-/*
- * 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());
- }
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.objects.utils;\r
+\r
+import java.util.*;\r
+\r
+/**\r
+ * MapList Simple way of bijectively mapping a non-contiguous linear range to\r
+ * another non-contiguous linear range Use at your own risk! TODO: efficient\r
+ * implementation of private posMap method TODO: test/ensure that sense of from\r
+ * and to ratio start position is conserved (codon start position recovery)\r
+ * TODO: optimize to use int[][] arrays rather than vectors.\r
+ */\r
+public class MapList {\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see java.lang.Object#equals(java.lang.Object)\r
+ */\r
+ public boolean equals(MapList obj) {\r
+ if (obj == this)\r
+ return true;\r
+ if (obj != null && obj.fromRatio == fromRatio && obj.toRatio == toRatio\r
+ && obj.fromShifts != null && obj.toShifts != null) {\r
+ int i, iSize = fromShifts.size(), j, jSize = obj.fromShifts.size();\r
+ if (iSize != jSize)\r
+ return false;\r
+ for (i = 0, iSize = fromShifts.size(), j = 0, jSize = obj.fromShifts\r
+ .size(); i < iSize;) {\r
+ int[] mi = (int[]) fromShifts.elementAt(i++);\r
+ int[] mj = (int[]) obj.fromShifts.elementAt(j++);\r
+ if (mi[0] != mj[0] || mi[1] != mj[1])\r
+ return false;\r
+ }\r
+ iSize = toShifts.size();\r
+ jSize = obj.toShifts.size();\r
+ if (iSize != jSize)\r
+ return false;\r
+ for (i = 0, j = 0; i < iSize;) {\r
+ int[] mi = (int[]) toShifts.elementAt(i++);\r
+ int[] mj = (int[]) obj.toShifts.elementAt(j++);\r
+ if (mi[0] != mj[0] || mi[1] != mj[1])\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ public Vector fromShifts;\r
+\r
+ public Vector toShifts;\r
+\r
+ int fromRatio; // number of steps in fromShifts to one toRatio unit\r
+\r
+ int toRatio; // number of steps in toShifts to one fromRatio\r
+\r
+ /**\r
+ * \r
+ * @return series of intervals mapped in from\r
+ */\r
+ public int[] getFromRanges() {\r
+ return getRanges(fromShifts);\r
+ }\r
+\r
+ public int[] getToRanges() {\r
+ return getRanges(toShifts);\r
+ }\r
+\r
+ private int[] getRanges(Vector shifts) {\r
+ int[] rnges = new int[2 * shifts.size()];\r
+ Enumeration e = shifts.elements();\r
+ int i = 0;\r
+ while (e.hasMoreElements()) {\r
+ int r[] = (int[]) e.nextElement();\r
+ rnges[i++] = r[0];\r
+ rnges[i++] = r[1];\r
+ }\r
+ return rnges;\r
+ }\r
+\r
+ /**\r
+ * lowest and highest value in the from Map\r
+ */\r
+ int[] fromRange = null;\r
+\r
+ /**\r
+ * lowest and highest value in the to Map\r
+ */\r
+ int[] toRange = null;\r
+\r
+ /**\r
+ * \r
+ * @return length of mapped phrase in from\r
+ */\r
+ public int getFromRatio() {\r
+ return fromRatio;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return length of mapped phrase in to\r
+ */\r
+ public int getToRatio() {\r
+ return toRatio;\r
+ }\r
+\r
+ public int getFromLowest() {\r
+ return fromRange[0];\r
+ }\r
+\r
+ public int getFromHighest() {\r
+ return fromRange[1];\r
+ }\r
+\r
+ public int getToLowest() {\r
+ return toRange[0];\r
+ }\r
+\r
+ public int getToHighest() {\r
+ return toRange[1];\r
+ }\r
+\r
+ private void ensureRange(int[] limits, int pos) {\r
+ if (limits[0] > pos)\r
+ limits[0] = pos;\r
+ if (limits[1] < pos)\r
+ limits[1] = pos;\r
+ }\r
+\r
+ public MapList(int from[], int to[], int fromRatio, int toRatio) {\r
