org.jcvi.jillion.trace.fastq.DefaultFastqFileDataStore Maven / Gradle / Ivy

Show more of this group Show more artifacts with this name
Show all versions of jillion Show documentation
An open source genomics software library written in Java to support sequence and assembly analysis
There is a newer version: 6.0.2
/*******************************************************************************
 * Jillion development code
 * 
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public License.  This should
 * be distributed with the code.  If you do not have a copy,
 *  see:
 * 
 *          http://www.gnu.org/copyleft/lesser.html
 * 
 * 
 * Copyright for this code is held jointly by the individual authors.  These should be listed in the @author doc comments.
 * 
 * Information about Jillion can be found on its homepage
 * 
 *         http://jillion.sourceforge.net
 * 
 * Contributors:
 *     Danny Katzel - initial API and implementation
 ******************************************************************************/
/*
 * Created on Oct 9, 2009
 *
 * @author dkatzel
 */
package org.jcvi.jillion.trace.fastq;

import java.io.File;
import java.io.IOException;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.function.Predicate;

import org.jcvi.jillion.core.datastore.DataStore;
import org.jcvi.jillion.core.util.Builder;
/**
 * {@code DefaultFastqFileDataStore} is the default implementation
 * of {@link FastqDataStore} which stores
 * all {@link FastqRecord}s from a file in memory.  This is only recommended for small fastq
 * files that won't take up too much memory.
 * @author dkatzel
 *
 */
final class DefaultFastqFileDataStore{
	
	private DefaultFastqFileDataStore(){
		//can not instantiate
	}


   /**
	 * Create a new {@link FastqDataStore} instance for the {@link FastqRecord}s
	 * that are accepted by the given {@link DataStoreFilter} that are contained in
	 * the given fastq file. Any records that are not accepted by the filter
	 * will not be included in the returned {@link FastqDataStore}. All of those
	 * records must have their qualities encoded a manner that can be parsed by
	 * the given {@link FastqQualityCodec} (if provided).
	 * 
	 * @param parser
	 *            the {@link FastqParser} instance to parse, must exist and can not be null.
	 * @param filter
	 *            an instance of {@link DataStoreFilter} that can be used to filter
	 *            out some {@link FastqRecord}s from the datastore.
	 * @param qualityCodec
	 *            the {@link FastqQualityCodec} needed to parse the encoded
	 *            quality values in each record. If this value is null, then the
	 *            datastore implementation will try to guess the codec used
	 *            which might have a performance penalty associated with it.
	 * @return a new {@link FastqFileDataStore} instance containing only those
	 *         records that pass the filter.
	 * @throws IOException
	 *             if thre is a problem parsing the fastq file.
	 * @throws NullPointerException
	 *             if either fastqFile or filter is null.
	 */
	public static FastqFileDataStore create(FastqParser parser,
			FastqQualityCodec qualityCodec, Predicate filter, Predicate recordFilter)
			throws IOException {
		DefaultFastqFileDataStoreBuilderVisitor2 visitor = new DefaultFastqFileDataStoreBuilderVisitor2(
		        qualityCodec,filter, recordFilter, parser.getFile().orElse(null));
		   
		   parser.parse(visitor);

		   return visitor.build();
	}
    
	private static final class DefaultFastqFileDataStoreBuilderVisitor2 implements FastqVisitor, Builder {
		private final Predicate filter;
		private final Predicate recordFilter;
		private final FastqQualityCodec qualityCodec;
		private final Map map = new LinkedHashMap<>();

		private final File fastqFile;
		
		public DefaultFastqFileDataStoreBuilderVisitor2(
				FastqQualityCodec qualityCodec, Predicate filter, Predicate recordFilter,
				File fastqFile) {
			if(qualityCodec==null){
				throw new NullPointerException("quality codec can not be null");
			}
			if(filter==null){
				throw new NullPointerException("filter can not be null");
			}
			
			this.qualityCodec = qualityCodec;
			this.filter = filter;
			this.recordFilter = recordFilter;
			this.fastqFile = fastqFile;
		}

		@Override
		public FastqRecordVisitor visitDefline(FastqVisitorCallback callback,
				String id, String optionalComment) {
			if(!filter.test(id)){
				return null;
			}
			return new AbstractFastqRecordVisitor(id,optionalComment, qualityCodec) {
				
				@Override
				protected void visitRecord(FastqRecord record) {
				    if(recordFilter==null || recordFilter.test(record)){
					map.put(record.getId(), record);	
				    }
				}
			};
		}

		@Override
		public void visitEnd() {
			//no-op
		}
		@Override
		public void halted() {
			//no-op			
		}
		@Override
		public FastqFileDataStore build() {
			return new FastqFileDataStoreImpl(DataStore.of(map, FastqDataStore.class),
			                                    qualityCodec, fastqFile);
		}

	}
}