/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * 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
{
- /* (non-Javadoc)
- * @see java.lang.Object#equals(java.lang.Object)
+
+ /*
+ * Subregions (base 1) described as { [start1, end1], [start2, end2], ...}
*/
- 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;
- }
+ private List<int[]> fromShifts = new ArrayList<int[]>();
+
+ /*
+ * Same format as fromShifts, for the 'mapped to' sequence
+ */
+ private List<int[]> toShifts = new ArrayList<int[]>();
+
+ /*
+ * 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;
+
+ /**
+ * 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)
+ {
+ // TODO should also override hashCode to ensure equal objects have equal
+ // hashcodes
+ if (o == null || !(o instanceof MapList))
+ {
+ return false;
+ }
+
+ MapList obj = (MapList) o;
+ if (obj == this)
+ {
return true;
}
- return false;
+ 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());
}
- 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
+
/**
- * lowest and highest value in the from Map
+ * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
*/
- int[] fromRange=null;
+ public List<int[]> getFromRanges()
+ {
+ return fromShifts;
+ }
+
/**
- * lowest and highest value in the to Map
+ * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List<int[]> 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<int[]> 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
*/
- int[] toRange=null;
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 getFromLowest()
+ {
+ return fromLowest;
}
- public int getToLowest() {
- return toRange[0];
+
+ public int getFromHighest()
+ {
+ return fromHighest;
}
- public int getToHighest() {
- return toRange[1];
+
+ public int getToLowest()
+ {
+ return toLowest;
}
- private void ensureRange(int[] limits, int pos) {
- if (limits[0]>pos)
- limits[0]=pos;
- if (limits[1]<pos)
- limits[1]=pos;
+
+ public int getToHighest()
+ {
+ return toHighest;
}
+
+ /**
+ * Constructor.
+ *
+ * @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)
{
- 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)
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
+ fromLowest = from[0];
+ fromHighest = from[1];
+ for (int i = 0; i < from.length; i += 2)
{
- ensureRange(fromRange, from[i]);
- ensureRange(fromRange, from[i+1]);
+ fromLowest = Math.min(fromLowest, from[i]);
+ fromHighest = Math.max(fromHighest, from[i + 1]);
- fromShifts.addElement(new int[]
- {from[i], from[i + 1]});
+ fromShifts.add(new int[] { from[i], from[i + 1] });
}
- toShifts = new Vector();
- for (int i=0;i<to.length; i+=2)
+
+ toLowest = to[0];
+ toHighest = to[1];
+ 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]});
+ toLowest = Math.min(toLowest, to[i]);
+ toHighest = Math.max(toHighest, to[i + 1]);
+ toShifts.add(new int[] { to[i], to[i + 1] });
}
- this.fromRatio=fromRatio;
- this.toRatio=toRatio;
}
+
+ /**
+ * Copy constructor. Creates an identical mapping.
+ *
+ * @param map
+ */
public MapList(MapList map)
{
- this.fromRange = new int[]
- { map.fromRange[0], map.fromRange[1] };
- this.toRange = new int[]
- { map.toRange[0], map.toRange[1] };
+ // 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)
{
- this.fromShifts = new Vector();
- Enumeration e = map.fromShifts.elements();
- while (e.hasMoreElements())
+ for (int[] r : map.fromShifts)
{
- int[] el = (int[]) e.nextElement();
- fromShifts.addElement(new int[]
- { el[0], el[1] });
+ fromShifts.add(new int[] { r[0], r[1] });
}
}
if (map.toShifts != null)
{
- this.toShifts = new Vector();
- Enumeration e = map.toShifts.elements();
- while (e.hasMoreElements())
+ for (int[] r : map.toShifts)
{
- int[] el = (int[]) e.nextElement();
- toShifts.addElement(new int[]
- { el[0], el[1] });
+ toShifts.add(new int[] { r[0], r[1] });
}
}
}
+
+ /**
+ * Constructor given ranges as lists of [start, end] positions
+ *
+ * @param fromRange
+ * @param toRange
+ * @param fromRatio
+ * @param toRatio
+ */
+ public MapList(List<int[]> fromRange, List<int[]> toRange, int fromRatio,
+ int toRatio)
+ {
+ this.fromShifts = fromRange;
+ this.toShifts = toRange;
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
+
+ fromLowest = Integer.MAX_VALUE;
+ fromHighest = 0;
+ for (int[] range : fromRange)
+ {
+ fromLowest = Math.min(fromLowest, range[0]);
+ fromHighest = Math.max(fromHighest, range[1]);
+ }
+
+ toLowest = Integer.MAX_VALUE;
+ toHighest = 0;
+ for (int[] range : toRange)
+ {
+ toLowest = Math.min(toLowest, range[0]);
+ toHighest = Math.max(toHighest, range[1]);
+ }
+ }
+
/**
* 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()
+ 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()
+ protected int[][] makeToMap()
{
- return posMap(toShifts,toRatio, fromShifts, fromRatio);
+ // 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
+ *
+ * @param shiftTo
+ * @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)
+ private int[][] posMap(List<int[]> shiftTo, int ratio,
+ List<int[]> shiftFrom, int toRatio)
{
- int iv=0,ivSize = intVals.size();
- if (iv>=ivSize)
+ // TODO not used - remove??