+ fromRange = new int[] { from[0], from[1] };\r
+ toRange = new int[] { to[0], to[1] };\r
+\r
+ fromShifts = new Vector();\r
+ for (int i = 0; i < from.length; i += 2) {\r
+ ensureRange(fromRange, from[i]);\r
+ ensureRange(fromRange, from[i + 1]);\r
+\r
+ fromShifts.addElement(new int[] { from[i], from[i + 1] });\r
+ }\r
+ toShifts = new Vector();\r
+ for (int i = 0; i < to.length; i += 2) {\r
+ ensureRange(toRange, to[i]);\r
+ ensureRange(toRange, to[i + 1]);\r
+ toShifts.addElement(new int[] { to[i], to[i + 1] });\r
+ }\r
+ this.fromRatio = fromRatio;\r
+ this.toRatio = toRatio;\r
+ }\r
+\r
+ public MapList(MapList map) {\r
+ this.fromRange = new int[] { map.fromRange[0], map.fromRange[1] };\r
+ this.toRange = new int[] { map.toRange[0], map.toRange[1] };\r
+ this.fromRatio = map.fromRatio;\r
+ this.toRatio = map.toRatio;\r
+ if (map.fromShifts != null) {\r
+ this.fromShifts = new Vector();\r
+ Enumeration e = map.fromShifts.elements();\r
+ while (e.hasMoreElements()) {\r
+ int[] el = (int[]) e.nextElement();\r
+ fromShifts.addElement(new int[] { el[0], el[1] });\r
+ }\r
+ }\r
+ if (map.toShifts != null) {\r
+ this.toShifts = new Vector();\r
+ Enumeration e = map.toShifts.elements();\r
+ while (e.hasMoreElements()) {\r
+ int[] el = (int[]) e.nextElement();\r
+ toShifts.addElement(new int[] { el[0], el[1] });\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * get all mapped positions from 'from' to 'to'\r
+ * \r
+ * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int\r
+ * [fromFinish-fromStart+2] { toStart..toFinish mappings}}\r
+ */\r
+ public int[][] makeFromMap() {\r
+ return posMap(fromShifts, fromRatio, toShifts, toRatio);\r
+ }\r
+\r
+ /**\r
+ * get all mapped positions from 'to' to 'from'\r
+ * \r
+ * @return int[to position]=position mapped in from\r
+ */\r
+ public int[][] makeToMap() {\r
+ return posMap(toShifts, toRatio, fromShifts, fromRatio);\r
+ }\r
+\r
+ /**\r
+ * construct an int map for intervals in intVals\r
+ * \r
+ * @param intVals\r
+ * @return int[] { from, to pos in range }, int[range.to-range.from+1]\r
+ * returning mapped position\r
+ */\r
+ private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,\r
+ int toRatio) {\r
+ int iv = 0, ivSize = intVals.size();\r
+ if (iv >= ivSize) {\r
+ return null;\r
+ }\r
+ int[] intv = (int[]) intVals.elementAt(iv++);\r
+ int from = intv[0], to = intv[1];\r
+ if (from > to) {\r
+ from = intv[1];\r
+ to = intv[0];\r
+ }\r
+ while (iv < ivSize) {\r
+ intv = (int[]) intVals.elementAt(iv++);\r
+ if (intv[0] < from) {\r
+ from = intv[0];\r
+ }\r
+ if (intv[1] < from) {\r
+ from = intv[1];\r
+ }\r
+ if (intv[0] > to) {\r
+ to = intv[0];\r
+ }\r
+ if (intv[1] > to) {\r
+ to = intv[1];\r
+ }\r
+ }\r
+ int tF = 0, tT = 0;\r
+ int mp[][] = new int[to - from + 2][];\r
+ for (int i = 0; i < mp.length; i++) {\r
+ int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);\r
+ if (m != null) {\r
+ if (i == 0) {\r
+ tF = tT = m[0];\r
+ } else {\r
+ if (m[0] < tF) {\r
+ tF = m[0];\r
+ }\r
+ if (m[0] > tT) {\r
+ tT = m[0];\r
+ }\r
+ }\r
+ }\r
+ mp[i] = m;\r
+ }\r
+ int[][] map = new int[][] { new int[] { from, to, tF, tT },\r
+ new int[to - from + 2] };\r
+\r
+ map[0][2] = tF;\r
+ map[0][3] = tT;\r
+\r
+ for (int i = 0; i < mp.length; i++) {\r
