/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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 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.
+ * 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)
*/
public class MapList
{
+
/*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
+ * 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
*/
- public boolean equals(MapList obj)
+ 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 != 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;
+ 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
-
/**
+ * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
*
- * @return series of intervals mapped in from
+ * @return
*/
- public int[] getFromRanges()
+ public List<int[]> getFromRanges()
{
- return getRanges(fromShifts);
+ return fromShifts;
}
- public int[] getToRanges()
+ /**
+ * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...}
+ *
+ * @return
+ */
+ public List<int[]> getToRanges()
{
- return getRanges(toShifts);
+ return toShifts;
}
- private int[] getRanges(Vector shifts)
+ /**
+ * 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()];
- Enumeration e = shifts.elements();
int i = 0;
- while (e.hasMoreElements())
+ for (int[] r : shifts)
{
- int r[] = (int[]) e.nextElement();
rnges[i++] = r[0];
rnges[i++] = r[1];
}
}
/**
- * 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 getFromLowest()
{
- return fromRange[0];
+ return fromLowest;
}
public int getFromHighest()
{
- return fromRange[1];
+ return fromHighest;
}
public int getToLowest()
{
- return toRange[0];
+ return toLowest;
}
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;
+ 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();
+ 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();
+
+ 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}}
*/
- public int[][] makeFromMap()
+ protected int[][] makeFromMap()
{
+ // TODO not used - remove??
return posMap(fromShifts, fromRatio, toShifts, toRatio);
}
*
* @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
+ * @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();
+ // TODO not used - remove??
+ int iv = 0, ivSize = shiftTo.size();
if (iv >= ivSize)
{
return null;
}
- int[] intv = (int[]) intVals.elementAt(iv++);
+ int[] intv = shiftTo.get(iv++);
int from = intv[0], to = intv[1];
if (from > to)
{
}
while (iv < ivSize)
{
- intv = (int[]) intVals.elementAt(iv++);
+ 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;
* shifts.insertElementAt(new int[] { pos, shift}, sidx); else
* rshift[1]+=shift; }
*/
+
/**
* shift from pos to To(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, 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, toCount);
+ 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] };
+ 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();
+ 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
{
{
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(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 };
+ int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
+ int[] intv = { 0, 0 };
while (iv < ivSize)
{
- intv = (int[]) intVals.elementAt(iv++);
+ 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
{
* find series of intervals mapping from start-end in the From map.
*
* @param start
- * position in to map
+ * position mapped 'to'
* @param end
- * position in to map
- * @return series of ranges in from map
+ * 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);
- 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;
+ // needs to be inclusive of end of symbol position
+ int fromEnd[] = shiftTo(end);
+
+ return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
}
/**
* find series of intervals mapping from start-end in the to map.
*
* @param start
- * position in from map
+ * position mapped 'from'
* @param end
- * position in from map
- * @return series of ranges in to map
+ * position mapped 'from'
+ * @return series of [start, end] ranges in sequence mapped 'to'
*/
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;
+ 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
+ * @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
*/
- private int[] getIntervals(Vector fromShifts2, int[] fromStart,
- int[] fromEnd, int fromRatio2)
+ protected static int[] getIntervals(List<int[]> shiftFrom,
+ int[] fromStart, int[] fromEnd, int fromRatio2)
{
+ if (fromStart == null || fromEnd == null)
+ {
+ return null;
+ }
int startpos, endpos;
startpos = fromStart[0]; // first position in fromStart
endpos = fromEnd[0]; // last position in fromEnd
int endindx = (fromRatio2 - 1); // additional positions to get to last
// position from endpos
- int intv = 0, intvSize = fromShifts2.size();
+ 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 = (int[]) fromShifts2.elementAt(intv++);
+ iv = shiftFrom.get(intv++);
if (fe_s > -1)
{
endpos = iv[0]; // start counting from beginning of interval
i++;
}
if (fs == fe && fe == -1)
+ {
return null;
- Vector ranges = new Vector();
+ }
+ List<int[]> ranges = new ArrayList<int[]>();
if (fs <= fe)
{
intv = fs;
i = fs;
// truncate initial interval
- iv = (int[]) fromShifts2.elementAt(intv++);
- iv = new int[]
- { iv[0], iv[1] };// clone
+ 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
+ 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.addElement(iv); // add only - or final range
+ }
+ ranges.add(iv); // add only - or final range
}
else
{
// walk from end of interval.
- i = fromShifts2.size() - 1;
+ 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)
{
}
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
+ ranges.add(iv); // add (truncated) reversed interval
+ iv = shiftFrom.get(i);
+ iv = new int[] { iv[1], iv[0] }; // reverse and clone
}
if (i == fe)
{
// interval is already reversed
iv[1] = endpos;
}
- ranges.addElement(iv); // add only - or final range
+ ranges.add(iv); // add only - or final range
}
// create array of start end intervals.
int[] range = null;
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;
*/
public int getToPosition(int mpos)
{
+ // TODO not used - remove??
int[] mp = shiftTo(mpos);
if (mp != null)
{
int[] mp = shiftTo(mpos);
if (mp != null)
{
- return new int[]
- { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
+ return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
}
return null;
}
*/
public int getMappedPosition(int pos)
{
+ // TODO not used - remove??
int[] mp = shiftFrom(pos);
if (mp != null)
{
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 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");
- }
- 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");
- }
- 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) ? "," : ";"));
- }
- }
- 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 boolean containsEither(boolean local, MapList map)
{
+ // TODO not used - remove?
if (local)
{
return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= 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