X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=dc5bee876134fee1ea42afc4a767a51c90fe893f;hb=34abca821ae5c3f9220bfc246c3055e3ba9f39c3;hp=defa670dcf0792f4bdb791b98e755a0109d8d23a;hpb=1e3af75ad546eb9e8d57b92946903eace01a198e;p=jalview.git
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index defa670..dc5bee8 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,280 +1,1116 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
/**
- * MapList
- * Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range
+ * A 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.
+ *
+ * TODO: test/ensure that sense of from and to ratio start position is conserved
+ * (codon start position recovery)
*/
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
+
+ /*
+ * Subregions (base 1) described as { [start1, end1], [start2, end2], ...}
+ */
+ private List fromShifts;
+
+ /*
+ * Same format as fromShifts, for the 'mapped to' sequence
+ */
+ private List toShifts;
+
+ /*
+ * number of steps in fromShifts to one toRatio unit
+ */
+ private int fromRatio;
+
+ /*
+ * number of steps in toShifts to one fromRatio
+ */
+ private int toRatio;
+
+ /*
+ * lowest and highest value in the from Map
+ */
+ private int fromLowest;
+
+ private int fromHighest;
+
+ /*
+ * lowest and highest value in the to Map
+ */
+ private int toLowest;
+
+ private int toHighest;
+
+ /**
+ * Constructor
+ */
+ public MapList()
+ {
+ fromShifts = new ArrayList();
+ toShifts = new ArrayList();
+ }
+
+ /**
+ * Two MapList objects are equal if they are the same object, or they both
+ * have populated shift ranges and all values are the same.
+ */
+ @Override
+ public boolean equals(Object o)
+ {
+ if (o == null || !(o instanceof MapList))
+ {
+ return false;
+ }
+
+ MapList obj = (MapList) o;
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj.fromRatio != fromRatio || obj.toRatio != toRatio
+ || obj.fromShifts == null || obj.toShifts == null)
+ {
+ return false;
+ }
+ return Arrays
+ .deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
+ && Arrays
+ .deepEquals(toShifts.toArray(), obj.toShifts.toArray());
+ }
+
+ /**
+ * Returns a hashcode made from the fromRatio, toRatio, and from/to ranges
+ */
+ @Override
+ public int hashCode()
+ {
+ int hashCode = 31 * fromRatio;
+ hashCode = 31 * hashCode + toRatio;
+ hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
+ hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+ return hashCode;
+ }
+
+ /**
+ * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List getFromRanges()
+ {
+ return fromShifts;
+ }
+
+ /**
+ * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List getToRanges()
+ {
+ return toShifts;
+ }
+
+ /**
+ * Flattens a list of [start, end] into a single [start1, end1, start2,
+ * end2,...] array.
+ *
+ * @param shifts
+ * @return
+ */
+ protected static int[] getRanges(List shifts)
+ {
+ int[] rnges = new int[2 * shifts.size()];
+ int i = 0;
+ for (int[] r : shifts)
+ {
+ rnges[i++] = r[0];
+ rnges[i++] = r[1];
+ }
+ return rnges;
+ }
+
+ /**
+ *
+ * @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 fromLowest;
+ }
+
+ public int getFromHighest()
+ {
+ return fromHighest;
+ }
+
+ public int getToLowest()
+ {
+ return toLowest;
+ }
+
+ public int getToHighest()
+ {
+ return toHighest;
+ }
+
+ /**
+ * Constructor given from and to ranges as [start1, end1, start2, end2,...].
+ * If any end is equal to the next start, the ranges will be merged. There is
+ * no validation check that the ranges do not overlap each other.
+ *
+ * @param from
+ * contiguous regions as [start1, end1, start2, end2, ...]
+ * @param to
+ * same format as 'from'
+ * @param fromRatio
+ * phrase length in 'from' (e.g. 3 for dna)
+ * @param toRatio
+ * phrase length in 'to' (e.g. 1 for protein)
+ */
public MapList(int from[], int to[], int fromRatio, int toRatio)
{
- fromShifts = new Vector();
- for (int i=0;i 0 && from[i] == fromShifts.get(added - 1)[1])
+ {
+ /*
+ * this range starts where the last ended - just extend it
+ */
+ fromShifts.get(added - 1)[1] = from[i + 1];
+ }
+ else
+ {
+ fromShifts.add(new int[] { from[i], from[i + 1] });
+ added++;
+ }
+ }
+
+ toLowest = Integer.MAX_VALUE;
+ toHighest = Integer.MIN_VALUE;
+ added = 0;
+ for (int i = 0; i < to.length; i += 2)
+ {
+ toLowest = Math.min(toLowest, Math.min(to[i], to[i + 1]));
+ toHighest = Math.max(toHighest, Math.max(to[i], to[i + 1]));
+ if (added > 0 && to[i] == toShifts.get(added - 1)[1])
+ {
+ toShifts.get(added - 1)[1] = to[i + 1];
+ }
+ else
+ {
+ toShifts.add(new int[] { to[i], to[i + 1] });
+ added++;
+ }
+ }
+ }
+
+ /**
+ * Copy constructor. Creates an identical mapping.
+ *
+ * @param map
+ */
+ public MapList(MapList map)
+ {
+ this();
+ // TODO not used - remove?
+ this.fromLowest = map.fromLowest;
+ this.fromHighest = map.fromHighest;
+ this.toLowest = map.toLowest;
+ this.toHighest = map.toHighest;
+
+ this.fromRatio = map.fromRatio;
+ this.toRatio = map.toRatio;
+ if (map.fromShifts != null)
+ {
+ for (int[] r : map.fromShifts)
+ {
+ fromShifts.add(new int[] { r[0], r[1] });
+ }
+ }
+ if (map.toShifts != null)
+ {
+ for (int[] r : map.toShifts)
+ {
+ toShifts.add(new int[] { r[0], r[1] });
+ }
+ }
+ }
+
+ /**
+ * Constructor given ranges as lists of [start, end] positions. There is no
+ * validation check that the ranges do not overlap each other.
+ *
+ * @param fromRange
+ * @param toRange
+ * @param fromRatio
+ * @param toRatio
+ */
+ public MapList(List fromRange, List toRange, int fromRatio,
+ int toRatio)
+ {
+ this();
+ fromRange = coalesceRanges(fromRange);
+ toRange = coalesceRanges(toRange);
+ this.fromShifts = fromRange;
+ this.toShifts = toRange;
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
+
+ fromLowest = Integer.MAX_VALUE;
+ fromHighest = Integer.MIN_VALUE;
+ for (int[] range : fromRange)
+ {
+ fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
+ fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
+ }
+
+ toLowest = Integer.MAX_VALUE;
+ toHighest = Integer.MIN_VALUE;
+ for (int[] range : toRange)
+ {
+ toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
+ toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
+ }
}
+
+ /**
+ * Consolidates a list of ranges so that any contiguous ranges are merged.
+ * This assumes the ranges are already in start order (does not sort them).
+ *
+ * @param ranges
+ * @return the same list (if unchanged), else a new merged list, leaving the
+ * input list unchanged
+ */
+ public static List coalesceRanges(final List ranges)
+ {
+ if (ranges == null || ranges.size() < 2) {
+ return ranges;
+ }
+
+ boolean changed = false;
+ List merged = new ArrayList();
+ int[] lastRange = ranges.get(0);
+ int lastDirection = lastRange[1] >= lastRange[0] ? 1 : -1;
+ lastRange = new int[] { lastRange[0], lastRange[1] };
+ merged.add(lastRange);
+ boolean first = true;
+
+ for (final int[] range : ranges)
+ {
+ if (first)
+ {
+ first = false;
+ continue;
+ }
+ if (range[0] == lastRange[0] && range[1] == lastRange[1])
+ {
+ // drop duplicate range
+ changed = true;
+ continue;
+ }
+
+ /*
+ * drop this range if it lies within the last range
+ */
+ if ((lastDirection == 1 && range[0] >= lastRange[0]
+ && range[0] <= lastRange[1] && range[1] >= lastRange[0] && range[1] <= lastRange[1])
+ || (lastDirection == -1 && range[0] <= lastRange[0]
+ && range[0] >= lastRange[1]
+ && range[1] <= lastRange[0] && range[1] >= lastRange[1]))
+ {
+ changed = true;
+ continue;
+ }
+
+ int direction = range[1] >= range[0] ? 1 : -1;
+
+ /*
+ * if next range is in the same direction as last and contiguous,
+ * just update the end position of the last range
+ */
+ boolean sameDirection = range[1] == range[0] || direction == lastDirection;
+ boolean extending = range[0] == lastRange[1] + lastDirection;
+ boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0] && range[0] <= lastRange[1])
+ || (lastDirection == -1 && range[0] <= lastRange[0] && range[0] >= lastRange[1]);
+ if (sameDirection && (overlapping || extending))
+ {
+ lastRange[1] = range[1];
+ changed = true;
+ }
+ else
+ {
+ lastRange = new int[] { range[0], range[1] };
+ merged.add(lastRange);
+ // careful: merging [5, 5] after [7, 6] should keep negative direction
+ lastDirection = (range[1] == range[0]) ? lastDirection : direction;
+ }
+ }
+
+ return changed ? merged : ranges;
+ }
+
/**
* get all mapped positions from 'from' to 'to'
- * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
+ *
+ * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int
+ * [fromFinish-fromStart+2] { toStart..toFinish mappings}}
*/
- public int[][] makeFromMap() {
- return posMap(fromShifts, fromRatio, toShifts, toRatio);
+ protected int[][] makeFromMap()
+ {
+ // TODO not used - remove??
+ 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);
+ protected int[][] makeToMap()
+ {
+ // TODO not used - remove??
+ 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];
- }
- while (iv.hasNext()) {
- intv = (int[]) iv.next();
- 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;itT) {
- tT=m[0];
- }
- }
+ *
+ * @param shiftTo
+ * @return int[] { from, to pos in range }, int[range.to-range.from+1]
+ * returning mapped position
+ */
+ private int[][] posMap(List shiftTo, int ratio,
+ List shiftFrom, int toRatio)
+ {
+ // TODO not used - remove??
+ int iv = 0, ivSize = shiftTo.size();
+ if (iv >= ivSize)
+ {
+ return null;
+ }
+ int[] intv = shiftTo.get(iv++);
+ int from = intv[0], to = intv[1];
+ if (from > to)
+ {
+ from = intv[1];
+ to = intv[0];
+ }
+ while (iv < ivSize)
+ {
+ intv = shiftTo.get(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, shiftTo, ratio, shiftFrom, toRatio);
+ if (m != null)
+ {
+ if (i == 0)
+ {
+ tF = tT = m[0];
+ }
+ else
+ {
+ if (m[0] < tF)
+ {
+ tF = 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 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;
+ }
+ 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 shiftTo, int fromRatio,
+ List shiftFrom, int toRatio)
+ {
+ // TODO: javadoc; tests
+ int[] fromCount = countPos(shiftTo, pos);
+ if (fromCount == null)
+ {
+ return null;
+ }
+ int fromRemainder = (fromCount[0] - 1) % fromRatio;
+ int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
+ int[] toPos = countToPos(shiftFrom, 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 shiftTo
* @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;
- }
- }
+ protected static int[] countPos(List shiftTo, int pos)
+ {
+ int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
+ while (iv < ivSize)
+ {
+ intv = shiftTo.get(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;
+ }
}
- 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 shiftFrom
* @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;
- }
- }
+ protected static int[] countToPos(List shiftFrom, int pos)
+ {
+ int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+ int[] intv = { 0, 0 };
+ while (iv < ivSize)
+ {
+ intv = shiftFrom.get(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 mapped 'to'
+ * @param end
+ * position mapped 'to'
+ * @return series of [start, end] ranges in sequence mapped 'from'
+ */
+ public int[] locateInFrom(int start, int end)
+ {
+ // inefficient implementation
+ int fromStart[] = shiftTo(start);
+ // needs to be inclusive of end of symbol position
+ int fromEnd[] = shiftTo(end);
+
+ return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
+ }
+
+ /**
+ * find series of intervals mapping from start-end in the to map.
+ *
+ * @param start
+ * position mapped 'from'
+ * @param end
+ * position mapped 'from'
+ * @return series of [start, end] ranges in sequence mapped 'to'
+ */
+ public int[] locateInTo(int start, int end)
+ {
+ int toStart[] = shiftFrom(start);
+ int toEnd[] = shiftFrom(end);
+ return getIntervals(toShifts, toStart, toEnd, toRatio);
+ }
+
+ /**
+ * like shift - except returns the intervals in the given vector of shifts
+ * which were spanned in traversing fromStart to fromEnd
+ *
+ * @param shiftFrom
+ * @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
+ */
+ protected static int[] getIntervals(List shiftFrom,
+ int[] fromStart, int[] fromEnd, int fromRatio2)
+ {
+ if (fromStart == null || fromEnd == null)
+ {
+ return null;
+ }
+ 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 = shiftFrom.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 = shiftFrom.get(intv++);
+ if (fe_s > -1)
+ {
+ endpos = iv[0]; // start counting from beginning of interval
+ endindx--; // inclusive of endpos
}
- 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!");
+ 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
+ }
+ }
+ }
}
- 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
+ {
+ 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 (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!
+ 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;
+ }
+ List ranges = new ArrayList();
+ if (fs <= fe)
+ {
+ intv = fs;
+ i = fs;
+ // truncate initial interval
+ iv = shiftFrom.get(intv++);
+ iv = new int[] { iv[0], iv[1] };// clone
+ if (i == fs)
+ {
+ iv[0] = startpos;
+ }
+ while (i != fe)
+ {
+ ranges.add(iv); // add initial range
+ iv = shiftFrom.get(intv++); // get next interval
+ iv = new int[] { iv[0], iv[1] };// clone
+ i++;
+ }
+ if (i == fe)
+ {
+ iv[1] = endpos;
+ }
+ ranges.add(iv); // add only - or final range
+ }
+ else
+ {
+ // walk from end of interval.