+ if (mp[i] != null) {\r
+ map[1][i] = mp[i][0] - tF;\r
+ } else {\r
+ map[1][i] = -1; // indicates an out of range mapping\r
+ }\r
+ }\r
+ return map;\r
+ }\r
+\r
+ /**\r
+ * addShift\r
+ * \r
+ * @param pos\r
+ * start position for shift (in original reference frame)\r
+ * @param shift\r
+ * length of shift\r
+ * \r
+ * public void addShift(int pos, int shift) { int sidx = 0; int[]\r
+ * rshift=null; while (sidx<shifts.size() && (rshift=(int[])\r
+ * shifts.elementAt(sidx))[0]<pos) sidx++; if (sidx==shifts.size())\r
+ * shifts.insertElementAt(new int[] { pos, shift}, sidx); else\r
+ * rshift[1]+=shift; }\r
+ */\r
+ /**\r
+ * shift from pos to To(pos)\r
+ * \r
+ * @param pos\r
+ * int\r
+ * @return int shifted position in To, frameshift in From, direction of mapped\r
+ * symbol in To\r
+ */\r
+ public int[] shiftFrom(int pos) {\r
+ return shift(pos, fromShifts, fromRatio, toShifts, toRatio);\r
+ }\r
+\r
+ /**\r
+ * inverse of shiftFrom - maps pos in To to a position in From\r
+ * \r
+ * @param pos\r
+ * (in To)\r
+ * @return shifted position in From, frameshift in To, direction of mapped\r
+ * symbol in From\r
+ */\r
+ public int[] shiftTo(int pos) {\r
+ return shift(pos, toShifts, toRatio, fromShifts, fromRatio);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param fromShifts\r
+ * @param fromRatio\r
+ * @param toShifts\r
+ * @param toRatio\r
+ * @return\r
+ */\r
+ private int[] shift(int pos, Vector fromShifts, int fromRatio,\r
+ Vector toShifts, int toRatio) {\r
+ int[] fromCount = countPos(fromShifts, pos);\r
+ if (fromCount == null) {\r
+ return null;\r
+ }\r
+ int fromRemainder = (fromCount[0] - 1) % fromRatio;\r
+ int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);\r
+ int[] toPos = countToPos(toShifts, toCount);\r
+ if (toPos == null) {\r
+ return null; // throw new Error("Bad Mapping!");\r
+ }\r
+ // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);\r
+ return new int[] { toPos[0], fromRemainder, toPos[1] };\r
+ }\r
+\r
+ /**\r
+ * count how many positions pos is along the series of intervals.\r
+ * \r
+ * @param intVals\r
+ * @param pos\r
+ * @return number of positions or null if pos is not within intervals\r
+ */\r
+ private int[] countPos(Vector intVals, int pos) {\r
+ int count = 0, intv[], iv = 0, ivSize = intVals.size();\r
+ while (iv < ivSize) {\r
+ intv = (int[]) intVals.elementAt(iv++);\r
+ if (intv[0] <= intv[1]) {\r
+ if (pos >= intv[0] && pos <= intv[1]) {\r
+ return new int[] { count + pos - intv[0] + 1, +1 };\r
+ } else {\r
+ count += intv[1] - intv[0] + 1;\r
+ }\r
+ } else {\r
+ if (pos >= intv[1] && pos <= intv[0]) {\r
+ return new int[] { count + intv[0] - pos + 1, -1 };\r
+ } else {\r
+ count += intv[0] - intv[1] + 1;\r
+ }\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * count out pos positions into a series of intervals and return the position\r
+ * \r
+ * @param intVals\r
+ * @param pos\r
+ * @return position pos in interval set\r
+ */\r
+ private int[] countToPos(Vector intVals, int pos) {\r
+ int count = 0, diff = 0, iv = 0, ivSize = intVals.size(), intv[] = { 0, 0 };\r
+ while (iv < ivSize) {\r
+ intv = (int[]) intVals.elementAt(iv++);\r
+ diff = intv[1] - intv[0];\r
+ if (diff >= 0) {\r
+ if (pos <= count + 1 + diff) {\r
+ return new int[] { pos - count - 1 + intv[0], +1 };\r
