/*
 *                    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 01-21-2010
 *
 * @author Richard Holland
 * @author Scooter Willis
 * @author Paolo Pavan
 *
 */
package org.biojava.nbio.core.sequence.template;

import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.AccessionID;
import org.biojava.nbio.core.sequence.DataSource;
import org.biojava.nbio.core.sequence.Strand;
import org.biojava.nbio.core.sequence.TaxonomyID;
import org.biojava.nbio.core.sequence.features.*;
import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
import org.biojava.nbio.core.sequence.location.SequenceLocation;
import org.biojava.nbio.core.sequence.location.SimpleLocation;
import org.biojava.nbio.core.sequence.location.template.Location;
import org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.*;

/**
 *
 * The base class for DNA, RNA and Protein sequences.
 * @param <C>
 */
public abstract class AbstractSequence<C extends Compound> implements Sequence<C> {

	private final static Logger logger = LoggerFactory.getLogger(AbstractSequence.class);

	private TaxonomyID taxonomy;
	private AccessionID accession;
	private SequenceReader<C> sequenceStorage = null;
	private CompoundSet<C> compoundSet;
	private AnnotationType annotationType = AnnotationType.UNKNOWN;
	private String description;
	private String originalHeader;
	private Collection<Object> userCollection;
	private Integer bioBegin = null;
	private Integer bioEnd = null;
	private AbstractSequence<?> parentSequence = null;
	private String source = null;
	private ArrayList<String> notesList = new ArrayList<String>();
	private Double sequenceScore = null;
	private FeaturesKeyWordInterface featuresKeyWord = null;
	private DatabaseReferenceInterface databaseReferences = null;
	private FeatureRetriever featureRetriever = null;
	private ArrayList<FeatureInterface<AbstractSequence<C>, C>> features =
			new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
	private LinkedHashMap<String, ArrayList<FeatureInterface<AbstractSequence<C>, C>>> groupedFeatures =
			new LinkedHashMap<String, ArrayList<FeatureInterface<AbstractSequence<C>, C>>>();

	public AbstractSequence() {
	}

	/**
	 * Create a Sequence from a simple string where the values should be found in compoundSet
	 * @param seqString
	 * @param compoundSet
	 * @throws CompoundNotFoundException
	 */
	public AbstractSequence(String seqString, CompoundSet<C> compoundSet) throws CompoundNotFoundException {
		setCompoundSet(compoundSet);
		sequenceStorage = new ArrayListSequenceReader<C>();
		sequenceStorage.setCompoundSet(this.getCompoundSet());
		sequenceStorage.setContents(seqString);
	}

	/**
	 * A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location
	 * of the sequence data. A variety of use cases are possible. A ProxySequenceReader that knows the offset and of the sequence in
	 * a large fasta file. A ProxySequenceReader that can pull Sequence data from UniProt, NCBI or a custom database.
	 * If the ProxySequenceReader implements various interfaces then the sequence will set those interfaces so that calls to
	 * various methods will be valid.
	 *
	 * @param proxyLoader
	 * @param compoundSet
	 */
	public AbstractSequence(SequenceReader<C> proxyLoader, CompoundSet<C> compoundSet) {
		setCompoundSet(compoundSet);
		setProxySequenceReader(proxyLoader);
	}

	/**
	 * Very important method that allows external mappings of sequence data and features. This method
	 * will gain additional interface inspection that allows external data sources with knowledge
	 * of features for a sequence to be supported.
	 *
	 * @param proxyLoader
	 */
	public void setProxySequenceReader(SequenceReader<C> proxyLoader) {
		this.sequenceStorage = proxyLoader;
		if (proxyLoader instanceof FeaturesKeyWordInterface) {
			this.setFeaturesKeyWord((FeaturesKeyWordInterface) sequenceStorage);
		}
		if (proxyLoader instanceof DatabaseReferenceInterface) {
			this.setDatabaseReferences((DatabaseReferenceInterface) sequenceStorage);
		}

