79 lines
2.7 KiB
Java
79 lines
2.7 KiB
Java
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package org.broadinstitute.sting.gatk.executive;
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import org.broadinstitute.sting.gatk.io.storage.Storage;
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import org.broadinstitute.sting.gatk.io.OutputTracker;
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import java.util.Collection;
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import java.util.ArrayList;
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/**
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* User: hanna
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* Date: Apr 30, 2009
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* Time: 4:04:38 PM
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* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
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* Software and documentation are copyright 2005 by the Broad Institute.
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* All rights are reserved.
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*
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* Users acknowledge that this software is supplied without any warranty or support.
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* The Broad Institute is not responsible for its use, misuse, or
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* functionality.
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*/
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/**
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* Hold pointers to the output and error streams, and state to indicate whether
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* a write is complete. Not generally thread-safe. Calls to isComplete()/complete()
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* can be made at any time from any thread, but complete() should be called on the
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* thread which is doing the writing.
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*/
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public class OutputMergeTask {
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/**
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* The output streams which should be written to.
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*/
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private final Collection<MergeOperation<?>> mergeOperations = new ArrayList<MergeOperation<?>>();
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/**
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* Add a new merge operation to this merge task.
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* @param targetStream Target for stream output.
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* @param temporaryStorage Temporary storage.
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* @param <StreamType> Type of the output stream.
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*/
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public <StreamType> void addMergeOperation( StreamType targetStream, Storage<StreamType> temporaryStorage ) {
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mergeOperations.add( new MergeOperation<StreamType>(targetStream,temporaryStorage) );
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}
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/**
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* Merge data from output streams into target storage.
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*/
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public synchronized void merge() {
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for( MergeOperation mergeOperation: mergeOperations )
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mergeOperation.temporaryStorage.mergeInto(mergeOperation.targetStream);
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}
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/**
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* Represents a single file needed to be merged.
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* @param <StreamType> Type of the file to be merged.
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*/
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private class MergeOperation<StreamType> {
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/**
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* Destination for the temporary file's output.
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*/
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public final StreamType targetStream;
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/**
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* Temporary storage location for the file.
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*/
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public final Storage<StreamType> temporaryStorage;
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/**
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* Create a new merge file object with the given output stream and storage placeholder.
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* @param targetStream Target for temporary data.
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* @param temporaryStorage The temporary data itself.
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*/
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public MergeOperation( StreamType targetStream, Storage<StreamType> temporaryStorage ) {
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this.targetStream = targetStream;
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this.temporaryStorage = temporaryStorage;
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}
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}
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}
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