105 lines
3.0 KiB
Java
105 lines
3.0 KiB
Java
|
package org.broadinstitute.sting.utils.threading;
|
||
|
|
|
||
|
|
import org.broadinstitute.sting.utils.GenomeLoc;
|
||
|
|
|
||
|
|
import java.util.List;
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Created by IntelliJ IDEA.
|
||
|
|
* User: depristo
|
||
|
|
* Date: 1/13/11
|
||
|
|
* Time: 9:38 AM
|
||
|
|
* To change this template use File | Settings | File Templates.
|
||
|
|
*/
|
||
|
|
public abstract class GenomeLocProcessingTracker {
|
||
|
|
/**
|
||
|
|
* Information about processing locations and their owners
|
||
|
|
*/
|
||
|
|
public static final class ProcessingLoc {
|
||
|
|
GenomeLoc loc;
|
||
|
|
String owner;
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Create an unowned loc
|
||
|
|
* @param loc
|
||
|
|
*/
|
||
|
|
public ProcessingLoc(GenomeLoc loc) {
|
||
|
|
this(loc, null);
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Create a loc that's already owned
|
||
|
|
* @param loc
|
||
|
|
* @param owner
|
||
|
|
*/
|
||
|
|
public ProcessingLoc(GenomeLoc loc, String owner) {
|
||
|
|
this.loc = loc;
|
||
|
|
this.owner = owner;
|
||
|
|
}
|
||
|
|
|
||
|
|
public GenomeLoc getLoc() {
|
||
|
|
return loc;
|
||
|
|
}
|
||
|
|
|
||
|
|
public String getOwner() {
|
||
|
|
return owner;
|
||
|
|
}
|
||
|
|
|
||
|
|
public void setOwner(String owner) {
|
||
|
|
this.owner = owner;
|
||
|
|
}
|
||
|
|
|
||
|
|
public boolean isOwned() { return owner != null; }
|
||
|
|
}
|
||
|
|
|
||
|
|
// --------------------------------------------------------------------------------
|
||
|
|
//
|
||
|
|
// Code to claim intervals for processing and query for their ownership
|
||
|
|
//
|
||
|
|
// --------------------------------------------------------------------------------
|
||
|
|
/**
|
||
|
|
* Queries the current database if a location is owned. Does not guarantee that the
|
||
|
|
* loc can be owned in a future call, though.
|
||
|
|
*
|
||
|
|
* @param loc
|
||
|
|
* @return
|
||
|
|
*/
|
||
|
|
public boolean locIsOwned(GenomeLoc loc) {
|
||
|
|
return findOwner(loc) != null;
|
||
|
|
}
|
||
|
|
|
||
|
|
public ProcessingLoc findOwner(GenomeLoc loc) {
|
||
|
|
for ( ProcessingLoc l : getProcessingLocs() ) {
|
||
|
|
if ( l.getLoc().equals(loc) )
|
||
|
|
return l;
|
||
|
|
}
|
||
|
|
|
||
|
|
return null;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* The workhorse routine. Attempt to claim processing ownership of loc, with my name.
|
||
|
|
* This is an atomic operation -- other threads / processes will wait until this function
|
||
|
|
* returns. The return result is the ProcessingLoc object describing who owns this
|
||
|
|
* location. If the location isn't already claimed and we now own the location, the pl owner
|
||
|
|
* will be myName. Otherwise, the name of the owner can found in the pl.
|
||
|
|
*
|
||
|
|
* @param loc
|
||
|
|
* @param myName
|
||
|
|
* @return
|
||
|
|
*/
|
||
|
|
public abstract ProcessingLoc claimOwnership(GenomeLoc loc, String myName);
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Returns the list of currently owned locations, updating the database as necessary.
|
||
|
|
* DO NOT MODIFY THIS LIST! As with all parallelizing data structures, the list may be
|
||
|
|
* out of date immediately after the call returns, or may be updating on the fly.
|
||
|
|
*
|
||
|
|
* This is really useful for printing, counting, etc. operations that aren't mission critical
|
||
|
|
*
|
||
|
|
* @return
|
||
|
|
*/
|
||
|
|
protected abstract List<ProcessingLoc> getProcessingLocs();
|
||
|
|
}
|