		if (proxyLoader instanceof FeatureRetriever) {
			this.setFeatureRetriever((FeatureRetriever) sequenceStorage);
			HashMap<String, ArrayList<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
			for (String k: ff.keySet()){
				for (AbstractFeature f: ff.get(k)){
					this.addFeature(f);
				}
			}
			// success of next statement guaranteed because source is a compulsory field
			//DBReferenceInfo dbQualifier = (DBReferenceInfo)ff.get("source").get(0).getQualifiers().get("db_xref");
			ArrayList<DBReferenceInfo> dbQualifiers = (ArrayList)ff.get("source").get(0).getQualifiers().get("db_xref");
			DBReferenceInfo dbQualifier = dbQualifiers.get(0);

			if (dbQualifier != null) this.setTaxonomy(new TaxonomyID(dbQualifier.getDatabase()+":"+dbQualifier.getId(), DataSource.UNKNOWN));
		}

		if(getAccession() == null && proxyLoader instanceof UniprotProxySequenceReader){ // we have lots of unsupported operations for this call so quick fix to allow this tow rork
			this.setAccession(proxyLoader.getAccession());
		}
	}

	public SequenceReader<C> getProxySequenceReader() {
		return sequenceStorage;
	}

	/**
	 * @return the bioBegin
	 */
	public Integer getBioBegin() {
		if (bioBegin == null) {
			return 1;
		} else {
			return bioBegin;
		}
	}

	/**
	 * @param bioBegin the bioBegin to set
	 */
	public void setBioBegin(Integer begin) {
		this.bioBegin = begin;
	}

	/**
	 * @return the bioEnd
	 */
	public Integer getBioEnd() {
		if (bioEnd == null) {
			return this.getLength();
		} else {
			return bioEnd;
		}
	}

	/**
	 * @param bioEnd the bioEnd to set
	 */
	public void setBioEnd(Integer end) {
		this.bioEnd = end;
	}

	/**
	 * Provided for convince if the developer needs to associate data with a sequence
	 *
	 * @return
	 */
	public Collection<Object> getUserCollection() {

		return userCollection;
	}

	/**
	 *
	 * @param userCollection
	 */
	public void setUserCollection(Collection<Object> userCollection) {
		this.userCollection = userCollection;
	}

	/**
	 * @return the annotation
	 */
	public AnnotationType getAnnotationType() {
		return annotationType;
	}

	/**
	 * @param annotation the annotation to set
	 */
	public void setAnnotationType(AnnotationType annotationType) {
		this.annotationType = annotationType;
	}

	/**
	 * @return the description
	 */
	public String getDescription() {
		return description;
	}

	/**
	 * @param description the description to set
	 */
	public void setDescription(String description) {
		this.description = description;
	}

	/**
	 * @return the originalHeader
	 */
	public String getOriginalHeader() {
		return originalHeader;
	}

	/**
	 * @param originalHeader the originalHeader to set
	 */
	public void setOriginalHeader(String originalHeader) {
		this.originalHeader = originalHeader;
	}

	/**
	 * @return the parentSequence
	 */
	public AbstractSequence<?> getParentSequence() {
		return parentSequence;
	}

	/**
	 * @param parentSequence the parentSequence to set
	 */
	public void setParentSequence(AbstractSequence<?> parentSequence) {
		this.parentSequence = parentSequence;
	}

	/**
	 * Added support for the source of this sequence for GFF3 export
	 * If a sub sequence doesn't have  source then check for parent source
	 * @return the source
	 */
	public String getSource() {
		if (source != null) {
			return source;
		}
		if (parentSequence != null) {
			return parentSequence.getSource();
		}
		return null;
	}

	/**
	 * Added support for the source of this sequence for GFF3 export
	 * @param source the source to set
	 */
	public void setSource(String source) {

		this.source = source;
	}

	/**
	 * Add notes about this sequence that will get exported for GFF3
	 * @param note
	 */
	public void addNote(String note) {
		notesList.add(note);
	}

	public void removeNote(String note) {
		notesList.remove(note);
	}

	/**
	 * @return the notesList
	 */
	public ArrayList<String> getNotesList() {
		return notesList;
	}

	/**
	 * @param notesList the notesList to set
	 */
	public void setNotesList(ArrayList<String> notesList) {
		this.notesList = notesList;
	}

	/**
	 * Provide place holder for a metric that indicate a score associated with the sequence
	 * @return the sequenceScore
	 */
	public Double getSequenceScore() {
		return sequenceScore;
	}

