X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=d71272189564505f99c2989f99e04df51a40b543;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=5da89b058aedc78aea8c2d8ed3fb8ffa0bbc7fd2;hpb=1698842ec6755d1995dae7c1a590efbfc8f6e4d5;p=jalview.git
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 5da89b0..d712721 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,224 +1,316 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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
{
- /* (non-Javadoc)
- * @see java.lang.Object#clone()
- */
- protected Object clone() throws CloneNotSupportedException {
- // TODO Auto-generated method stub
- return super.clone();
- }
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#equals(java.lang.Object)
*/
- public boolean equals(MapList obj) {
- if (obj==this)
+ 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) {
- Iterator i,j;
- for (i=fromShifts.iterator(),j=obj.fromShifts.iterator(); i.hasNext();) {
- int[] mi=(int[]) i.next();
- if (!j.hasNext())
- return false;
- int[] mj=(int[]) j.next();
- if (mi[0]!=mj[0] || mi[1]!=mj[1])
+ 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;
}
- if (j.hasNext())
+ iSize = toShifts.size();
+ jSize = obj.toShifts.size();
+ if (iSize != jSize)
return false;
- for (i=toShifts.iterator(),j=obj.toShifts.iterator(); i.hasNext();) {
- int[] mi=(int[]) i.next();
- if (!j.hasNext())
- return false;
- int[] mj=(int[]) j.next();
- if (mi[0]!=mj[0] || mi[1]!=mj[1])
+ 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;
}
- if (j.hasNext())
- 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;
+ int[] fromRange = null;
+
/**
* lowest and highest value in the to Map
*/
- int[] toRange=null;
+ 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() {
+
+ public int getFromLowest()
+ {
return fromRange[0];
}
- public int getFromHighest() {
+
+ public int getFromHighest()
+ {
return fromRange[1];
}
- public int getToLowest() {
+
+ public int getToLowest()
+ {
return toRange[0];
}
- public int getToHighest() {
+
+ 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[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] };
+ fromRange = new int[]
+ { from[0], from[1] };
+ toRange = new int[]
+ { to[0], to[1] };
fromShifts = new Vector();
- for (int i=0;i= ivSize)
{
return null;
}
- int[] intv=(int[]) iv.next();
- int from=intv[0],to=intv[1];
+ int[] intv = (int[]) intVals.elementAt(iv++);
+ int from = intv[0], to = intv[1];
if (from > to)
{
from = intv[1];
- to=intv[0];
+ to = intv[0];
}
- while (iv.hasNext())
+ while (iv < ivSize)
{
- intv = (int[]) iv.next();
- 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, intVals, ratio, toIntVals, 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]};
+ { new int[]
+ { from, to, tF, tT }, new int[to - from + 2] };
map[0][2] = tF;
map[0][3] = tT;
@@ -227,7 +319,7 @@ public class MapList
{
if (mp[i] != null)
{
- map[1][i] = mp[i][0]-tF;
+ map[1][i] = mp[i][0] - tF;
}
else
{
@@ -236,28 +328,28 @@ public class MapList
}
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= intv[0] && pos <= intv[1])
{
return new int[]
- {
- count + pos - intv[0] + 1, +1};
+ { count + pos - intv[0] + 1, +1 };
}
else
{
- count+=intv[1]-intv[0]+1;
+ count += intv[1] - intv[0] + 1;
}
}
else
@@ -331,43 +427,42 @@ public class MapList
if (pos >= intv[1] && pos <= intv[0])
{
return new int[]
- {
- count + intv[0] - pos + 1, -1};
+ { 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 pos
* @return position pos in interval set
*/
- private int[] countToPos(Iterator intVals, int pos)
+ private int[] countToPos(Vector intVals, int pos)
{
- int count = 0, diff = 0, intv[] =
- {
- 0, 0};
- while (intVals.hasNext())
+ int count = 0, diff = 0, iv = 0, ivSize = intVals.size(), intv[] =
+ { 0, 0 };
+ while (iv < ivSize)
{
- intv = (int[])intVals.next();
- diff = intv[1]-intv[0];
+ 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};
+ { pos - count - 1 + intv[0], +1 };
}
else
{
- count+=1+diff;
+ count += 1 + diff;
}
}
else
@@ -375,126 +470,195 @@ public class MapList
if (pos <= count + 1 - diff)