+ i = shiftFrom.size() - 1;
+ while (i > fs)
+ {
+ i--;
+ }
+ iv = shiftFrom.get(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.add(iv); // add (truncated) reversed interval
+ iv = shiftFrom.get(i);
+ iv = new int[] { iv[1], iv[0] }; // reverse and clone
+ }
+ if (i == fe)
+ {
+ // interval is already reversed
+ iv[1] = endpos;
+ }
+ ranges.add(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 = ranges.get(intv);
+ range[i++] = iv[0];
+ range[i++] = iv[1];
+ ranges.set(intv++, null); // 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)
+ {
+ // TODO not used - remove??
+ 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)
+ {
+ // TODO not used - remove??
+ int[] mp = shiftFrom(pos);
+ if (mp != null)
+ {
+ return mp[0];
+ }
+ return pos;
+ }
+
+ public int[] getMappedWord(int pos)
+ {
+ // TODO not used - remove??
+ int[] mp = shiftFrom(pos);
+ if (mp != null)
+ {
+ return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
+ }
+ return null;
+ }
+
+ /**
+ *
+ * @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)
+ {
+ // TODO not used - remove?
+ 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()));
+ }
+ }
+
+ /**
+ * String representation - for debugging, not guaranteed not to change
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder(64);
+ sb.append("[");
+ for (int[] shift : fromShifts)
+ {
+ sb.append(" ").append(Arrays.toString(shift));
+ }
+ sb.append(" ] ");
+ sb.append(fromRatio).append(":").append(toRatio);
+ sb.append(" to [");
+ for (int[] shift : toShifts)
+ {
+ sb.append(" ").append(Arrays.toString(shift));
+ }
+ sb.append(" ]");
+ return sb.toString();
}
+
+ /**
+ * Extend this map list by adding the given map's ranges. There is no
+ * validation check that the ranges do not overlap existing ranges (or each
+ * other), but contiguous ranges are merged.
+ *
+ * @param map
+ */
+ public void addMapList(MapList map)
+ {
+ if (this.equals(map))
+ {
+ return;
+ }
+ this.fromLowest = Math.min(fromLowest, map.fromLowest);
+ this.toLowest = Math.min(toLowest, map.toLowest);
+ this.fromHighest = Math.max(fromHighest, map.fromHighest);
+ this.toHighest = Math.max(toHighest, map.toHighest);
+
+ for (int[] range : map.getFromRanges())
+ {
+ addRange(range, fromShifts);
+ }
+ for (int[] range : map.getToRanges())
+ {
+ addRange(range, toShifts);
+ }
+ }
+
+ /**
+ * Adds the given range to a list of ranges. If the new range just extends
+ * existing ranges, the current endpoint is updated instead.
+ *
+ * @param range
+ * @param addTo
+ */
+ static void addRange(int[] range, List addTo)
+ {
+ /*
+ * list is empty - add to it!
+ */
+ if (addTo.size() == 0)
+ {
+ addTo.add(range);
+ return;
+ }
+
+ int[] last = addTo.get(addTo.size() - 1);
+ boolean lastForward = last[1] >= last[0];
+ boolean newForward = range[1] >= range[0];
+
+ /*
+ * contiguous range in the same direction - just update endpoint
+ */
+ if (lastForward == newForward && last[1] == range[0])
+ {
+ last[1] = range[1];
+ return;
+ }
+
+ /*
+ * next range starts at +1 in forward sense - update endpoint
+ */
+ if (lastForward && newForward && range[0] == last[1] + 1)
+ {
+ last[1] = range[1];
+ return;
+ }
+
+ /*
+ * next range starts at -1 in reverse sense - update endpoint
+ */
+ if (!lastForward && !newForward && range[0] == last[1] - 1)
+ {
+ last[1] = range[1];
+ return;
+ }
+
+ /*
+ * just add the new range
+ */
+ addTo.add(range);
+ }
+
+ /**
+ * Returns true if mapping is from forward strand, false if from reverse
+ * strand. Result is just based on the first 'from' range that is not a single
+ * position. Default is true unless proven to be false. Behaviour is not well
+ * defined if the mapping has a mixture of forward and reverse ranges.
+ *
+ * @return
+ */
+ public boolean isFromForwardStrand()
+ {
+ boolean forwardStrand = true;
+ for (int[] range : getFromRanges())
+ {
+ if (range[1] > range[0])
+ {
+ break; // forward strand confirmed
+ }
+ else if (range[1] < range[0])
+ {
+ forwardStrand = false;
+ break; // reverse strand confirmed
+ }
+ }
+ return forwardStrand;
+ }
+
+ /**
+ *
+ * @return true if from, or to is a three to 1 mapping
+ */
+ public boolean isTripletMap()
+ {
+ return (toRatio == 3 && fromRatio == 1)
+ || (fromRatio == 3 && toRatio == 1);
+ }
+
}