/*
- * 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
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.util;
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)
+ * 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
{
- 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
+ /*
+ * (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)
- fromShifts.add(new int[] { from[i], from[i+1]});
+ 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)
- toShifts.add(new int[] { to[i], to[i+1]});
- this.fromRatio=fromRatio;
- this.toRatio=toRatio;
+ 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}}
+ *
+ * @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
+ * @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]<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];
- }
- }
+ 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];
}
- 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
+ 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;
}
- return map;
+ 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;
- }
-*/
+ *
+ * @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
+ *
+ * @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);
+ 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
+ *
+ * @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);
+ public int[] shiftTo(int pos)
+ {
+ return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
}
+
/**
*
* @param fromShifts
* @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, 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(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(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;
+ }
}
- 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(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]; // last position in fromEnd
+ int endindx = (fromRatio2 - 1); // additional positions to get to last
+ // position from endpos
+ int intv = 0, intvSize = fromShifts2.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 = (int[]) fromShifts2.elementAt(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 (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])
+ {
+ 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 -= endpos - iv[1]; // skip all this interval too
+ }
+ }
+ }
+ }
+ 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");
}
- 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)
- System.out.println("ShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
- else
- System.out.println("ShiftTo("+too[0]+")=="+"NaN! - not Bijective Mapping!");
+ 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");
}
- 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(",");
+ }
+ }
+ 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) ? "," : ";"));
}
- 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!
+ }
+ 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);
+ MapList mldna = new MapList(new int[]
+ { 2, 2, 6, 8, 12, 16 }, new int[]
+ { 1, 3 }, 3, 1);
+ int[] frm = mldna.locateInFrom(1, 1);
+ testLocateFrom(mldna, 1, 1, new int[]
+ { 2, 2, 6, 7 });
+ MapList.testMap(mldna, 1, 3);
+ /*
+ * 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!
+ }
+
+ private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
+ {
+ int[] frm = mldna.locateInFrom(i, j);
+ if (frm == ks || java.util.Arrays.equals(frm, ks))
+ {
+ System.out.println("Success test locate from " + i + " to " + j);
+ }
+ else
+ {
+ System.err.println("Failed test locate from " + i + " to " + j);
+ for (int c = 0; c < frm.length; c++)
+ {
+ System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
+ }
+ System.err.println("Expected");
+ for (int c = 0; c < ks.length; c++)
+ {
+ System.err.print(ks[c] + ((c % 2 == 0) ? "," : ";"));
+ }
+ }
+ }
+
+ /**
+ *
+ * @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)
+ {
+ 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()));
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff