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)
+ /*
+ * (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) {
- int i,iSize=fromShifts.size(),j,jSize=obj.fromShifts.size();
- if (iSize!=jSize)
+ 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])
+ 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)
+ 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])
+ 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
{
return getRanges(fromShifts);
}
+
public int[] getToRanges()
{
return getRanges(toShifts);
}
-
+
private int[] getRanges(Vector shifts)
{
- int[] rnges = new int[2*shifts.size()];
+ int[] rnges = new int[2 * shifts.size()];
Enumeration e = shifts.elements();
- int i=0;
+ int i = 0;
while (e.hasMoreElements())
{
int r[] = (int[]) e.nextElement();
}
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
{
return fromRatio;
}
+
/**
*
* @return length of mapped phrase in to
{
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[1]=pos;
+
+ 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] };
+ 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)
+ for (int i = 0; i < from.length; i += 2)
{
ensureRange(fromRange, from[i]);
- ensureRange(fromRange, from[i+1]);
+ ensureRange(fromRange, from[i + 1]);
fromShifts.addElement(new int[]
- {from[i], from[i + 1]});
+ { from[i], from[i + 1] });
}
toShifts = new Vector();
- for (int i=0;i<to.length; i+=2)
+ for (int i = 0; i < to.length; i += 2)
{
ensureRange(toRange, to[i]);
- ensureRange(toRange, to[i+1]);
+ ensureRange(toRange, to[i + 1]);
toShifts.addElement(new int[]
- {to[i], to[i + 1]});
+ { to[i], to[i + 1] });
}
- this.fromRatio=fromRatio;
- this.toRatio=toRatio;
+ this.fromRatio = fromRatio;
+ this.toRatio = toRatio;
}
+
public MapList(MapList map)
{
this.fromRange = new int[]
}
}
}
+
/**
* 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);
}
+
/**
* 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);
+ 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)
+ int toRatio)
{
- int iv=0,ivSize = intVals.size();
- if (iv>=ivSize)
+ int iv = 0, ivSize = intVals.size();
+ if (iv >= ivSize)
{
return null;
}
- int[] intv=(int[]) intVals.elementAt(iv++);
- 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<ivSize)
+ while (iv < ivSize)
{
intv = (int[]) intVals.elementAt(iv++);
- if (intv[0]<from)
+ if (intv[0] < from)
{
- from=intv[0];
+ from = intv[0];
}
- if (intv[1]<from)
+ if (intv[1] < from)
{
- from=intv[1];
+ from = intv[1];
}
- if (intv[0]>to)
+ if (intv[0] > to)
{
- to=intv[0];
+ to = intv[0];
}
- if (intv[1]>to)
+ if (intv[1] > to)
{
- to=intv[1];
+ to = intv[1];
}
}
- int tF=0,tT=0;
- int mp[][] = new int[to-from+2][];
+ int tF = 0, tT = 0;
+ int mp[][] = new int[to - from + 2][];
for (int i = 0; i < mp.length; i++)
{
- int[] m = shift(i+from,intVals,ratio,toIntVals, toRatio);
+ int[] m = shift(i + from, 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;
{
if (mp[i] != null)
{
- map[1][i] = mp[i][0]-tF;
+ map[1][i] = mp[i][0] - tF;
}
else
{
}
return map;
}
+
/**
* addShift
- * @param pos start position for shift (in original reference frame)
- * @param shift length of shift
- *
- public void addShift(int pos, int shift)
- {
- int sidx = 0;
- int[] rshift=null;
- while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
- sidx++;
- if (sidx==shifts.size())
- shifts.insertElementAt(new int[] { pos, shift}, sidx);
- else
- rshift[1]+=shift;
- }
+ *
+ * @param pos
+ * start position for shift (in original reference frame)
+ * @param shift
+ * length of shift
+ *
+ * public void addShift(int pos, int shift) { int sidx = 0; int[] rshift=null;
+ * while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+ * sidx++; if (sidx==shifts.size()) shifts.insertElementAt(new int[] { pos,
+ * shift}, sidx); else rshift[1]+=shift; }
*/
/**
* shift from pos to To(pos)
- *
- * @param pos int
- * @return int shifted position in To, frameshift in From, direction of mapped symbol in To
+ *
+ * @param pos
+ * int
+ * @return int shifted position in To, frameshift in From, direction of mapped
+ * symbol in To
*/
public int[] shiftFrom(int pos)
{
/**
* inverse of shiftFrom - maps pos in To to a position in From
- * @param pos (in To)
- * @return shifted position in From, frameshift in To, direction of mapped symbol in From
+ *
+ * @param pos
+ * (in To)
+ * @return shifted position in From, frameshift in To, direction of mapped
