001    /*
002     *                    BioJava development code
003     *
004     * This code may be freely distributed and modified under the
005     * terms of the GNU Lesser General Public Licence.  This should
006     * be distributed with the code.  If you do not have a copy,
007     * see:
008     *
009     *      http://www.gnu.org/copyleft/lesser.html
010     *
011     * Copyright for this code is held jointly by the individual
012     * authors.  These should be listed in @author doc comments.
013     *
014     * For more information on the BioJava project and its aims,
015     * or to join the biojava-l mailing list, visit the home page
016     * at:
017     *
018     *      http://www.biojava.org/
019     *
020     * Created on 01-21-2010
021     */
022    
023    package org.biojava3.core.sequence.io;
024    
025    import java.util.List;
026    
027    import org.biojava3.core.sequence.DNASequence;
028    import org.biojava3.core.sequence.compound.NucleotideCompound;
029    import org.biojava3.core.sequence.io.template.SequenceCreatorInterface;
030    import org.biojava3.core.sequence.loader.ArrayListProxySequenceReader;
031    import org.biojava3.core.sequence.template.AbstractSequence;
032    import org.biojava3.core.sequence.template.CompoundSet;
033    import org.biojava3.core.sequence.template.ProxySequenceReader;
034    
035    /**
036     * A helper class that allows different ways to read a string and create a DNA sequence. Used in FastaReaderHelper
037     * and probably a layer that isn't needed
038     *
039     * @author Scooter Willis <willishf at gmail dot com>
040     */
041    public class DNASequenceCreator implements
042        SequenceCreatorInterface<NucleotideCompound> {
043    
044      private final CompoundSet<NucleotideCompound> compoundSet;
045    
046      /**
047       *
048       * @param compoundSet
049       */
050      public DNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet) {
051        this.compoundSet = compoundSet;
052      }
053    
054    /**
055     *
056     * @param sequence The Sequence from a String
057     * @param index Currently not used
058     * @return
059     */
060      public AbstractSequence<NucleotideCompound> getSequence(String sequence,
061          long index) {
062        return new DNASequence(sequence, compoundSet);
063      }
064    /**
065     *
066     * @param proxyLoader The Sequence from a ProxySequenceReader
067     * @param index Currently not used
068     * @return
069     */
070      public AbstractSequence<NucleotideCompound> getSequence(
071          ProxySequenceReader<NucleotideCompound> proxyLoader, long index) {
072        return new DNASequence(proxyLoader, compoundSet);
073      }
074    
075      /**
076       *
077       * @param list
078       * @return
079       */
080      public AbstractSequence<NucleotideCompound> getSequence(
081          List<NucleotideCompound> list) {
082        ArrayListProxySequenceReader<NucleotideCompound> store = new ArrayListProxySequenceReader<NucleotideCompound>();
083        store.setCompoundSet(compoundSet);
084        store.setContents(list);
085        return new DNASequence(store);
086      }
087    }