/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.engine.datasources.providers;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList;
import org.broadinstitute.gatk.utils.GenomeLoc;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
/**
* User: hanna
* Date: May 21, 2009
* Time: 2:49:17 PM
* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
* Software and documentation are copyright 2005 by the Broad Institute.
* All rights are reserved.
*
* Users acknowledge that this software is supplied without any warranty or support.
* The Broad Institute is not responsible for its use, misuse, or
* functionality.
*/
/**
* A view into the reference-ordered data in the provider.
*/
public class ManagingReferenceOrderedView implements ReferenceOrderedView {
/**
* The data sources along with their current states.
*/
private List<ReferenceOrderedDataState> states = new ArrayList<ReferenceOrderedDataState>();
/**
* Create a new view of reference-ordered data.
* @param provider
*/
public ManagingReferenceOrderedView( LocusShardDataProvider provider ) {
for( ReferenceOrderedDataSource dataSource: provider.getReferenceOrderedData() )
states.add(new ReferenceOrderedDataState(dataSource, dataSource.seek(provider.getLocus())));
provider.register(this);
}
public Collection<Class<? extends View>> getConflictingViews() { return Collections.emptyList(); }
/**
* Gets an object which can track the reference-ordered data at every locus.
* @param loc Locus at which to track.
* @return A tracker containing information about this locus.
*/
@Override
public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc ) {
if ( states.isEmpty() )
return RefMetaDataTracker.EMPTY_TRACKER;
else {
List<RODRecordList> bindings = new ArrayList<RODRecordList>(states.size());
for ( ReferenceOrderedDataState state: states )
// todo -- warning, I removed the reference to the name from states
bindings.add( state.iterator.seekForward(loc) );
return new RefMetaDataTracker(bindings);
}
}
/**
* Closes the current view.
*/
public void close() {
for( ReferenceOrderedDataState state: states )
state.dataSource.close( state.iterator );
// Clear out the existing data so that post-close() accesses to this data will fail-fast.
states = null;
}
}
/**
* Models the traversal state of a given ROD lane.
*/
class ReferenceOrderedDataState {
public final ReferenceOrderedDataSource dataSource;
public final LocationAwareSeekableRODIterator iterator;
public ReferenceOrderedDataState( ReferenceOrderedDataSource dataSource, LocationAwareSeekableRODIterator iterator ) {
this.dataSource = dataSource;
this.iterator = iterator;
}
}