+ } else {\r
+ count += 1 + diff;\r
+ }\r
+ } else {\r
+ if (pos <= count + 1 - diff) {\r
+ return new int[] { intv[0] - (pos - count - 1), -1 };\r
+ } else {\r
+ count += 1 - diff;\r
+ }\r
+ }\r
+ }\r
+ return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);\r
+ }\r
+\r
+ /**\r
+ * find series of intervals mapping from start-end in the From map.\r
+ * \r
+ * @param start\r
+ * position in to map\r
+ * @param end\r
+ * position in to map\r
+ * @return series of ranges in from map\r
+ */\r
+ public int[] locateInFrom(int start, int end) {\r
+ // inefficient implementation\r
+ int fromStart[] = shiftTo(start);\r
+ int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol\r
+ // position\r
+ if (fromStart == null || fromEnd == null)\r
+ return null;\r
+ int iv[] = getIntervals(fromShifts, fromStart, fromEnd, fromRatio);\r
+ return iv;\r
+ }\r
+\r
+ /**\r
+ * find series of intervals mapping from start-end in the to map.\r
+ * \r
+ * @param start\r
+ * position in from map\r
+ * @param end\r
+ * position in from map\r
+ * @return series of ranges in to map\r
+ */\r
+ public int[] locateInTo(int start, int end) {\r
+ // inefficient implementation\r
+ int toStart[] = shiftFrom(start);\r
+ int toEnd[] = shiftFrom(end);\r
+ if (toStart == null || toEnd == null)\r
+ return null;\r
+ int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);\r
+ return iv;\r
+ }\r
+\r
+ /**\r
+ * like shift - except returns the intervals in the given vector of shifts\r
+ * which were spanned in traversing fromStart to fromEnd\r
+ * \r
+ * @param fromShifts2\r
+ * @param fromStart\r
+ * @param fromEnd\r
+ * @param fromRatio2\r
+ * @return series of from,to intervals from from first position of starting\r
+ * region to final position of ending region inclusive\r
+ */\r
+ private int[] getIntervals(Vector fromShifts2, int[] fromStart,\r
+ int[] fromEnd, int fromRatio2) {\r
+ int startpos, endpos;\r
+ startpos = fromStart[0]; // first position in fromStart\r
+ endpos = fromEnd[0] + fromEnd[2] * (fromRatio2 - 1); // last position in\r
+ // fromEnd\r
+ int intv = 0, intvSize = fromShifts2.size();\r
+ int iv[], i = 0, fs = -1, fe = -1; // containing intervals\r
+ while (intv < intvSize && (fs == -1 || fe == -1)) {\r
+ iv = (int[]) fromShifts2.elementAt(intv++);\r
+ if (iv[0] <= iv[1]) {\r
+ if (fs == -1 && startpos >= iv[0] && startpos <= iv[1]) {\r
+ fs = i;\r
+ }\r
+ if (fe == -1 && endpos >= iv[0] && endpos <= iv[1]) {\r
+ fe = i;\r
+ }\r
+ } else {\r
+ if (fs == -1 && startpos <= iv[0] && startpos >= iv[1]) {\r
+ fs = i;\r
+ }\r
+ if (fe == -1 && endpos <= iv[0] && endpos >= iv[1]) {\r
+ fe = i;\r
+ }\r
+ }\r
+ i++;\r
+ }\r
+ if (fs == fe && fe == -1)\r
+ return null;\r
+ Vector ranges = new Vector();\r
+ if (fs <= fe) {\r
+ intv = fs;\r
+ i = fs;\r
+ // truncate initial interval\r
+ iv = (int[]) fromShifts2.elementAt(intv++);\r
+ iv = new int[] { iv[0], iv[1] };// clone\r
+ if (i == fs)\r
+ iv[0] = startpos;\r
+ while (i != fe) {\r
+ ranges.addElement(iv); // add initial range\r
+ iv = (int[]) fromShifts2.elementAt(intv++); // get next interval\r
+ iv = new int[] { iv[0], iv[1] };// clone\r
+ i++;\r
+ }\r
+ if (i == fe)\r
+ iv[1] = endpos;\r
+ ranges.addElement(iv); // add only - or final range\r
+ } else {\r
+ // walk from end of interval.\r
