/*
 *                    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/
 *
 */

package org.biojava.bio.seq.impl;

import java.util.Collections;
import java.util.Iterator;

import org.biojava.bio.Annotatable;
import org.biojava.bio.Annotation;
import org.biojava.bio.BioError;
import org.biojava.bio.BioException;
import org.biojava.bio.SimpleAnnotation;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.FeatureFilter;
import org.biojava.bio.seq.FeatureHolder;
import org.biojava.bio.seq.FilterUtils;
import org.biojava.bio.seq.RealizingFeatureHolder;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SimpleFeatureHolder;
import org.biojava.bio.symbol.Location;
import org.biojava.bio.symbol.SymbolList;
import org.biojava.ontology.OntoTools;
import org.biojava.ontology.Term;
import org.biojava.utils.AbstractChangeable;
import org.biojava.utils.ChangeEvent;
import org.biojava.utils.ChangeForwarder;
import org.biojava.utils.ChangeListener;
import org.biojava.utils.ChangeSupport;
import org.biojava.utils.ChangeType;
import org.biojava.utils.ChangeVetoException;

/**
 * A no-frills implementation of a feature.
 * 
 * @author Matthew Pocock
 * @author Thomas Down
 * @author Kalle N�slund
 * @author Paul Seed
 * @author Len Trigg
 * @see org.biojavax.bio.seq.SimpleRichFeature
 */

public class SimpleFeature
extends
 AbstractChangeable
implements
 Feature,
 RealizingFeatureHolder,
 java.io.Serializable
{
  private transient ChangeListener annotationForwarder;
  private transient ChangeListener featureForwarder;

  /**
   * The FeatureHolder that we will delegate the FeatureHolder interface too.
   * This is lazily instantiated.
   */
  private SimpleFeatureHolder featureHolder;

  /**
   * The location of this feature.
   */
  private Location loc;
  /**
   * The type of this feature - something like Exon.
   * This is included for cheap interoperability with GFF.
   */
  private String type;
  /**
   * The source of this feature - the program that generated it.
   * This is included for cheap interoperability with GFF.
   */
  private String source;
  /**
   * Our parent FeatureHolder.
   */
  private FeatureHolder parent;
  /**
   * The annotation object.
   * This is lazily instantiated.
   */
  private Annotation annotation;

  private Term typeTerm;
  private Term sourceTerm;

  /**
   * A utility function to retrieve the feature holder delegate, creating it if
   * necessary.
   *
   * @return  the FeatureHolder delegate
   */
  protected SimpleFeatureHolder getFeatureHolder() {
    if(featureHolder == null) {
      featureHolder = new SimpleFeatureHolder();
    }
    return featureHolder;
  }

  /**
   * A utility function to find out if the feature holder delegate has been
   * instantiated yet. If it has not, we may avoid instantiating it by returning
   * some pre-canned result.
   *
   * @return true if the feature holder delegate has been created and false
   *         otherwise
   */
  protected boolean featureHolderAllocated() {
    return featureHolder != null;
  }

  protected ChangeSupport getChangeSupport(ChangeType ct) {
    ChangeSupport cs = super.getChangeSupport(ct);

    if(
      (annotationForwarder == null) &&
      (ct.isMatchingType(Annotatable.ANNOTATION) || Annotatable.ANNOTATION.isMatchingType(ct))
    ) {
      annotationForwarder =
              new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY);
      getAnnotation().addChangeListener(
        annotationForwarder,
        Annotatable.ANNOTATION
      );
    }

    if(
      (featureForwarder == null) &&
      (ct == null || ct == FeatureHolder.FEATURES)
    ) {
      featureForwarder = new ChangeForwarder(
        this,
        cs
      );
      getFeatureHolder().addChangeListener(
        featureForwarder,
        FeatureHolder.FEATURES
      );
    }

    return cs;
  }

  public Location getLocation() {
    return loc;
  }

  public void setLocation(Location loc)
  throws ChangeVetoException {
    if(hasListeners()) {
      ChangeSupport cs = getChangeSupport(LOCATION);
      synchronized(cs) {
        ChangeEvent ce = new ChangeEvent(this, LOCATION, loc, this.loc);
        cs.firePreChangeEvent(ce);
        this.loc = loc;
        cs.firePostChangeEvent(ce);
      }
    } else {
      this.loc = loc;
    }
  }

  public Term getTypeTerm() {
      return typeTerm;
  }

  public String getType() {
    if(type != null) {
      return type;
    } else if (typeTerm != null) {
        return typeTerm.getName();
    } else {
        return "";
    }
  }

  public void setType(String type)
  throws ChangeVetoException {
    if(hasListeners()) {
      ChangeSupport cs = getChangeSupport(TYPE);
      synchronized(cs) {
        ChangeEvent ce = new ChangeEvent(this, TYPE, type, this.type);
        cs.firePreChangeEvent(ce);
        this.type = type;
        cs.firePostChangeEvent(ce);
      }
    } else {
      this.type = type;
    }
  }

    public void setTypeTerm(Term t)
        throws ChangeVetoException
    {
        if(hasListeners()) {
            ChangeSupport cs = getChangeSupport(TYPE);
            synchronized (cs) {
                ChangeEvent ce_term = new ChangeEvent(this, TYPETERM, t, this.getTypeTerm());
                ChangeEvent ce_name = new ChangeEvent(this, TYPE, t.getName(), this.getType());
                cs.firePreChangeEvent(ce_term);
                cs.firePreChangeEvent(ce_name);
                this.typeTerm = t;
                cs.firePostChangeEvent(ce_term);
                cs.firePostChangeEvent(ce_name);
            }
        } else {
            this.typeTerm = t;
        }
    }