+ * symbol in From
*/
public int[] shiftTo(int pos)
{
return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
}
+
/**
- *
+ *
* @param fromShifts
* @param fromRatio
* @param toShifts
* @return
*/
private int[] shift(int pos, Vector fromShifts, int fromRatio,
- Vector toShifts, int toRatio)
+ Vector toShifts, int toRatio)
{
int[] fromCount = countPos(fromShifts, pos);
- if (fromCount==null)
+ if (fromCount == null)
{
return null;
}
- int fromRemainder=(fromCount[0]-1) % fromRatio;
- int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
+ int fromRemainder = (fromCount[0] - 1) % fromRatio;
+ int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
int[] toPos = countToPos(toShifts, toCount);
- if (toPos==null)
+ if (toPos == null)
{
return null; // throw new Error("Bad Mapping!");
}
- //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
+ // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
return new int[]
- {
- toPos[0], fromRemainder, toPos[1]};
+ { 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(Vector intVals, int pos)
{
- int count=0,intv[],iv=0,ivSize=intVals.size();
- while (iv<ivSize)
+ int count = 0, intv[], iv = 0, ivSize = intVals.size();
+ while (iv < ivSize)
{
- intv = (int[])intVals.elementAt(iv++);
+ 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};
+ { count + pos - intv[0] + 1, +1 };
}
else
{
- count+=intv[1]-intv[0]+1;
+ count += intv[1] - intv[0] + 1;
}
}
else
if (pos >= intv[1] && pos <= intv[0])
{
return new int[]
- {
- count + intv[0] - pos + 1, -1};
+ { 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(Vector intVals, int pos)
{
- int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
- {
- 0, 0};
- while (iv<ivSize)
+ int count = 0, diff = 0, iv = 0, ivSize = intVals.size(), intv[] =
+ { 0, 0 };
+ while (iv < ivSize)
{
- intv = (int[])intVals.elementAt(iv++);
- 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
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); // needs to be inclusive of end of symbol position
- 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 series of from,to intervals from from first position of starting region to final position of ending region inclusive
+ * @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]+fromEnd[2]*(fromRatio2-1); // last position in fromEnd
- int intv=0,intvSize= fromShifts2.size();
- int iv[],i=0,fs=-1,fe=-1; // containing intervals
- while (intv<intvSize && (fs==-1 || fe==-1)) {
+ 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 (iv[0]<=iv[1]) {
- if (fs==-1 && startpos>=iv[0] && startpos<=iv[1]) {
+ if (fe_s>-1)
+ {
+ endpos = iv[0]; // start counting from beginning of interval
+ endindx--; // inclusive of endpos
+ }
+ if (iv[0] <= iv[1])
+ {
+ if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
+ {
fs = i;
}
- if (fe==-1 && endpos>=iv[0] && endpos<=iv[1]) {
- fe = i;
+ if (endpos >= iv[0] && endpos <= iv[1])
+ {
+ if (fe_s == -1)
+ {
+ fe_s = i;
+ }
+ if (fe_s != -1)
+ {
+ if (endpos + endindx <= iv[1])
+ {
+ fe = i;
+ endpos = endpos + endindx; // end of end token is within this interval
+ }
+ else
+ {
+ endindx -= iv[1] - endpos; // skip all this interval too
+ }
+ }
}
- } else {
- if (fs==-1 && startpos<=iv[0] && startpos>=iv[1]) {
+ }
+ else
+ {
+ if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
+ {
fs = i;
}
- if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
- fe = i;
+ if (endpos <= iv[0] && endpos >= iv[1])
+ {
+ if (fe_s == -1)
+ {
+ fe_s = i;
+ }
+ if (fe_s != -1)
+ {
+ if (endpos - endindx >= iv[1])
+ {
+ fe = i;
+ endpos = endpos - endindx; // end of end token is within this interval
+ }
+ else
+ {
+ endindx -= endpos-iv[1]; // skip all this interval too
+ }
+ }
}
}
i++;
}
- if (fs==fe && fe==-1)
+ if (fs == fe && fe == -1)
return null;
- Vector ranges=new Vector();
- if (fs<=fe) {
+ Vector ranges = new Vector();
+ if (fs <= fe)
+ {
intv = fs;
- i=fs;
+ i = fs;
// truncate initial interval
iv = (int[]) fromShifts2.elementAt(intv++);
- iv = new int[] { iv[0], iv[1]};// clone
- if (i==fs)
+ iv = new int[]
+ { iv[0], iv[1] };// clone
+ if (i == fs)
iv[0] = startpos;
- while (i!=fe) {
+ 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
+ iv = new int[]
+ { iv[0], iv[1] };// clone
i++;
}
- if (i==fe)
+ if (i == fe)
iv[1] = endpos;
ranges.addElement(iv); // add only - or final range
- } else {
+ }
+ else
+ {
// walk from end of interval.
