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ProgressMeter optimization: don't do genome loc formatting, but instead create an object that only formats when printing is actually needed

This commit is contained in:
Mark DePristo 2012-12-17 15:55:21 -05:00
parent 1de2f527b9
commit 67fe81391c
1 changed files with 62 additions and 6 deletions
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68
public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java
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@ -145,7 +145,7 @@ public class ProgressMeter {
private final SimpleTimer timer = new SimpleTimer();
private GenomeLoc maxGenomeLoc = null;
private String positionMessage = "starting";
private Position position = new Position(PositionStatus.STARTING);
private long nTotalRecordsProcessed = 0;
final ProgressMeterDaemon progressMeterDaemon;
@ -234,9 +234,65 @@ public class ProgressMeter {
this.nTotalRecordsProcessed = Math.max(this.nTotalRecordsProcessed, nTotalRecordsProcessed);
// a pretty name for our position
this.positionMessage = maxGenomeLoc == null
? "unmapped reads"
: String.format("%s:%d", maxGenomeLoc.getContig(), maxGenomeLoc.getStart());
this.position = maxGenomeLoc == null ? new Position(PositionStatus.IN_UNMAPPED_READS) : new Position(maxGenomeLoc);
}
/**
* Describes the status of this position marker, such as starting up, done, in the unmapped reads,
* or somewhere on the genome
*/
private enum PositionStatus {
STARTING("Starting"),
DONE("done"),
IN_UNMAPPED_READS("unmapped reads"),
ON_GENOME(null);
public final String message;
private PositionStatus(String message) {
this.message = message;
}
}
/**
* A pair of position status and the genome loc, if necessary. Used to get a
* status update message as needed, without the computational cost of formatting
* the genome loc string every time a progress notification happens (which is almost
* always not printed)
*/
private class Position {
final PositionStatus type;
final GenomeLoc maybeLoc;
/**
* Create a position object of any type != ON_GENOME
* @param type
*/
@Requires({"type != null", "type != PositionStatus.ON_GENOME"})
private Position(PositionStatus type) {
this.type = type;
this.maybeLoc = null;
}
/**
* Create a position object of type ON_GENOME at genomeloc loc
* @param loc
*/
@Requires("loc != null")
private Position(GenomeLoc loc) {
this.type = PositionStatus.ON_GENOME;
this.maybeLoc = loc;
}
/**
* @return a human-readable representation of this position
*/
private String getMessage() {
if ( type == PositionStatus.ON_GENOME )
return maxGenomeLoc.getContig() + ":" + maxGenomeLoc.getStart();
else
return type.message;
}
}
/**
@ -267,7 +323,7 @@ public class ProgressMeter {
updateLoggerPrintFrequency(estTotalRuntime.getTimeInSeconds());
logger.info(String.format("%15s %5.2e %s %s %5.1f%% %s %s",
positionMessage, progressData.getUnitsProcessed()*1.0, elapsed, unitRate,
position.getMessage(), progressData.getUnitsProcessed()*1.0, elapsed, unitRate,
100*fractionGenomeTargetCompleted, estTotalRuntime, timeToCompletion));
}
@ -317,7 +373,7 @@ public class ProgressMeter {
public void notifyDone(final long nTotalRecordsProcessed) {
// print out the progress meter
this.nTotalRecordsProcessed = nTotalRecordsProcessed;
this.positionMessage = "done";
this.position = new Position(PositionStatus.DONE);
printProgress(true);
logger.info(String.format("Total runtime %.2f secs, %.2f min, %.2f hours",