/*
- * 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 2.9.0b1)
+ * 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
{
- 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<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;
+ }
+ 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 the 'from' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List<int[]> getFromRanges()
+ {
+ return fromShifts;
+ }
+
+ /**
+ * 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
+ */
+ 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.
+ *
+ * @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();
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
+ fromLowest = from[0];
+ fromHighest = from[1];
for (int i = 0; i < from.length; i += 2)
{
- fromShifts.add(new int[]
- {from[i], from[i + 1]});
+ fromLowest = Math.min(fromLowest, from[i]);
+ fromHighest = Math.max(fromHighest, from[i + 1]);
+
+ fromShifts.add(new int[] { from[i], from[i + 1] });
}
- toShifts = new Vector();
+
+ toLowest = to[0];
+ toHighest = to[1];
for (int i = 0; i < to.length; i += 2)
{
- toShifts.add(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] });
}
+ }
+
+ /**
+ * Copy constructor. Creates an identical mapping.
+ *
+ * @param map
+ */
+ public MapList(MapList map)
+ {
+ // 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
+ *
+ * @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()
{
+ // 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)
{
- Iterator iv = intVals.iterator();
- if (!iv.hasNext())
+ // TODO not used - remove??
+ int iv = 0, ivSize = shiftTo.size();
+ if (iv >= ivSize)
{
return null;
}
- int[] intv = (int[]) iv.next();
+ int[] intv = shiftTo.get(iv++);
int from = intv[0], to = intv[1];
if (from > to)
{
from = intv[1];
to = intv[0];
}
- while (iv.hasNext())
+ while (iv < ivSize)
{
- intv = (int[]) iv.next();
+ intv = shiftTo.get(iv++);
if (intv[0] < from)
{
from = intv[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)
}
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;
/**
* 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)
{
/**
* 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)
{
}
/**
- *
- * @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.iterator(), pos);
+ // 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.iterator(), toCount);
+ 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};
+ // 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)
+ protected static int[] countPos(List<int[]> shiftTo, int pos)
{
- int count = 0, intv[];
- while (intVals.hasNext())
+ int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
+ while (iv < ivSize)
{
- intv = (int[]) intVals.next();
+ 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
{
{
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 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)
+ protected static int[] countToPos(List<int[]> shiftFrom, int pos)
{
- int count = 0, diff = 0, intv[] =
- {
- 0, 0};
- while (intVals.hasNext())
+ int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+ int[] intv = { 0, 0 };
+ while (iv < ivSize)
{
- intv = (int[]) intVals.next();
+ 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
{
{
if (pos <= count + 1 - diff)
{
- return new int[]
- {
- intv[0] - (pos - count - 1), -1};
+ return new int[] { intv[0] - (pos - count - 1), -1 };
}
else
{
}
}
}
- 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 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);
}
- public static void testMap(MapList ml, int fromS, int fromE)
+ /**
+ * 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)
{
- for (int from = 1; from <= 25; from++)
+ 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<int[]> shiftFrom,
+ int[] fromStart, int[] fromEnd, int fromRatio2)
+ {
+ if (fromStart == null || fromEnd == null)
{
- int[] too = ml.shiftFrom(from);
- System.out.print("ShiftFrom(" + from + ")==");
- if (too == 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)
{
- System.out.print("NaN\n");
+ endpos = iv[0]; // start counting from beginning of interval
+ endindx--; // inclusive of endpos
}
- else
+ if (iv[0] <= iv[1])
{
- System.out.print(too[0] + " % " + too[1]);
- System.out.print("\t+--+\t");
- int[] toofrom = ml.shiftTo(too[0]);
- if (toofrom != null)
+ if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
+ {
+ fs = i;
+ }
+ if (endpos >= iv[0] && endpos <= iv[1])
{
- if (toofrom[0] != from)
+ if (fe_s == -1)
+ {
+ fe_s = i;
+ }
+ if (fe_s != -1)
{
- System.err.println("Mapping not reflexive:" + from + " " + too[0] +
- "->" + toofrom[0]);
+ 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
+ }
}
- System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
- toofrom[1]);
}
- else
+ }
+ else
+ {
+ if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
{
- System.out.println("ShiftTo(" + too[0] + ")==" +
- "NaN! - not Bijective Mapping!");
+ 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;
+ }
+ List<int[]> ranges = new ArrayList<int[]>();
+ 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
}
- 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++)
+ else
{
- if (mmap[1][i - 1] == -1)
+ // walk from end of interval.
+ i = shiftFrom.size() - 1;
+ while (i > fs)
{
- System.out.print(i + "=XXX");
-
+ i--;
}
- else
+ iv = shiftFrom.get(i);
+ iv = new int[] { iv[1], iv[0] };// reverse and clone
+ // truncate initial interval
+ if (i == fs)
{
- System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+ 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 % 20 == 0)
+ if (i == fe)
{
- System.out.print("\n");
+ // interval is already reversed
+ iv[1] = endpos;
}
- else
+ 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)
{
- System.out.print(",");
+ iv = ranges.get(intv);
+ range[i++] = iv[0];
+ range[i++] = iv[1];
+ ranges.set(intv++, null); // remove
}
}
- System.out.print("\n");
+ 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;
}
- public static void main(String argv[])
+ /**
+ * 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)
{
- 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!
+ 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("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