+ int iv = 0, ivSize = shiftTo.size();
+ if (iv >= ivSize)
{
return null;
}
- int[] intv=(int[]) intVals.elementAt(iv++);
- int from=intv[0],to=intv[1];
+ int[] intv = shiftTo.get(iv++);
+ int from = intv[0], to = intv[1];
if (from > to)
{
from = intv[1];
- to=intv[0];
+ to = intv[0];
}
- while (iv<ivSize)
+ while (iv < ivSize)
{
- intv = (int[]) intVals.elementAt(iv++);
- if (intv[0]<from)
+ intv = shiftTo.get(iv++);
+ if (intv[0] < from)
{
- from=intv[0];
+ from = intv[0];
}
- if (intv[1]<from)
+ if (intv[1] < from)
{
- from=intv[1];
+ from = intv[1];
}
- if (intv[0]>to)
+ if (intv[0] > to)
{
- to=intv[0];
+ to = intv[0];
}
- if (intv[1]>to)
+ if (intv[1] > to)
{
- to=intv[1];
+ to = intv[1];
}
}
- int tF=0,tT=0;
- int mp[][] = new int[to-from+2][];
+ 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);
+ int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio);
if (m != null)
{
if (i == 0)
{
- tF=tT=m[0];
+ tF = tT = m[0];
}
else
{
if (m[0] < tF)
{
- tF=m[0];
+ tF = m[0];
}
if (m[0] > tT)
{
- tT=m[0];
+ tT = m[0];
}
}
}
mp[i] = m;
}
- int[][] map = new int[][]
- {
- new int[]
- {
- from, to, tF, tT}, new int[to - from + 2]};
+ int[][] map = new int[][] { new int[] { from, to, tF, tT },
+ new int[to - from + 2] };
map[0][2] = tF;
map[0][3] = tT;
{
if (mp[i] != null)
{
- map[1][i] = mp[i][0]-tF;
+ map[1][i] = mp[i][0] - tF;
}
else
{
}
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;
- }
+ *
+ * @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
+ *
+ * @param pos
+ * int
+ * @return int shifted position in To, frameshift in From, direction of mapped
+ * symbol in To
*/
public int[] shiftFrom(int pos)
{
/**
* 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
+ *
+ * @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 shiftTo
* @param fromRatio
- * @param toShifts
+ * @param shiftFrom
* @param toRatio
* @return
*/
- private int[] shift(int pos, Vector fromShifts, int fromRatio,
- Vector toShifts, int toRatio)
+ protected static int[] shift(int pos, List<int[]> shiftTo, int fromRatio,
+ List<int[]> shiftFrom, int toRatio)
{
- int[] fromCount = countPos(fromShifts, pos);
- if (fromCount==null)
+ // 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(toShifts, toCount);
- if (toPos==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]};
+ // 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(Vector intVals, int pos)
+ protected static int[] countPos(List<int[]> shiftTo, int pos)
{
- int count=0,intv[],iv=0,ivSize=intVals.size();
- while (iv<ivSize)
+ int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
+ while (iv < ivSize)
{
- intv = (int[])intVals.elementAt(iv++);
+ 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};
+ return new int[] { count + pos - intv[0] + 1, +1 };
}
else
{
- count+=intv[1]-intv[0]+1;
+ count += intv[1] - intv[0] + 1;
}
}
else
{
if (pos >= intv[1] && pos <= intv[0])
{
- return new int[]
- {
- count + intv[0] - pos + 1, -1};
+ return new int[] { count + intv[0] - pos + 1, -1 };
}
else
{
- count+=intv[0]-intv[1]+1;
+ 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(Vector intVals, int pos)
+ protected static int[] countToPos(List<int[]> shiftFrom, int pos)
{
- int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
- {
- 0, 0};
- while (iv<ivSize)
+ int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+ int[] intv = { 0, 0 };
+ while (iv < ivSize)
{
- intv = (int[])intVals.elementAt(iv++);