{
return new int[]
- {
- intv[0] - (pos - count - 1), -1};
+ { 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
+ *
+ * @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) {
+ public int[] locateInFrom(int start, int end)
+ {
// inefficient implementation
int fromStart[] = shiftTo(start);
- int fromEnd[] = shiftTo(end);
- if (fromStart==null || fromEnd==null)
+ 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);
+ 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
+ *
+ * @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) {
+ public int[] locateInTo(int start, int end)
+ {
// inefficient implementation
int toStart[] = shiftFrom(start);
int toEnd[] = shiftFrom(end);
- if (toStart==null || toEnd==null)
+ 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
+ * 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
+ * @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)
- {
- // correct for word direction for start and end
- int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1);
- int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1);
- Iterator intv = fromShifts2.iterator();
- int iv[],i=0,fs=-1,fe=-1; // containing intervals
- while (intv.hasNext() && (fs==-1 || fe==-1)) {
- iv = (int[]) intv.next();
- if (iv[0]<=iv[1]) {
- if (fs==-1 && startpos>=iv[0] && startpos<=iv[1]) {
- fs = i;
+ 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 (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]) {
- fs = i;
+ }
+ 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) {
- intv = fromShifts2.iterator();
- i=0;
- while (ifs) {
+ i = fromShifts2.size() - 1;
+ while (i > fs)
+ {
i--;
}
iv = (int[]) fromShifts2.elementAt(i);
- iv = new int[] { iv[1], iv[0]};// reverse and clone
+ 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) {
+ 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
+ iv = (int[]) fromShifts2.elementAt(i);
+ iv = new int[]
+ { iv[1], iv[0] }; // reverse and clone
}
- if (i==fe) {
+ if (i == fe)
+ {
// interval is already reversed
iv[1] = endpos;
}
@@ -502,23 +666,90 @@ public class MapList
}
// 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];
- intv = ranges.iterator();
- i=0;
- while (intv.hasNext())
+ range = new int[ranges.size() * 2];
+ intv = 0;
+ intvSize = ranges.size();
+ i = 0;
+ while (intv < intvSize)
{
- iv = (int[]) intv.next();
+ iv = (int[]) ranges.elementAt(intv);
range[i++] = iv[0];
range[i++] = iv[1];
- intv.remove();
+ 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
@@ -527,49 +758,49 @@ public class MapList
{
for (int from = 1; from <= 25; from++)
{
- int[] too=ml.shiftFrom(from);
- System.out.print("ShiftFrom("+from+")==");
- if (too==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(too[0] + " % " + too[1] + " (" + too[2] + ")");
System.out.print("\t+--+\t");
- int[] toofrom=ml.shiftTo(too[0]);
+ int[] toofrom = ml.shiftTo(too[0]);
if (toofrom != null)
{
- if (toofrom[0]!=from)
+ if (toofrom[0] != from)
{
- System.err.println("Mapping not reflexive:" + from + " " + too[0] +
- "->" + toofrom[0]);
+ System.err.println("Mapping not reflexive:" + from + " "
+ + too[0] + "->" + toofrom[0]);
}
- System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
- toofrom[1]+" ("+toofrom[2]+")");
+ System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
+ + " % " + toofrom[1] + " (" + toofrom[2] + ")");
}
else
{
- System.out.println("ShiftTo(" + too[0] + ")==" +
- "NaN! - not Bijective Mapping!");
+ 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] + " ");
+ 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");
+ System.out.print(i + "=XXX");
}
else
{
- System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
+ System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
}
- if (i % 20==0)
+ if (i % 20 == 0)
{
System.out.print("\n");
}
@@ -578,17 +809,19 @@ public class MapList
System.out.print(",");
}
}
- //test range function
+ // test range function
System.out.print("\nTest locateInFrom\n");
{
- int f=mmap[0][2],t=mmap[0][3];
- while (f= 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()));
+ }
}
}