--- /dev/null
+/*
+ * 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());
+ }
+}
--- /dev/null
+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.
+ }
+}
git://source.jalview.org / vamsas.git / commitdiff