public class Mapping {
/**
* Contains the
- * start-end pairs mapping from
- * the associated sequence to the
- * sequence in the database
+ * start-end pairs mapping from
+ * the associated sequence to the
+ * sequence in the database
* coordinate system
* it also takes care of step difference between coordinate systems
*/
this(to, new MapList(exon, is, i, j));
}
/**
- * create a duplicate (and independent) mapping object with
+ * create a duplicate (and independent) mapping object with
* the same reference to any SequenceI being mapped to.
* @param map2
*/
public Mapping(Mapping map2)
{
if (map2!=this && map2!=null) {
- if (map2.map!=null)
+ if (map2.map!=null)
{
map=new MapList(map2.map);
}
/**
* Equals that compares both the to references and MapList mappings.
* @param other
- * @return
+ * @return
*/
public boolean equals(Mapping other) {
if (other==null)
* @param mpos
* @return
*/
- public int getPosition(int mpos)
+ public int getPosition(int mpos)
{
if (map!=null) {
int[] mp = map.shiftTo(mpos);
if (map!=null) {
int[] mp=map.shiftTo(mpos);
if (mp!=null) {
- return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)};
+ return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)};
}
}
return null;
}
/**
- * width of mapped unit in associated sequence
- *
+ * width of mapped unit in associated sequence
+ *
*/
public int getWidth() {
if (map!=null) {
return null;
}
/**
- * locates the region of feature f in the associated sequence's reference frame
+ * locates the region of feature f in the associated sequence's reference frame
* @param f
* @return one or more features corresponding to f
*/
public SequenceFeature[] locateFeature(SequenceFeature f)
{
- // this is a stopgap - features broken over exon boundaries will not be
- // broken into a collection of feature fragments.
- // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence
- // need a function like int [] fromrange = map.getRange(from,to)
- // need to make subgrouped sequence features.
- if (true) {
+ if (true) { // f.getBegin()!=f.getEnd()) {
if (map!=null) {
int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
SequenceFeature[] vf = new SequenceFeature[frange.length/2];
return vf;
}
}
- if (false){
+ if (false) //else
+ {
int[] word = getWord(f.getBegin());
- if (word[0]<word[1])
+ if (word[0]<word[1])
{
f.setBegin(word[0]);
} else {
f.setBegin(word[1]);
}
word = getWord(f.getEnd());
- if (word[0]>word[1])
+ if (word[0]>word[1])
{
f.setEnd(word[0]);
} else {
// give up and just return the feature.
return new SequenceFeature[] { f };
}
-
+
/**
* return a series of contigs on the associated sequence corresponding to
* the from,to interval on the mapped reference frame
* @return
*/
public int[] locateMappedRange(int from, int to) {
- //TODO
+ //TODO
return null;
}
}