- diff = intv[1]-intv[0];
+ 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};
+ return new int[] { pos - count - 1 + intv[0], +1 };
}
else
{
- count+=1+diff;
+ count += 1 + diff;
}
}
else
{
if (pos <= count + 1 - diff)
{
- return new int[]
- {
- intv[0] - (pos - count - 1), -1};
+ return new int[] { intv[0] - (pos - count - 1), -1 };
}
else
{
- count+=1-diff;
+ count += 1 - diff;
}
}
}
- return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);
+ 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
+ *
+ * @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) {
+ 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);
- if (fromStart==null || fromEnd==null)
- return null;
- int iv[] = getIntervals(fromShifts, fromStart, fromEnd,fromRatio);
- return iv;
+
+ return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
}
/**
* 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
+ *
+ * @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) {
- // inefficient implementation
+ public int[] locateInTo(int start, int end)
+ {
int toStart[] = shiftFrom(start);
int toEnd[] = shiftFrom(end);
- if (toStart==null || toEnd==null)
- return null;
- int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
- return iv;
+ 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 fromShifts2
+ * 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
+ * @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)
+ protected static int[] getIntervals(List<int[]> shiftFrom,
+ int[] fromStart, int[] fromEnd, int fromRatio2)
{
- // correct for word direction for start and end
- int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1);
- int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1);
- 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]) {
+ 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
+ }
+ 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;
+ if (endpos >= iv[0] && endpos <= iv[1])
+ {
+ if (fe_s == -1)
+ {
+ fe_s = i;
+ }
+ if (fe_s != -1)
+ {
+ if (endpos + endindx <= iv[1])
+ {
+ fe = i;
+ endpos = endpos + endindx; // end of end token is within this
+ // interval
+ }
+ else
+ {
+ endindx -= iv[1] - endpos; // skip all this interval too
+ }
+ }
}
- } else {
- if (fs==-1 && startpos<=iv[0] && startpos>=iv[1]) {
+ }
+ else
+ {
+ if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
+ {
fs = i;
}
- if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
- fe = i;
+ if (endpos <= iv[0] && endpos >= iv[1])
+ {
+ if (fe_s == -1)
+ {
+ fe_s = i;
+ }
+ if (fe_s != -1)
+ {
+ if (endpos - endindx >= iv[1])
+ {
+ fe = i;
+ endpos = endpos - endindx; // end of end token is within this
+ // interval
+ }
+ else
+ {
+ endindx -= endpos - iv[1]; // skip all this interval too
+ }
+ }
}
}
i++;
}
- if (fs==fe && fe==-1)
+ if (fs == fe && fe == -1)
+ {
return null;
- Vector ranges=new Vector();
- if (fs<=fe) {
+ }
+ List<int[]> ranges = new ArrayList<int[]>();
+ if (fs <= fe)
+ {
intv = fs;
- i=fs;
+ i = fs;
// truncate initial interval
- iv = (int[]) fromShifts2.elementAt(intv++);
- iv = new int[] { iv[0], iv[1]};// clone
- if (i==fs)
+ iv = shiftFrom.get(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
+ }
+ 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)
+ if (i == fe)
+ {
iv[1] = endpos;
- ranges.addElement(iv); // add only - or final range
- } else {
+ }
+ ranges.add(iv); // add only - or final range
+ }
+ else
+ {
// walk from end of interval.