	/**
	 * @param sequenceScore the sequenceScore to set
	 */
	public void setSequenceScore(Double sequenceScore) {
		this.sequenceScore = sequenceScore;
	}

	/**
	 * Return features at a sequence position by type
	 * @param featureType
	 * @param bioSequencePosition
	 * @return
	 */
	public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(String featureType, int bioSequencePosition) {
		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureHits =
				new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
		List<FeatureInterface<AbstractSequence<C>, C>> features = getFeaturesByType(featureType);
		if (features != null) {
			for (FeatureInterface<AbstractSequence<C>, C> feature : features) {
				if (bioSequencePosition >= feature.getLocations().getStart().getPosition() && bioSequencePosition <= feature.getLocations().getEnd().getPosition()) {
					featureHits.add(feature);
				}
			}
		}
		return featureHits;
	}

	/**
	 * Return features at a sequence position
	 * @param featureType
	 * @param bioSequencePosition
	 * @return
	 */
	public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(int bioSequencePosition) {
		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureHits =
				new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
		if (features != null) {
			for (FeatureInterface<AbstractSequence<C>, C> feature : features) {
				if (bioSequencePosition >= feature.getLocations().getStart().getPosition() && bioSequencePosition <= feature.getLocations().getEnd().getPosition()) {
					featureHits.add(feature);
				}
			}
		}
		return featureHits;
	}

	/**
	 *
	 * @return
	 */
	public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures() {
		return features;
	}

	/**
	 * Method to help set the proper details for a feature as it relates to a sequence
	 * where the feature needs to have a location on the sequence
	 * @param bioStart
	 * @param bioEnd
	 * @param feature
	 */
	public void addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>, C> feature) {
		SequenceLocation<AbstractSequence<C>, C> sequenceLocation =
				new SequenceLocation<AbstractSequence<C>, C>(bioStart, bioEnd, this);
		feature.setLocation(sequenceLocation);
		addFeature(feature);
	}

	/**
	 * Add a feature to this sequence. The feature will be added to the collection where the order is start position and if more than
	 * one feature at the same start position then longest is added first. This helps on doing feature layout for displaying features
	 * in SequenceFeaturePanel
	 * @param feature
	 */
	public void addFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
		features.add(feature);
		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.get(feature.getType());
		if (featureList == null) {
			featureList = new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
			groupedFeatures.put(feature.getType(), featureList);
		}
		featureList.add(feature);
		Collections.sort(features, AbstractFeature.LOCATION_LENGTH);
		Collections.sort(featureList, AbstractFeature.LOCATION_LENGTH);
	}

	/**
	 * Remove a feature from the sequence
	 * @param feature
	 */
	public void removeFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
		features.remove(feature);
		ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.get(feature.getType());
		if (featureList != null) {
			featureList.remove(feature);
			if (featureList.isEmpty()) {
				groupedFeatures.remove(feature.getType());
			}
		}
	}

	/**
	 *
	 * @param type
	 * @return
	 */
	public List<FeatureInterface<AbstractSequence<C>, C>> getFeaturesByType(String type) {
		List<FeatureInterface<AbstractSequence<C>, C>> features = groupedFeatures.get(type);
		if (features == null) {
			features = new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
		}
		return features;
	}

	/**
	 * @return the featuresKeyWord
	 */
	public FeaturesKeyWordInterface getFeaturesKeyWord() {
		return featuresKeyWord;
	}

	/**
	 * @param featuresKeyWord the featuresKeyWord to set
	 */
	public void setFeaturesKeyWord(FeaturesKeyWordInterface featuresKeyWord) {
		this.featuresKeyWord = featuresKeyWord;
	}

	/**
	 * @return the databaseReferences
	 */
	public DatabaseReferenceInterface getDatabaseReferences() {
		return databaseReferences;
	}

	/**
	 * @param databaseReferences the databaseReferences to set
	 */
	public void setDatabaseReferences(DatabaseReferenceInterface databaseReferences) {
		this.databaseReferences = databaseReferences;
	}

	public FeatureRetriever getFeatureRetriever() {
		return featureRetriever;
	}

	public void setFeatureRetriever(FeatureRetriever featureRetriever) {
		this.featureRetriever = featureRetriever;
	}



	public enum AnnotationType {

		CURATED, PREDICTED, UNKNOWN;
	}

	/**
	 * @return the accession
	 */
	@Override
	public AccessionID getAccession() {
		return accession;
	}

