/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*/
public class MapList
{
- 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
+ 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
public MapList(int from[], int to[], int fromRatio, int toRatio)
{
fromShifts = new Vector();
- for (int i=0;i<from.length; i+=2)
- fromShifts.add(new int[] { from[i], from[i+1]});
+ for (int i = 0; i < from.length; i += 2)
+ {
+ fromShifts.add(new int[]
+ {from[i], from[i + 1]});
+ }
toShifts = new Vector();
- for (int i=0;i<to.length; i+=2)
- toShifts.add(new int[] { to[i], to[i+1]});
- this.fromRatio=fromRatio;
- this.toRatio=toRatio;
+ for (int i = 0; i < to.length; i += 2)
+ {
+ toShifts.add(new int[]
+ {to[i], to[i + 1]});
+ }
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
}
+
/**
* 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);
+ 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);
+ 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) {
- Iterator iv = intVals.iterator();
- if (!iv.hasNext())
- return null;
- int[] intv=(int[]) iv.next();
- int from=intv[0],to=intv[1];
- if (from>to) {
- from = intv[1];
- to=intv[0];
+ private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
+ int toRatio)
+ {
+ Iterator iv = intVals.iterator();
+ if (!iv.hasNext())
+ {
+ return null;
+ }
+ int[] intv = (int[]) iv.next();
+ int from = intv[0], to = intv[1];
+ if (from > to)
+ {
+ from = intv[1];
+ to = intv[0];
+ }
+ while (iv.hasNext())
+ {
+ intv = (int[]) iv.next();
+ if (intv[0] < from)
+ {
+ from = intv[0];
+ }
+ if (intv[1] < from)
+ {
+ from = intv[1];
+ }
+ if (intv[0] > to)
+ {
+ to = intv[0];
}
- while (iv.hasNext()) {
- intv = (int[]) iv.next();
- 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];
+ 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];
- }
- }
+ }
+ 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];
}
- mp[i] = m;
+ if (m[0] > tT)
+ {
+ tT = m[0];
+ }
+ }
}
- int[][] map=new int[][] { new int[]{from, to, tF, tT}, new int[to-from+2]};
+ 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
- }
+ 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;
+ }
+ 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)
- {
+ public void addShift(int pos, int shift)
+ {
int sidx = 0;
int[] rshift=null;
- while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+ 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)
*
*/
public int[] shiftFrom(int pos)
{
- return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
+ return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
}
/**
* @param pos (in To)
* @return shifted position in From, frameshift in To
*/
- public int[] shiftTo(int pos) {
- return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
+ 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.iterator(), pos);
- if (fromCount==null)
- return null;
- int fromRemainder=(fromCount[0]-1) % fromRatio;
- int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
- int[] toPos = countToPos(toShifts.iterator(), 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};
+ private int[] shift(int pos, Vector fromShifts, int fromRatio,
+ Vector toShifts, int toRatio)
+ {
+ int[] fromCount = countPos(fromShifts.iterator(), pos);
+ if (fromCount == null)
+ {
+ return null;
+ }
+ int fromRemainder = (fromCount[0] - 1) % fromRatio;
+ int toCount = 1 + ( ( (fromCount[0] - 1) / fromRatio) * toRatio);
+ int[] toPos = countToPos(toShifts.iterator(), 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};
}
+
/**
* 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(Iterator intVals, int pos) {
- int count=0,intv[];
- while (intVals.hasNext()) {
- intv = (int[])intVals.next();
- 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;
- }
- }
+ private int[] countPos(Iterator intVals, int pos)
+ {
+ int count = 0, intv[];
+ while (intVals.hasNext())
+ {
+ intv = (int[]) intVals.next();
+ 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;
+ }
}
- return null;
+ 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(Iterator intVals, int pos) {
- int count=0,diff=0,intv[]={0,0};
- while (intVals.hasNext()) {
- intv = (int[])intVals.next();
- 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;
- }
- }
+ private int[] countToPos(Iterator intVals, int pos)
+ {
+ int count = 0, diff = 0, intv[] =
+ {
+ 0, 0};
+ while (intVals.hasNext())
+ {
+ intv = (int[]) intVals.next();
+ 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;
+ }
}
- return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);
+ 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);
}
- 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]);
- 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]);
- } else
- System.out.println("ShiftTo("+too[0]+")=="+"NaN! - not Bijective Mapping!");
- }
+
+ 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");
}
- 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]));
+ else
+ {
+ System.out.print(too[0] + " % " + too[1]);
+ 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]);
}
- if (i % 20==0)
- System.out.print("\n");
- else
- System.out.print(",");
+ System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
+ toofrom[1]);
+ }
+ 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]));
}
- System.out.print("\n");
+ if (i % 20 == 0)
+ {
+ System.out.print("\n");
+ }
+ else
+ {
+ System.out.print(",");
+ }
+ }
+ 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);
-
- // test internal consistency
- int to[] = new int[51];
- MapList.testMap(ml, 1, 25);
- /*
- 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!
+
+ 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);
+
+ // test internal consistency
+ int to[] = new int[51];
+ MapList.testMap(ml, 1, 25);
+ /*
+ 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!
}
}
git://source.jalview.org / jalview.git / blobdiff