+ i = fromShifts2.size() - 1;\r
+ while (i > fs) {\r
+ i--;\r
+ }\r
+ iv = (int[]) fromShifts2.elementAt(i);\r
+ iv = new int[] { iv[1], iv[0] };// reverse and clone\r
+ // truncate initial interval\r
+ if (i == fs) {\r
+ iv[0] = startpos;\r
+ }\r
+ while (--i != fe) { // fix apparent logic bug when fe==-1\r
+ ranges.addElement(iv); // add (truncated) reversed interval\r
+ iv = (int[]) fromShifts2.elementAt(i);\r
+ iv = new int[] { iv[1], iv[0] }; // reverse and clone\r
+ }\r
+ if (i == fe) {\r
+ // interval is already reversed\r
+ iv[1] = endpos;\r
+ }\r
+ ranges.addElement(iv); // add only - or final range\r
+ }\r
+ // create array of start end intervals.\r
+ int[] range = null;\r
+ if (ranges != null && ranges.size() > 0) {\r
+ range = new int[ranges.size() * 2];\r
+ intv = 0;\r
+ intvSize = ranges.size();\r
+ i = 0;\r
+ while (intv < intvSize) {\r
+ iv = (int[]) ranges.elementAt(intv);\r
+ range[i++] = iv[0];\r
+ range[i++] = iv[1];\r
+ ranges.setElementAt(null, intv++); // remove\r
+ }\r
+ }\r
+ return range;\r
+ }\r
+\r
+ /**\r
+ * get the 'initial' position of mpos in To\r
+ * \r
+ * @param mpos\r
+ * position in from\r
+ * @return position of first word in to reference frame\r
+ */\r
+ public int getToPosition(int mpos) {\r
+ int[] mp = shiftTo(mpos);\r
+ if (mp != null) {\r
+ return mp[0];\r
+ }\r
+ return mpos;\r
+ }\r
+\r
+ /**\r
+ * get range of positions in To frame for the mpos word in From\r
+ * \r
+ * @param mpos\r
+ * position in From\r
+ * @return null or int[] first position in To for mpos, last position in to\r
+ * for Mpos\r
+ */\r
+ public int[] getToWord(int mpos) {\r
+ int[] mp = shiftTo(mpos);\r
+ if (mp != null) {\r
+ return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get From position in the associated reference frame for position pos in the\r
+ * associated sequence.\r
+ * \r
+ * @param pos\r
+ * @return\r
+ */\r
+ public int getMappedPosition(int pos) {\r
+ int[] mp = shiftFrom(pos);\r
+ if (mp != null) {\r
+ return mp[0];\r
+ }\r
+ return pos;\r
+ }\r
+\r
+ public int[] getMappedWord(int pos) {\r
+ int[] mp = shiftFrom(pos);\r
+ if (mp != null) {\r
+ return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * test routine. not incremental.\r
+ * \r
+ * @param ml\r
+ * @param fromS\r
+ * @param fromE\r
+ */\r
+ public static void testMap(MapList ml, int fromS, int fromE) {\r
+ for (int from = 1; from <= 25; from++) {\r
+ int[] too = ml.shiftFrom(from);\r
+ System.out.print("ShiftFrom(" + from + ")==");\r
+ if (too == null) {\r
+ System.out.print("NaN\n");\r
+ } else {\r
+ System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");\r
+ System.out.print("\t+--+\t");\r
+ int[] toofrom = ml.shiftTo(too[0]);\r
+ if (toofrom != null) {\r
+ if (toofrom[0] != from) {\r
+ System.err.println("Mapping not reflexive:" + from + " " + too[0]\r
+ + "->" + toofrom[0]);\r
+ }\r
+ System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % "\r
+ + toofrom[1] + " (" + toofrom[2] + ")");\r
+ } else {\r
+ System.out.println("ShiftTo(" + too[0] + ")=="\r
+ + "NaN! - not Bijective Mapping!");\r
+ }\r
+ }\r
+ }\r
+ int mmap[][] = ml.makeFromMap();\r
+ System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "\r
+ + mmap[0][2] + " " + mmap[0][3] + " ");\r
+ for (int i = 1; i <= mmap[1].length; i++) {\r
