@Ensures("result != null")
public final String toString() {
if (GenomeLoc.isUnmapped(this)) return "unmapped";
if (throughEndOfContigP() && atBeginningOfContigP()) return getContig();
else if (throughEndOfContigP() || getStart() == getStop())
return String.format("%s:%d", getContig(), getStart());
else return String.format("%s:%d-%d", getContig(), getStart(), getStop());
}
/**
* Returns a new GenomeLoc that represents the region between the endpoints of this and that.
* Requires that this and that GenomeLoc are both mapped.
*/
@Requires({"that != null", "isUnmapped(this) == isUnmapped(that)"})
@Ensures("result != null")
public GenomeLoc endpointSpan(GenomeLoc that) throws ReviewedStingException {
if (GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
throw new ReviewedStingException("Cannot get endpoint span for unmerged genome locs");
}
if (!this.getContig().equals(that.getContig())) {
throw new ReviewedStingException(
"Cannot get endpoint span for genome locs on different contigs");
}
return new GenomeLoc(
getContig(),
this.contigIndex,
Math.min(getStart(), that.getStart()),
Math.max(getStop(), that.getStop()));
}
/**
* Returns a new GenomeLoc that represents the entire span of this and that. Requires that this
* and that GenomeLoc are contiguous and both mapped
*/
@Requires({"that != null", "isUnmapped(this) == isUnmapped(that)"})
@Ensures("result != null")
public GenomeLoc merge(GenomeLoc that) throws ReviewedStingException {
if (GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
if (!GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
throw new ReviewedStingException("Tried to merge a mapped and an unmapped genome loc");
return UNMAPPED;
}
if (!(this.contiguousP(that))) {
throw new ReviewedStingException("The two genome loc's need to be contigous");
}
return new GenomeLoc(
getContig(),
this.contigIndex,
Math.min(getStart(), that.getStart()),
Math.max(getStop(), that.getStop()));
}
@Requires("that != null")
@Ensures("result != null")
public GenomeLoc intersect(GenomeLoc that) throws ReviewedStingException {
if (GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
if (!GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
throw new ReviewedStingException("Tried to intersect a mapped and an unmapped genome loc");
return UNMAPPED;
}
if (!(this.overlapsP(that))) {
throw new ReviewedStingException(
"GenomeLoc::intersect(): The two genome loc's need to overlap");
}
return new GenomeLoc(
getContig(),
this.contigIndex,
Math.max(getStart(), that.getStart()),
Math.min(getStop(), that.getStop()));
}
@Requires("that != null")
@Ensures("result == 0 || result == 1 || result == -1")
public int compareTo(GenomeLoc that) {
int result = 0;
if (this == that) {
result = 0;
} else if (GenomeLoc.isUnmapped(this)) result = 1;
else if (GenomeLoc.isUnmapped(that)) result = -1;
else {
final int cmpContig = compareContigs(that);
if (cmpContig != 0) {
result = cmpContig;
} else {
if (this.getStart() < that.getStart()) result = -1;
if (this.getStart() > that.getStart()) result = 1;
}
}
return result;
}
@Requires("that != null")
public final List<GenomeLoc> subtract(final GenomeLoc that) {
if (GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
if (!GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
throw new ReviewedStingException("Tried to intersect a mapped and an unmapped genome loc");
return Arrays.asList(UNMAPPED);
}
if (!(this.overlapsP(that))) {
throw new ReviewedStingException("GenomeLoc::minus(): The two genome loc's need to overlap");
}
if (equals(that)) {
return Collections.emptyList();
} else if (containsP(that)) {
List<GenomeLoc> l = new ArrayList<GenomeLoc>(2);
/**
* we have to create two new region, one for the before part, one for the after The old
* region: |----------------- old region (g) -------------| |----- to delete (e) ------|
*
* <p>product (two new regions): |------| + |--------|
*/
int afterStop = this.getStop(), afterStart = that.getStop() + 1;
int beforeStop = that.getStart() - 1, beforeStart = this.getStart();
if (afterStop - afterStart >= 0) {
GenomeLoc after = new GenomeLoc(this.getContig(), getContigIndex(), afterStart, afterStop);
l.add(after);
}
if (beforeStop - beforeStart >= 0) {
GenomeLoc before =
new GenomeLoc(this.getContig(), getContigIndex(), beforeStart, beforeStop);
l.add(before);
}
return l;
} else if (that.containsP(this)) {
/**
* e completely contains g, delete g, but keep looking, there may be more regions i.e.:
* |--------------------- e --------------------| |--- g ---| |---- others ----|
*/
return Collections.emptyList(); // don't need to do anything
} else {
/**
* otherwise e overlaps some part of g
*
* <p>figure out which region occurs first on the genome. I.e., is it: |------------- g
* ----------| |------------- e ----------|
*
* <p>or: |------------- g ----------| |------------ e -----------|
*/
GenomeLoc n;
if (that.getStart() < this.getStart()) {
n = new GenomeLoc(this.getContig(), getContigIndex(), that.getStop() + 1, this.getStop());
} else {
n = new GenomeLoc(this.getContig(), getContigIndex(), this.getStart(), that.getStart() - 1);
}
// replace g with the new region
return Arrays.asList(n);
}
}
