range[i++] = iv[0];
+        range[i++] = iv[1];
+        ranges.setElementAt(null, intv++); // 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)
+{
+  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) {
+  int[] mp = shiftFrom(pos);
+  if (mp!=null)
+  {
+    return mp[0];
+  }
+  return pos;
+}
+public int[] getMappedWord(int pos) {
+  int[] mp = shiftFrom(pos);
+  if (mp!=null)
+  {
+    return new int[] { mp[0], mp[0]+mp[2]*(getToRatio()-1)};
+  }
+  return null;
+}
+
+  /**
+   * test routine. not incremental.
+   * @param ml
+   * @param fromS
+   * @param fromE
+   */
+  public static void testMap(MapList ml, int fromS, int fromE)
+  {
+    for (int from = 1; from <= 25; from++)
+    {
+      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!");
+        }
+      }
+    }
+    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++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
+        System.out.print(i+"=XXX");
+
+      }
+      else
+      {
+        System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
+      }
+      if (i % 20==0)
+      {
+        System.out.print("\n");
+      }
+      else
+      {
+        System.out.print(",");
+      }
+    }
+    //test range function
+    System.out.print("\nTest locateInFrom\n");
+    {
+      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--;
+      }
+    }
+    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++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
+        System.out.print(i+"=XXX");
+
+      }
+      else
+      {
+        System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
+      }
+      if (i % 20==0)
+      {
+        System.out.print("\n");
+      }
+      else
+      {
+        System.out.print(",");
+      }
+    }
+    System.out.print("\n");
+    //test range function
+    System.out.print("\nTest locateInTo\n");
+    {
+      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");
+      }
+    }
+
+  }
+
+  public static void main(String argv[])
+  {
+    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!
+  }
+  /**
+   * 
+   * @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());
+  }
+}
diff --git a/src/uk/ac/vamsas/objects/utils/Mapping.java b/src/uk/ac/vamsas/objects/utils/Mapping.java
new file mode 100644
index 0000000..b592c8c
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/Mapping.java
@@ -0,0 +1,386 @@
+package uk.ac.vamsas.objects.utils;
+/*
+ * This code was originated from
+ * 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
+ * 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.
+ *
+ * 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
+ */
+
+import java.util.Vector;
+
+public class Mapping
+{
+  /**
+   * Contains the start-end pairs mapping from the associated sequence to the
+   * sequence in the database coordinate system it also takes care of step
+   * difference between coordinate systems
+   */
+  MapList map = null;
+
+  /**
+   * The seuqence that map maps the associated seuqence to (if any).
+  SequenceI to = null;
+  */
+  public Mapping(MapList map)
+  {
+    super();
+    this.map = map;
+  }
+
+/*  public Mapping(SequenceI to, MapList map)
+  {
+    this(map);
+    this.to = to;
+  }
+*/
+  /**
+   * create a new mapping from
+   * 
+   *  (in Jalview) param to was
+   *          the destination sequence being mapped
+   * @param local
+   *          int[] {start,end,start,end} series on associated sequence
+   * @param mapped
+   *          int[] {start,end,...} ranges on the reference frame being mapped
+   *          to
+   * @param i
+   *          step size on associated sequence
+   * @param j
+   *          step size on mapped frame
+   */
+  public Mapping(//SequenceI to, 
+      int[] local, int[] mapped, int i, int j)
+  {
+    this(new MapList(local, mapped, i, j));
+  }
+
+  /**
+   * create a duplicate (and independent) mapping object with the same reference
+   * to any SequenceI being mapped to.
+   * 
+   * @param map2
+   */
+  public Mapping(Mapping map2)
+  {
+    if (map2 != this && map2 != null)
+    {
+      if (map2.map != null)
+      {
+        map = new MapList(map2.map);
+      }
+    }
+  }
+
+  /**
+   * @return the map
+   */
+  public MapList getMap()
+  {
+    return map;
+  }
+
+  /**
+   * @param map
+   *          the map to set
+   */
+  public void setMap(MapList map)
+  {
+    this.map = map;
+  }
+
+  /**
+   * Equals that compares both the to references and MapList mappings.
+   * 
+   * @param other
+   * @return
+   */
+  public boolean equals(Mapping other)
+  {
+    if (other == null)
+      return false;
+    if (other == this)
+      return true;
+    if ((map != null && other.map == null)
+            || (map == null && other.map != null))
+      return false;
+    if (map.equals(other.map))
+      return true;
+    return false;
+  }
+
+  /**
+   * get the 'initial' position in the associated sequence for a position in the
+   * mapped reference frame
+   * 
+   * @param mpos
+   * @return
+   */
+  public int getPosition(int mpos)
+  {
+    if (map != null)
+    {
+      int[] mp = map.shiftTo(mpos);
+      if (mp != null)
+      {
+        return mp[0];
+      }
+    }
+    return mpos;
+  }
+
+  /**
+   * gets boundary in direction of mapping
+   * 
+   * @param position
+   *          in mapped reference frame
+   * @return int{start, end} positions in associated sequence (in direction of
+   *         mapped word)
+   */
+  public int[] getWord(int mpos)
+  {
+    if (map != null)
+    {
+      return map.getToWord(mpos);
+    }
+    return null;
+  }
+
+  /**
+   * width of mapped unit in associated sequence
+   * 
+   */
+  public int getWidth()
+  {
+    if (map != null)
+    {
+      return map.getFromRatio();
+    }
+    return 1;
+  }
+
+  /**
+   * width of unit in mapped reference frame
+   * 
+   * @return
+   */
+  public int getMappedWidth()
+  {
+    if (map != null)
+    {
+      return map.getToRatio();
+    }
+    return 1;
+  }
+
+  /**
+   * get mapped position in the associated reference frame for position pos in
+   * the associated sequence.
+   * 
+   * @param pos
+   * @return
+   */
+  public int getMappedPosition(int pos)
+  {
+    if (map != null)
+    {
+      int[] mp = map.shiftFrom(pos);
+      if (mp != null)
+      {
+        return mp[0];
+      }
+    }
+    return pos;
+  }
+
+  public int[] getMappedWord(int pos)
+  {
+    if (map != null)
+    {
+      int[] mp = map.shiftFrom(pos);
+      if (mp != null)
+      {
+        return new int[]
+        { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
+      }
+    }
+    return null;
+  }
+
+  /**
+   * locates the region of feature f in the associated (local) sequence's reference
+   * frame
+   * 
+   * @param f
+   * @return int[] { start1, end1, ... starti, endi } for the corresponding interval in local reference frame
+   */
+  public int[] locateFeature(int begin, int end)
+  {
+    if (true)
+    { // f.getBegin()!=f.getEnd()) {
+      if (map != null)
+      {
+        int[] frange = map.locateInFrom(begin, end); //f.getBegin(), f.getEnd());
+        /* left in as an example as to how this is used in Jalview
+         * SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
+        for (int i = 0, v = 0; i < frange.length; i += 2, v++)
+        {
+          vf[v] = new SequenceFeature(f);
+          vf[v].setBegin(frange[i]);
+          vf[v].setEnd(frange[i + 1]);
+          if (frange.length > 2)
+            vf[v].setDescription(f.getDescription() + "\nPart " + v);
+        }
+        */
+        return frange;
+      }
+    }
+    // give up and just return the interval unchanged - this might not be the correct behaviour
+    return new int[] { begin, end };
+  }
+
+  /**
+   * return a series of contigs on the associated sequence corresponding to the
+   * from,to interval on the mapped reference frame
+   * 
+   * @param from
+   * @param to
+   * @return int[] { from_i, to_i for i=1 to n contiguous regions in the
+   *         associated sequence}
+   */
+  public int[] locateRange(int from, int to)
+  {
+    if (map != null)
+    {
