@Override
protected void runTask() throws Exception {
progress.setState(State.RUNNING);
int mergeCount = 0;
T a = sourceA.hasNext() ? sourceA.read() : null;
T b = sourceB.hasNext() ? sourceB.read() : null;
while (a != null && b != null) {
final int c = comparator.compare(a, b);
if (c < 0) {
sink.write(a);
a = sourceA.hasNext() ? sourceA.read() : null;
} else if (c > 0) {
sink.write(b);
b = sourceB.hasNext() ? sourceB.read() : null;
} else {
sink.write(a);
sink.write(b);
a = sourceA.hasNext() ? sourceA.read() : null;
b = sourceB.hasNext() ? sourceB.read() : null;
}
++mergeCount;
if (mergeCount % 1000000 == 0) {
progress.setMessage(MessageFormat.format("Merged {0} unique items.", mergeCount));
}
}
while (a != null) {
sink.write(a);
a = sourceA.hasNext() ? sourceA.read() : null;
++mergeCount;
if (mergeCount % 1000000 == 0) {
progress.setMessage(MessageFormat.format("Merged {0} unique items.", mergeCount));
}
}
while (b != null) {
sink.write(b);
b = sourceB.hasNext() ? sourceB.read() : null;
++mergeCount;
if (mergeCount % 1000000 == 0) {
progress.setMessage(MessageFormat.format("Merged {0} unique items.", mergeCount));
}
}
progress.startAdjusting();
progress.setMessage(MessageFormat.format("Merged {0} unique items.", mergeCount));
progress.setState(State.COMPLETED);
progress.endAdjusting();
if (sink instanceof Flushable) ((Flushable) sink).flush();
}
@Override
public void runCommand() throws Exception {
if (LOG.isInfoEnabled()) LOG.info("Running filtering.");
if (LOG.isDebugEnabled()) LOG.debug(this);
if (filterFeatureMinFreq > 0) {
addFeaturesMinimumFrequency(filterFeatureMinFreq);
}
if (filterFeaturePattern != null) {
addFeaturesPattern(filterFeaturePattern);
}
if (filterFeatureWhitelist != null) {
addFeaturesWhitelist(
com.google.common.io.Files.readLines(filterFeatureWhitelist, getCharset()));
}
if (filterEntryMinFreq > 0) {
addEntryMinimumFrequency(filterEntryMinFreq);
}
if (filterEntryPattern != null) {
addEntryPattern(filterEntryPattern);
}
if (filterEntryWhitelist != null) {
addEntryWhitelist(com.google.common.io.Files.readLines(filterEntryWhitelist, getCharset()));
}
if (filterEventMinFreq > 0) {
addEventMinimumFrequency(filterEventMinFreq);
}
checkState();
activeEventsFile = inputEventsFile;
activeEntriesFile = inputEntriesFile;
activeFeaturesFile = inputFeaturesFile;
progress.addProgressListener(
new ProgressListener() {
@Override
public void progressChanged(ProgressEvent progressEvent) {
LOG.info(progressEvent.getSource().getProgressReport());
}
});
progress.setState(State.RUNNING);
progress.setProgressPercent(0);
// Run the filters forwards then backwards. Each filtering step may
// introduce additionaly filters for the other files, so continue
// looping until there is no work remaining. Depending on filters this
// very unlikely to take more than 3 passes
int passCount = 0;
int opCount = 0;
while (entryFilterRequired || eventFilterRequired || featureFilterRequired) {
// if (entryFilterRequired || eventFilterRequired) {
progress.setMessage("Running filtering pass (#" + (++passCount) + ").");
if (entryFilterRequired) {
filterEntries();
++opCount;
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 3
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
}
if (eventFilterRequired) {
filterEvents();
++opCount;
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 3
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
}
if (featureFilterRequired) {
filterFeatures();
++opCount;
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 3
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
}
// }
//
// if (featureFilterRequired || eventFilterRequired) {
//
// progress.setMessage("Running backwards filtering pass (#" + (++passCount) +
// ").");
//
// if (featureFilterRequired) {
// filterFeatures();
// ++opCount;
// progress.setProgressPercent(100 * opCount / (opCount
// + (entryFilterRequired ? 1 : 0)
// + (eventFilterRequired ? 1 : 0)
// + (featureFilterRequired ? 1 : 0)));
// }
if (eventFilterRequired) {
filterEvents();
++opCount;
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 3
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
}
if (entryFilterRequired) {
filterEntries();
++opCount;
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 3
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
}
// }
}
// Finished filtering so copy the results files to the outputs.
progress.setMessage("Copying final entries file.");
outputEntriesFile.delete();
if (!activeEntriesFile.renameTo(outputEntriesFile)) {
com.google.common.io.Files.copy(activeEntriesFile, outputEntriesFile);
if (!activeEntriesFile.equals(inputEntriesFile)) activeEntriesFile.delete();
}
++opCount;
progress.startAdjusting();
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 2
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
progress.setMessage("Copying finaly events file.");
progress.endAdjusting();
outputEventsFile.delete();
if (!activeEventsFile.renameTo(outputEventsFile)) {
com.google.common.io.Files.copy(activeEventsFile, outputEventsFile);
if (!activeEventsFile.equals(inputEventsFile)) activeEventsFile.delete();
}
++opCount;
progress.startAdjusting();
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 1
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
progress.setMessage("Copying final features file.");
progress.endAdjusting();
outputFeaturesFile.delete();
if (!activeFeaturesFile.renameTo(outputFeaturesFile)) {
com.google.common.io.Files.copy(activeFeaturesFile, outputFeaturesFile);
if (!activeFeaturesFile.equals(inputFeaturesFile)) activeFeaturesFile.delete();
}
++opCount;
progress.setProgressPercent(
100
* opCount
/ (opCount
+ 0
+ (entryFilterRequired ? 1 : 0)
+ (eventFilterRequired ? 1 : 0)
+ (featureFilterRequired ? 1 : 0)));
if (indexDeligate.isEnumeratorOpen()) {
indexDeligate.saveEnumerator();
indexDeligate.closeEnumerator();
}
progress.setState(State.COMPLETED);
}