- i=fromShifts2.size()-1;
- while (i>fs) {
+ 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) { // fix apparent logic bug when fe==-1
+ 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 = new int[]
+ { iv[1], iv[0] }; // reverse and clone
}
- if (i==fe) {
+ if (i == fe)
+ {
// interval is already reversed
iv[1] = endpos;
}
}
// create array of start end intervals.
int[] range = null;
- if (ranges!=null && ranges.size()>0)
+ if (ranges != null && ranges.size() > 0)
{
- range = new int[ranges.size()*2];
+ range = new int[ranges.size() * 2];
intv = 0;
- intvSize=ranges.size();
- i=0;
- while (intv<intvSize)
+ intvSize = ranges.size();
+ i = 0;
+ while (intv < intvSize)
{
iv = (int[]) ranges.elementAt(intv);
range[i++] = iv[0];
}
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)
+ * 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)
{
- return mp[0];
+ int[] mp = shiftTo(mpos);
+ if (mp != null)
+ {
+ return mp[0];
+ }
+ return mpos;
}
- 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)};
+
+ /**
+ * 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;
}
- 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)
+
+ /**
+ * get From position in the associated reference frame for position pos in the
+ * associated sequence.
+ *
+ * @param pos
+ * @return
+ */
+ public int getMappedPosition(int pos)
{
- return mp[0];
+ int[] mp = shiftFrom(pos);
+ if (mp != null)
+ {
+ return mp[0];
+ }
+ return pos;
}
- return pos;
-}
-public int[] getMappedWord(int pos) {
- int[] mp = shiftFrom(pos);
- if (mp!=null)
+
+ public int[] getMappedWord(int pos)
{
- return new int[] { mp[0], mp[0]+mp[2]*(getToRatio()-1)};
+ int[] mp = shiftFrom(pos);
+ if (mp != null)
+ {
+ return new int[]
+ { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
+ }
+ return null;
}
- return null;
-}
/**
* test routine. not incremental.
+ *
* @param ml
* @param fromS
* @param fromE
{
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");
}
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<=t) {
- System.out.println("Range "+f+" to "+t);
- int rng[] = ml.locateInFrom(f,t);
- if (rng!=null)
+ int f = mmap[0][2], t = mmap[0][3];
+ while (f <= t)
+ {
+ System.out.println("Range " + f + " to " + t);
+ int rng[] = ml.locateInFrom(f, t);
+ if (rng != null)
{
- for (int i=0; i<rng.length; i++) {
- System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ 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)
+ rng = ml.locateInFrom(t, f);
+ if (rng != null)
{
- for (int i=0; i<rng.length; i++) {
- System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ 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--;
+ 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] + " ");
+ 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");
+ 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");
}
}
}
System.out.print("\n");
- //test range function
+ // 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) ? "," : ";"));
+ 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)
+ rng = ml.locateInTo(t, f);
+ if (rng != null)
{
- for (int i=0; i<rng.length; i++) {
- System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ for (int i = 0; i < rng.length; i++)
+ {
+ System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
}
}
else
{
System.out.println("No range!");
}
- f++; t--;
+ 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);
+ { 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);
+ { 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!
+ * 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
+ * @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());
+ return new MapList(getToRanges(), getFromRanges(), getToRatio(),
+ getFromRatio());
}
}
git://source.jalview.org / jalview.git / commitdiff