	/**
	 * @param accession the accession to set
	 */
	public void setAccession(AccessionID accession) {
		this.accession = accession;
	}

	/**
	 * @return the species
	 */
	public TaxonomyID getTaxonomy() {
		return taxonomy;
	}

	/**
	 * @param species the species to set
	 */
	public void setTaxonomy(TaxonomyID taxonomy) {
		this.taxonomy = taxonomy;
	}

	@Override
	public CompoundSet<C> getCompoundSet() {
		if (compoundSet != null) {
			return compoundSet;
		}
		// This is invalid since the parentSequence isn't guaranteed to have the same compound set as this sequence,
		// e.g., the case where the parent sequence for a protein is a CDS.
		/*
		if (parentSequence != null) {
			return parentSequence.getCompoundSet();
		}
		*/
		return null;


	}

	public void setCompoundSet(CompoundSet<C> compoundSet) {
		this.compoundSet = compoundSet;
	}

	@Override
	public String toString() {
		return getSequenceAsString();
	}

	private SequenceReader<C> getSequenceStorage() {
		if (sequenceStorage != null) {
			return sequenceStorage;
		}
		if (parentSequence != null) {

			//return parentSequence.getSequenceStorage();

			if ( this.compoundSet.equals(parentSequence.getCompoundSet())){
				sequenceStorage = new ArrayListSequenceReader<C>();
				sequenceStorage.setCompoundSet(this.getCompoundSet());
				try {
					sequenceStorage.setContents(parentSequence.getSequenceAsString());
				} catch (CompoundNotFoundException e) {
					// TODO is there a better way to handle this exception?
					logger.error("Problem setting contents from parent sequence, some unrecognised compound: {}",e.getMessage());
				}
				return sequenceStorage;
			}

		}

		return null;
	}

	/**
	 *
	 * @param begin
	 * @param end
	 * @param strand
	 * @return
	 */
	public String getSequenceAsString(Integer bioStart, Integer bioEnd, Strand strand) {

		Location loc = new SimpleLocation(bioStart, bioEnd, strand);
		return loc.getSubSequence(this).getSequenceAsString();
	}

	/**
	 * Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
	 * @return
	 */
	@Override
	public String getSequenceAsString() {
		return SequenceMixin.toString(this);

	}

	/**
	 *
	 * @return
	 */
	@Override
	public List<C> getAsList() {
		return SequenceMixin.toList(this);
	}

	/**
	 *
	 * @param position The 1-indexed position of the amino acid
	 * @return
	 */
	@Override
	public C getCompoundAt(int position) {

		return getSequenceStorage().getCompoundAt(position);
	}

	/**
	 *
	 * @param compound
	 * @return The first index of compound in this sequence (1-based)
	 */
	@Override
	public int getIndexOf(C compound) {
		return getSequenceStorage().getIndexOf(compound);
	}

	/**
	 *
	 * @param compound
	 * @return The last index of compound in this sequence (1-based)
	 */
	@Override
	public int getLastIndexOf(C compound) {
		return getSequenceStorage().getLastIndexOf(compound);
	}

	/**
	 *
	 * @return
	 */
	@Override
	public int getLength() {
		return getSequenceStorage().getLength();
	}

	/**
	 *
	 * @param bioStart
	 * @param bioEnd
	 * @return
	 */
	@Override
	public SequenceView<C> getSubSequence(final Integer bioStart, final Integer bioEnd) {
		return new SequenceProxyView<C>(this, bioStart, bioEnd);
	}

	/**
	 *
	 * @return
	 */
	@Override
	public Iterator<C> iterator() {
		return getSequenceStorage().iterator();
	}

	/**
	 *
	 * @param compounds
	 * @return
	 */
	@Override
	public int countCompounds(C... compounds) {
		return SequenceMixin.countCompounds(this, compounds);
	}

	/**
	 *
	 * @return
	 */
	@Override
	public SequenceView<C> getInverse() {
		return SequenceMixin.inverse(this);
	}

	//TODO needs equals and hashcode
}