- i=fromShifts2.size()-1;
- while (i>fs) {
+ i = shiftFrom.size() - 1;
+ while (i > fs)
+ {
i--;
}
- iv = (int[]) fromShifts2.elementAt(i);
- iv = new int[] { iv[1], iv[0]};// reverse and clone
+ iv = shiftFrom.get(i);
+ iv = new int[] { iv[1], iv[0] };// reverse and clone
// truncate initial interval
- if (i==fs)
+ if (i == fs)
{
iv[0] = startpos;
}
- while (i!=fe) {
- ranges.addElement(iv); // add (truncated) reversed interval
- iv = (int[]) fromShifts2.elementAt(--i);
+ 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) {
+ if (i == fe)
+ {
// interval is already reversed
iv[1] = endpos;
}
- ranges.addElement(iv); // add only - or final range
+ ranges.add(iv); // add only - or final range
}
// create array of start end intervals.
int[] range = null;
- if (ranges!=null && ranges.size()>0)
+ if (ranges != null && ranges.size() > 0)
{
- range = new int[ranges.size()*2];
+ range = new int[ranges.size() * 2];
intv = 0;
- intvSize=ranges.size();
- i=0;
- while (intv<intvSize)
+ intvSize = ranges.size();
+ i = 0;
+ while (intv < intvSize)
{
- iv = (int[]) ranges.elementAt(intv);
+ iv = ranges.get(intv);
range[i++] = iv[0];
range[i++] = iv[1];
- ranges.setElementAt(null, intv++); // remove
+ ranges.set(intv++, null); // remove
}
}
return range;
}
+
/**
- * test routine. not incremental.
- * @param ml
- * @param fromS
- * @param fromE
+ * get the 'initial' position of mpos in To
+ *
+ * @param mpos
+ * position in from
+ * @return position of first word in to reference frame
*/
- public static void testMap(MapList ml, int fromS, int fromE)
+ public int getToPosition(int mpos)
{
- for (int from = 1; from <= 25; from++)
+ // TODO not used - remove??
+ int[] mp = shiftTo(mpos);
+ if (mp != null)
{
- 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!");
- }
- }
+ return mp[0];
}
- 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");
+ return mpos;
+ }
- }
- else
- {
- System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
- }
- if (i % 20==0)
- {
- System.out.print("\n");
- }
- else
- {
- System.out.print(",");
- }
+ /**
+ * 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) };
}
- //test range function
- System.out.print("\nTest locateInFrom\n");
+ 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)
{
- 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--;
- }
+ return mp[0];
}
- 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++)
+ return pos;
+ }
+
+ public int[] getMappedWord(int pos)
+ {
+ // TODO not used - remove??
+ int[] mp = shiftFrom(pos);
+ if (mp != null)
{
- if (mmap[1][i - 1] == -1)
- {
- System.out.print(i+"=XXX");
+ return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
+ }
+ return null;
+ }
- }
- else
- {
- System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
- }
- if (i % 20==0)
- {
- System.out.print("\n");
- }
- else
- {
- System.out.print(",");
- }
+ /**
+ *
+ * @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()));
}
- 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");
- }
+ else
+ {
+ return ((getToLowest() >= map.getToLowest() && getToHighest() <= map
+ .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map
+ .getToHighest()));
}
-
}
- public static void main(String argv[])
+ /**
+ * String representation - for debugging, not guaranteed not to change
+ */
+ @Override
+ public String toString()
{
- 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!
+ StringBuilder sb = new StringBuilder(64);
+ sb.append("From (").append(fromRatio).append(":").append(toRatio)
+ .append(") [");
+ for (int[] shift : fromShifts)
+ {
+ sb.append(" ").append(Arrays.toString(shift));
+ }
+ sb.append(" ] To [");
+ for (int[] shift : toShifts)
+ {
+ sb.append(" ").append(Arrays.toString(shift));
+ }
+ sb.append(" ]");
+ return sb.toString();
}
}
git://source.jalview.org / jalview.git / blobdiff