+ if (mmap[1][i - 1] == -1) {\r
+ System.out.print(i + "=XXX");\r
+\r
+ } else {\r
+ System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));\r
+ }\r
+ if (i % 20 == 0) {\r
+ System.out.print("\n");\r
+ } else {\r
+ System.out.print(",");\r
+ }\r
+ }\r
+ // test range function\r
+ System.out.print("\nTest locateInFrom\n");\r
+ {\r
+ int f = mmap[0][2], t = mmap[0][3];\r
+ while (f <= t) {\r
+ System.out.println("Range " + f + " to " + t);\r
+ int rng[] = ml.locateInFrom(f, t);\r
+ if (rng != null) {\r
+ for (int i = 0; i < rng.length; i++) {\r
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
+ }\r
+ } else {\r
+ System.out.println("No range!");\r
+ }\r
+ System.out.print("\nReversed\n");\r
+ rng = ml.locateInFrom(t, f);\r
+ if (rng != null) {\r
+ for (int i = 0; i < rng.length; i++) {\r
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
+ }\r
+ } else {\r
+ System.out.println("No range!");\r
+ }\r
+ System.out.print("\n");\r
+ f++;\r
+ t--;\r
+ }\r
+ }\r
+ System.out.print("\n");\r
+ mmap = ml.makeToMap();\r
+ System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "\r
+ + mmap[0][2] + " " + mmap[0][3] + " ");\r
+ for (int i = 1; i <= mmap[1].length; i++) {\r
+ if (mmap[1][i - 1] == -1) {\r
+ System.out.print(i + "=XXX");\r
+\r
+ } else {\r
+ System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));\r
+ }\r
+ if (i % 20 == 0) {\r
+ System.out.print("\n");\r
+ } else {\r
+ System.out.print(",");\r
+ }\r
+ }\r
+ System.out.print("\n");\r
+ // test range function\r
+ System.out.print("\nTest locateInTo\n");\r
+ {\r
+ int f = mmap[0][2], t = mmap[0][3];\r
+ while (f <= t) {\r
+ System.out.println("Range " + f + " to " + t);\r
+ int rng[] = ml.locateInTo(f, t);\r
+ if (rng != null) {\r
+ for (int i = 0; i < rng.length; i++) {\r
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
+ }\r
+ } else {\r
+ System.out.println("No range!");\r
+ }\r
+ System.out.print("\nReversed\n");\r
+ rng = ml.locateInTo(t, f);\r
+ if (rng != null) {\r
+ for (int i = 0; i < rng.length; i++) {\r
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
+ }\r
+ } else {\r
+ System.out.println("No range!");\r
+ }\r
+ f++;\r
+ t--;\r
+ System.out.print("\n");\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ public static void main(String argv[]) {\r
+ MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {\r
+ 51, 1 }, 1, 3);\r
+ MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 }, new int[] { 51, 1 },\r
+ 1, 3);\r
+ MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3, 1);\r
+ // test internal consistency\r
+ int to[] = new int[51];\r
+ MapList.testMap(ml, 1, 60);\r
+ /*\r
+ * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]\r
+ * toofrom=ml.shiftFrom(too[0]);\r
+ * System.out.println("ShiftFrom("+from+")=="+too\r
+ * [0]+" % "+too[1]+"\t+-+\tShiftTo("\r
+ * +too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }\r
+ */\r
+ System.out.print("Success?\n"); // if we get here - something must be\r
+ // working!\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return a MapList whose From range is this maplist's To Range, and vice\r
+ * versa\r
+ */\r
+ public MapList getInverse() {\r
+ return new MapList(getToRanges(), getFromRanges(), getToRatio(),\r
+ getFromRatio());\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff