/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
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= 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]; // last position in fromEnd
int endindx = (fromRatio2 - 1); // additional positions to get to last
// position from endpos
int intv = 0, intvSize = fromShifts2.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 = (int[]) fromShifts2.elementAt(intv++);
if (fe_s > -1)
{
endpos = iv[0]; // start counting from beginning of interval
endindx--; // inclusive of endpos
}
if (iv[0] <= iv[1])
{
if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
{
fs = i;
}
if (endpos >= iv[0] && endpos <= iv[1])
{
if (fe_s == -1)
{
fe_s = i;
}
if (fe_s != -1)
{
if (endpos + endindx <= iv[1])
{
fe = i;
endpos = endpos + endindx; // end of end token is within this
// interval
}
else
{
endindx -= iv[1] - endpos; // skip all this interval too
}
}
}
}
else
{
if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
{
fs = i;
}
if (endpos <= iv[0] && endpos >= iv[1])
{
if (fe_s == -1)
{
fe_s = i;
}
if (fe_s != -1)
{
if (endpos - endindx >= iv[1])
{
fe = i;
endpos = endpos - endindx; // end of end token is within this
// interval
}
else
{
endindx -= endpos - iv[1]; // skip all this interval too
}
}
}
}
i++;
}
if (fs == fe && fe == -1)
return null;
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);
MapList mldna = new MapList(new int[]
{ 2, 2, 6, 8, 12, 16 }, new int[]
{ 1, 3 }, 3, 1);
int[] frm = mldna.locateInFrom(1, 1);
testLocateFrom(mldna, 1, 1, new int[]
{ 2, 2, 6, 7 });
MapList.testMap(mldna, 1, 3);
/*
* 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!
}
private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
{
int[] frm = mldna.locateInFrom(i, j);
if (frm == ks || java.util.Arrays.equals(frm, ks))
{
System.out.println("Success test locate from " + i + " to " + j);
}
else
{
System.err.println("Failed test locate from " + i + " to " + j);
for (int c = 0; c < frm.length; c++)
{
System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
}
System.err.println("Expected");
for (int c = 0; c < ks.length; c++)
{
System.err.print(ks[c] + ((c % 2 == 0) ? "," : ";"));
}
}
}
/**
*
* @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)
{
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()));
}
}
}