+      if (from <= to)
+      {
+        from = (map.getToLowest() < from) ? from : map.getToLowest();
+        to = (map.getToHighest() > to) ? to : map.getToHighest();
+        if (from > to)
+          return null;
+      }
+      else
+      {
+        from = (map.getToHighest() > from) ? from : map.getToHighest();
+        to = (map.getToLowest() < to) ? to : map.getToLowest();
+        if (from < to)
+          return null;
+      }
+      return map.locateInFrom(from, to);
+    }
+    return new int[]
+    { from, to };
+  }
+
+  /**
+   * return a series of mapped contigs mapped from a range on the associated
+   * sequence
+   * 
+   * @param from
+   * @param to
+   * @return
+   */
+  public int[] locateMappedRange(int from, int to)
+  {
+    if (map != null)
+    {
+
+      if (from <= to)
+      {
+        from = (map.getFromLowest() < from) ? from : map.getFromLowest();
+        to = (map.getFromHighest() > to) ? to : map.getFromHighest();
+        if (from > to)
+          return null;
+      }
+      else
+      {
+        from = (map.getFromHighest() > from) ? from : map.getFromHighest();
+        to = (map.getFromLowest() < to) ? to : map.getFromLowest();
+        if (from < to)
+          return null;
+      }
+      return map.locateInTo(from, to);
+    }
+    return new int[]
+    { from, to };
+  }
+
+  /**
+   * return a new mapping object with a maplist modifed to only map the visible
+   * regions defined by viscontigs.
+   * 
+   * @param viscontigs
+   * @return
+   */
+  public Mapping intersectVisContigs(int[] viscontigs)
+  {
+    Mapping copy = new Mapping(this);
+    if (map != null)
+    {
+      Vector toRange = new Vector();
+      Vector fromRange = new Vector();
+      for (int vc = 0; vc < viscontigs.length; vc += 2)
+      {
+        // find a mapped range in this visible region
+        int[] mpr = locateMappedRange(1+viscontigs[vc], viscontigs[vc + 1]-1);
+        if (mpr != null)
+        {
+          for (int m = 0; m < mpr.length; m += 2)
+          {
+            toRange.addElement(new int[]
+            { mpr[m], mpr[m + 1] });
+            int[] xpos = locateRange(mpr[m], mpr[m + 1]);
+            for (int x = 0; x < xpos.length; x += 2)
+            {
+              fromRange.addElement(new int[]
+              { xpos[x], xpos[x + 1] });
+            }
+          }
+        }
+      }
+      int[] from = new int[fromRange.size()*2];
+      int[] to = new int[toRange.size()*2];
+      int[] r;
+      for (int f=0,fSize=fromRange.size(); f<fSize; f++)
+      {
+        r = (int[]) fromRange.elementAt(f);
+        from[f*2] = r[0];
+        from[f*2+1] = r[1];
+      }
+      for (int f=0,fSize=toRange.size(); f<fSize; f++)
+      {
+        r = (int[]) toRange.elementAt(f);
+        to[f*2] = r[0];
+        to[f*2+1] = r[1];
+      }
+      copy.setMap(new MapList(from, to, map.getFromRatio(), map.getToRatio()));
+    }
+    return copy;
+  }
+  public static void main(String[] args)
+  {
+    /**
+     * trite test of the intersectVisContigs method
+     * for a simple DNA -> Protein exon map and a range of visContigs
+     */
+    MapList fk = new MapList(new int[] { 1,6,8,13,15,23}, new int[] { 1,7}, 3, 1);
+    Mapping m = new Mapping(fk);
+    Mapping m_1 = m.intersectVisContigs(new int[] {fk.getFromLowest(), fk.getFromHighest()});
+    Mapping m_2 = m.intersectVisContigs(new int[] {1,7,11,20});
+    System.out.println(""+m_1.map.getFromRanges());
+    // this test was for debugging purposes only - it should run without exceptions, but the
+    // integrity of the mapping was checked using an interactive debugger rather than programmatically.
+  }
+}