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) {
/**
* 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}}
return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
}
/**
- *
+ *
* @param fromShifts
* @param fromRatio
* @param toShifts
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);
+ // 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<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++;
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 = 0;
intvSize=ranges.size();
- i=0;
- while (intv<intvSize)
+ 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)
+ {
+ 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