@Test
public void substractComplexExample() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 1, 20);
mSortedSet.add(e);
GenomeLoc r1 = genomeLocParser.createGenomeLoc(contigOneName, 3, 5);
GenomeLoc r2 = genomeLocParser.createGenomeLoc(contigOneName, 10, 12);
GenomeLoc r3 = genomeLocParser.createGenomeLoc(contigOneName, 16, 18);
GenomeLocSortedSet toExclude =
new GenomeLocSortedSet(genomeLocParser, Arrays.asList(r1, r2, r3));
GenomeLocSortedSet remaining = mSortedSet.subtractRegions(toExclude);
// logger.debug("Initial " + mSortedSet);
// logger.debug("Exclude " + toExclude);
// logger.debug("Remaining " + remaining);
assertEquals(mSortedSet.coveredSize(), 20);
assertEquals(toExclude.coveredSize(), 9);
assertEquals(remaining.coveredSize(), 11);
Iterator<GenomeLoc> it = remaining.iterator();
GenomeLoc p1 = it.next();
GenomeLoc p2 = it.next();
GenomeLoc p3 = it.next();
GenomeLoc p4 = it.next();
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 1, 2), p1);
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 6, 9), p2);
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 13, 15), p3);
assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 19, 20), p4);
}
@Test
public void testSizeBeforeLoc() {
GenomeLoc r1 = genomeLocParser.createGenomeLoc(contigOneName, 3, 5);
GenomeLoc r2 = genomeLocParser.createGenomeLoc(contigOneName, 10, 12);
GenomeLoc r3 = genomeLocParser.createGenomeLoc(contigOneName, 16, 18);
mSortedSet.addAll(Arrays.asList(r1, r2, r3));
testSizeBeforeLocX(2, 0);
testSizeBeforeLocX(3, 0);
testSizeBeforeLocX(4, 1);
testSizeBeforeLocX(5, 2);
testSizeBeforeLocX(6, 3);
testSizeBeforeLocX(10, 3);
testSizeBeforeLocX(11, 4);
testSizeBeforeLocX(12, 5);
testSizeBeforeLocX(13, 6);
testSizeBeforeLocX(15, 6);
testSizeBeforeLocX(16, 6);
testSizeBeforeLocX(17, 7);
testSizeBeforeLocX(18, 8);
testSizeBeforeLocX(19, 9);
testSizeBeforeLocX(50, 9);
testSizeBeforeLocX(50, (int) mSortedSet.coveredSize());
}
/**
* Create a new ProgressMeter
*
* @param performanceLogFile an optional performance log file where a table of performance logs
* will be written
* @param processingUnitName the name of the unit type being processed, suitable for saying X
* seconds per processingUnitName
* @param processingIntervals the intervals being processed
*/
public ProgressMeter(
final File performanceLogFile,
final String processingUnitName,
final GenomeLocSortedSet processingIntervals) {
if (processingUnitName == null)
throw new IllegalArgumentException("processingUnitName cannot be null");
if (processingIntervals == null)
throw new IllegalArgumentException("Target intervals cannot be null");
this.processingUnitName = processingUnitName;
this.regionsBeingProcessed = processingIntervals;
// setup the performance logger output, if requested
if (performanceLogFile != null) {
try {
this.performanceLog = new PrintStream(new FileOutputStream(performanceLogFile));
final List<String> pLogHeader =
Arrays.asList(
"elapsed.time",
"units.processed",
"processing.speed",
"bp.processed",
"bp.speed",
"genome.fraction.complete",
"est.total.runtime",
"est.time.remaining");
performanceLog.println(Utils.join("\t", pLogHeader));
} catch (FileNotFoundException e) {
throw new UserException.CouldNotCreateOutputFile(performanceLogFile, e);
}
} else {
performanceLog = null;
}
// cached for performance reasons
targetSizeInBP = processingIntervals.coveredSize();
// start up the timer
progressMeterDaemon = new ProgressMeterDaemon(this);
start();
}
