/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  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 @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on DATE
 *
 */
package org.biojava.nbio.core.sequence;

import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.loader.StringProxySequenceReader;
import org.biojava.nbio.core.sequence.template.*;
import org.biojava.nbio.core.sequence.transcription.Frame;
import org.biojava.nbio.core.sequence.transcription.TranscriptionEngine;
import org.biojava.nbio.core.sequence.views.ComplementSequenceView;
import org.biojava.nbio.core.sequence.views.ReversedSequenceView;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * This is class should model the attributes associated with a DNA sequence
 *
 * @author Scooter Willis
 */
public class DNASequence extends AbstractSequence<NucleotideCompound> {

	private final static Logger logger = LoggerFactory.getLogger(DNASequence.class);
/**
 * The type of DNA sequence
 */
	public enum DNAType {
		CHROMOSOME, MITOCHONDRIAL, PLASMID, PLASTID, UNKNOWN
	}
	private DNAType dnaType = DNAType.UNKNOWN;

	/**
	 * Shouldn't be used but makes it bean happy
	 */
	public DNASequence() {
//        throw new UnsupportedOperationException("Null constructor not supported");
	}

	/**
	 * String is king and create a sequence from DNA with default DNA compound set
	 * @param seqString
	 * @throws CompoundNotFoundException
	 */
	public DNASequence(String seqString) throws CompoundNotFoundException {
		super(seqString, DNACompoundSet.getDNACompoundSet());
	}

	/**
	 * Create a sequence where the actual storage of the sequence data is somewhere else
	 * @param proxyLoader
	 */
	public DNASequence(SequenceReader<NucleotideCompound> proxyLoader) {
		super(proxyLoader, DNACompoundSet.getDNACompoundSet());
	}

	/**
	 * Create a sequence from a string with user defined compound set
	 * @param seqString
	 * @param compoundSet
	 * @throws CompoundNotFoundException
	 */
	public DNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) throws CompoundNotFoundException {
		super(seqString, compoundSet);
	}

	/**
	 * Create a sequence from a ProxySequencereader and user defined compound set
	 * @param proxyLoader
	 * @param compoundSet
	 */
	public DNASequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) {
		super(proxyLoader, compoundSet);
	}

	/**
	 * Return the RNASequence equivalent of the DNASequence using default Transcription Engine. Not all
	 * species follow the same rules. If you don't know better use this method
	 * @return RNA sequence
	 */
	public RNASequence getRNASequence() {
	  return getRNASequence(Frame.getDefaultFrame());
	}

	/**
	 * Allow a user to pass in a rules engine to do the DNA to RNA translation
	 * @param engine
	 * @return RNA sequence
	 */
	public RNASequence getRNASequence(TranscriptionEngine engine) {
	  return getRNASequence(engine, Frame.getDefaultFrame());
	}

	/**
	 * Allows the user to pass in the Frame shift.
	 * @param frame
	 * @return rna sequence
	 */
	public RNASequence getRNASequence(Frame frame) {
	  return getRNASequence(TranscriptionEngine.getDefault(), frame);
	}

	public RNASequence getRNASequence(TranscriptionEngine engine, Frame frame) {
	  return (RNASequence) engine.getDnaRnaTranslator().createSequence(this, frame);
	}

	/**
	 * Get the GC count in the DNA Sequence
	 * @return GC count
	 */
	public int getGCCount() {
		return SequenceMixin.countGC(this);
	}

	/**
	 * Returns a Sequence which runs in the current reverse order
	 */
	public SequenceView<NucleotideCompound> getReverse() {
		return new ReversedSequenceView<NucleotideCompound>(this);
	}

	/**
	 * Returns a Sequence which will complement every base
	 */
	public SequenceView<NucleotideCompound> getComplement() {
		return new ComplementSequenceView<NucleotideCompound>(this);
	}

	/**
	 * Delegates to {@link #getInverse() } for the reverse complement
	 */
	public SequenceView<NucleotideCompound> getReverseComplement() {
		return getInverse();
	}

	/**
	 * @return the dnaType
	 */
	public DNAType getDNAType() {
		return dnaType;
	}

	/**
	 * @param dnaType the dnaType to set
	 */
	public void setDNAType(DNAType dnaType) {
		this.dnaType = dnaType;
	}

	public static void main(String[] args) throws Exception {
		DNASequence dnaSequence = new DNASequence("ATCG");
		logger.info("DNA Sequence: {}", dnaSequence.toString());

		StringProxySequenceReader<NucleotideCompound> sequenceStringProxyLoader =
				new StringProxySequenceReader<NucleotideCompound>("GCTA", DNACompoundSet.getDNACompoundSet());
		DNASequence dnaSequenceFromProxy = new DNASequence(sequenceStringProxyLoader);
		logger.info("DNA Sequence from Proxy: {}", dnaSequenceFromProxy.toString());
	}
}

@@ -4889,517 +4889,8 @@
 %0A%09%7D%0A
-%0A%09public static void main(String%5B%5D args) throws Exception %7B%0A%09%09DNASequence dnaSequence = new DNASequence(%22ATCG%22);%0A%09%09logger.info(%22DNA Sequence: %7B%7D%22, dnaSequence.toString());%0A%0A%09%09StringProxySequenceReader%3CNucleotideCompound%3E sequenceStringProxyLoader =%0A%09%09%09%09new StringProxySequenceReader%3CNucleotideCompound%3E(%22GCTA%22, DNACompoundSet.getDNACompoundSet());%0A%09%09DNASequence dnaSequenceFromProxy = new DNASequence(sequenceStringProxyLoader);%0A%09%09logger.info(%22DNA Sequence from Proxy: %7B%7D%22, dnaSequenceFromProxy.toString());%0A%09%7D
+%09
 %0A%7D%0A

remove DNASequence main