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)
* @see java.lang.Object#equals(java.lang.Object)
*/
public boolean equals(MapList obj) {
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();
+ 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();
+ 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;
/**
* lowest and highest value in the to Map
*/
- int[] toRange=null;
+ int[] toRange=null;
public int getFromRatio()
{
return fromRatio;
fromShifts = new Vector();
for (int i=0;i<from.length; i+=2)
- {
+ {
ensureRange(fromRange, from[i]);
ensureRange(fromRange, from[i+1]);
- fromShifts.add(new int[]
+ fromShifts.addElement(new int[]
{from[i], from[i + 1]});
}
toShifts = new Vector();
{
ensureRange(toRange, to[i]);
ensureRange(toRange, to[i+1]);
- toShifts.add(new int[]
+ toShifts.addElement(new int[]
{to[i], to[i + 1]});
}
this.fromRatio=fromRatio;
this.toRatio=toRatio;
}
+ public MapList(MapList map)
+ {
+ this.fromRange = new int[]
+ { map.fromRange[0], map.fromRange[1] };
+ this.toRange = new int[]
+ { map.toRange[0], map.toRange[1] };
+ this.fromRatio = map.fromRatio;
+ this.toRatio = map.toRatio;
+ if (map.fromShifts != null)
+ {
+ this.fromShifts = new Vector();
+ Enumeration e = map.fromShifts.elements();
+ while (e.hasMoreElements())
+ {
+ int[] el = (int[]) e.nextElement();
+ fromShifts.addElement(new int[]
+ { el[0], el[1] });
+ }
+ }
+ if (map.toShifts != null)
+ {
+ this.toShifts = new Vector();
+ Enumeration e = map.toShifts.elements();
+ while (e.hasMoreElements())
+ {
+ int[] el = (int[]) e.nextElement();
+ toShifts.addElement(new int[]
+ { el[0], el[1] });
+ }
+ }
+ }
/**
* get all mapped positions from 'from' to 'to'
* @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
int toRatio)
{
- Iterator iv = intVals.iterator();
- if (!iv.hasNext())
+ int iv=0,ivSize = intVals.size();
+ if (iv>=ivSize)
{
return null;
}
- int[] intv=(int[]) iv.next();
+ int[] intv=(int[]) intVals.elementAt(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 = (int[]) intVals.elementAt(iv++);
if (intv[0]<from)
{
from=intv[0];
return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
}
/**
- *
+ *
* @param fromShifts
* @param fromRatio
* @param toShifts
private int[] shift(int pos, Vector fromShifts, int fromRatio,
Vector toShifts, int toRatio)
{
- int[] fromCount = countPos(fromShifts.iterator(), pos);
+ int[] fromCount = countPos(fromShifts, pos);
if (fromCount==null)
{
return null;
}
int fromRemainder=(fromCount[0]-1) % fromRatio;
int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
- int[] toPos = countToPos(toShifts.iterator(), toCount);
+ int[] toPos = countToPos(toShifts, toCount);
if (toPos==null)
{
return null; // throw new Error("Bad Mapping!");
* @param pos
* @return number of positions or null if pos is not within intervals
*/
- private int[] countPos(Iterator intVals, int pos)
+ private int[] countPos(Vector intVals, int pos)
{
- int count=0,intv[];
- while (intVals.hasNext())
+ int count=0,intv[],iv=0,ivSize=intVals.size();
+ while (iv<ivSize)
{
- intv = (int[])intVals.next();
+ intv = (int[])intVals.elementAt(iv++);
if (intv[0] <= intv[1])
{
if (pos >= intv[0] && pos <= intv[1])
* @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[] =
+ int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
{
0, 0};
- while (intVals.hasNext())
+ while (iv<ivSize)
{
- intv = (int[])intVals.next();
+ intv = (int[])intVals.elementAt(iv++);
diff = intv[1]-intv[0];
if (diff >= 0)
{
public int[] locateInFrom(int start, int end) {
// inefficient implementation
int fromStart[] = shiftTo(start);
- int fromEnd[] = shiftTo(end);
+ 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);
*/
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();
+ // TODO: correct for word boundary w.r.t. fromStart->fromEnd direction for startpos and endpos.
+ // test is (1,8,12,17) to (1,5) and features on to : 2,2; 3,3; 4,3; 3,4; 4,4; 5,3; 3,5; 2,4; 4,2;
+ // correct for word direction for start and end :
+ int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1); // Math.min(fromStart[0], .. );
+ int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1); // Math.max(fromEnd[0],);
+ int intv=0,intvSize= fromShifts2.size();
int iv[],i=0,fs=-1,fe=-1; // containing intervals
- while (intv.hasNext() && (fs==-1 || fe==-1)) {
- iv = (int[]) intv.next();
+ 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]) {
- fs = i;
+ fs = i;
}
if (fe==-1 && endpos>=iv[0] && endpos<=iv[1]) {
- fe = i;
+ fe = i;
}
} else {
if (fs==-1 && startpos<=iv[0] && startpos>=iv[1]) {
- fs = i;
+ fs = i;
}
if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
- fe = i;
+ fe = i;
}
}
i++;
return null;
Vector ranges=new Vector();
if (fs<=fe) {
- intv = fromShifts2.iterator();
- i=0;
- while (i<fs) {
- intv.next();
- i++;
- }
+ intv = fs;
+ i=fs;
// truncate initial interval
- iv = (int[]) intv.next();
+ iv = (int[]) fromShifts2.elementAt(intv++);
iv = new int[] { iv[0], iv[1]};// clone
if (i==fs)
iv[0] = startpos;
while (i!=fe) {
ranges.addElement(iv); // add initial range
- iv = (int[]) intv.next(); // get next interval
+ iv = (int[]) fromShifts2.elementAt(intv++); // get next interval
iv = new int[] { iv[0], iv[1]};// clone
i++;
}
iv = (int[]) fromShifts2.elementAt(i);
iv = new int[] { iv[1], iv[0]};// reverse and clone
// truncate initial interval
- if (i==fs)
+ if (i==fs)
{
iv[0] = startpos;
}
}
// 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())
+ 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
System.out.print("\nTest locateInFrom\n");
{
int f=mmap[0][2],t=mmap[0][3];
- while (f<t) {
+ while (f<=t) {
System.out.println("Range "+f+" to "+t);
int rng[] = ml.locateInFrom(f,t);
if (rng!=null)
System.out.print("\n");
f++;t--;
}
- }
+ }
System.out.print("\n");
mmap = ml.makeToMap();
System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
System.out.print("\nTest locateInTo\n");
{
int f=mmap[0][2],t=mmap[0][3];
- while (f<t) {
+ while (f<=t) {
System.out.println("Range "+f+" to "+t);
int rng[] = ml.locateInTo(f,t);
if (rng!=null) {
f++; t--;
System.out.print("\n");
}
- }
+ }
}
git://source.jalview.org / jalview.git / blobdiff