  public String getSource() {
    if(source != null) {
      return source;
    } else if (sourceTerm != null) {
        return sourceTerm.getName();
    } else {
        return "";
    }
  }

  public Term getSourceTerm() {
      return sourceTerm;
  }

  public FeatureHolder getParent() {
    return parent;
  }

  public void setSource(String source)
  throws ChangeVetoException {
    if(hasListeners()) {
      ChangeSupport cs = getChangeSupport(SOURCE);
      synchronized(cs) {
        ChangeEvent ce = new ChangeEvent(this, SOURCE, this.source, source);
        cs.firePreChangeEvent(ce);
        this.source = source;
        cs.firePostChangeEvent(ce);
      }
    } else {
      this.source = source;
    }
  }


    public void setSourceTerm(Term t)
        throws ChangeVetoException
    {
        if(hasListeners()) {
            ChangeSupport cs = getChangeSupport(TYPE);
            synchronized (cs) {
                ChangeEvent ce_term = new ChangeEvent(this, SOURCETERM, t, this.getSourceTerm());
                ChangeEvent ce_name = new ChangeEvent(this, SOURCE, t.getName(), this.getSource());
                cs.firePreChangeEvent(ce_term);
                cs.firePreChangeEvent(ce_name);
                this.sourceTerm = t;
                cs.firePostChangeEvent(ce_term);
                cs.firePostChangeEvent(ce_name);
            }
        } else {
            this.sourceTerm = t;
        }
    }

    public Sequence getSequence() {
	FeatureHolder fh = this;
	while (fh instanceof Feature) {
	    fh = ((Feature) fh).getParent();
	}
	try {
	    return (Sequence) fh;
	} catch (ClassCastException ex) {
	    throw new BioError("Feature doesn't seem to have a Sequence ancestor: " + fh);
	}
    }

    public Annotation getAnnotation() {
	if(annotation == null)
	    annotation = new SimpleAnnotation();
	return annotation;
    }

    public SymbolList getSymbols() {
	return getLocation().symbols(getSequence());
    }

    public int countFeatures() {
	if(featureHolderAllocated())
	    return getFeatureHolder().countFeatures();
	return 0;
    }

    public Iterator features() {
	if(featureHolderAllocated())
	    return getFeatureHolder().features();
	return Collections.EMPTY_LIST.iterator();
    }

    public void removeFeature(Feature f)
    throws ChangeVetoException {
	getFeatureHolder().removeFeature(f);
    }

    public boolean containsFeature(Feature f) {
      if(featureHolderAllocated()) {
        return getFeatureHolder().containsFeature(f);
      } else {
        return false;
      }
    }


    public FeatureHolder filter(FeatureFilter ff) {
        FeatureFilter childFilter = new FeatureFilter.Not(FeatureFilter.top_level);

        if (FilterUtils.areDisjoint(ff, childFilter)) {
            return FeatureHolder.EMPTY_FEATURE_HOLDER;
        } else if (featureHolderAllocated()) {
            return getFeatureHolder().filter(ff);
        } else {
            return FeatureHolder.EMPTY_FEATURE_HOLDER;
        }
    }

    public FeatureHolder filter(FeatureFilter ff, boolean recurse) {
	if(featureHolderAllocated())
	    return getFeatureHolder().filter(ff, recurse);
	return FeatureHolder.EMPTY_FEATURE_HOLDER;
    }

    public Feature.Template makeTemplate() {
      Feature.Template ft = new Feature.Template();
      fillTemplate(ft);
      return ft;
    }

    protected void fillTemplate(Feature.Template ft) {
      ft.location = getLocation();
      ft.type = getType();
      ft.source = getSource();
      ft.annotation = getAnnotation();
      ft.sourceTerm = getSourceTerm();
      ft.typeTerm = getTypeTerm();
    }

    /**
     * Create a <code>SimpleFeature</code> on the given sequence.
     * The feature is created underneath the parent <code>FeatureHolder</code>
     * and populated directly from the template fields. However,
     * if the template annotation is the <code>Annotation.EMPTY_ANNOTATION</code>,
     * an empty <code>SimpleAnnotation</code> is attached to the feature instead.
     * @param sourceSeq the source sequence
     * @param parent the parent sequence or feature
     * @param template the template for the feature
     */
    public SimpleFeature(Sequence sourceSeq,
                         FeatureHolder parent,
                         Feature.Template template) {
        if (template.location == null) {
            throw new IllegalArgumentException(
		         "Location can not be null. Did you mean Location.EMPTY_LOCATION? " +
                 template.toString()
            );
        }
        if(!(parent instanceof Feature) && !(parent instanceof Sequence)) {
            throw new IllegalArgumentException("Parent must be sequence or feature, not: " + parent.getClass() + " " + parent);
        }

        if (template.location.getMin() < 1 || template.location.getMax() > sourceSeq.length()) {
            //throw new IllegalArgumentException("Location " + template.location.toString() + " is outside 1.." + sourceSeq.length());
        }

        this.parent = parent;
        this.loc = template.location;
        this.typeTerm = template.typeTerm != null ? template.typeTerm : OntoTools.ANY;
        this.sourceTerm = template.sourceTerm != null ? template.sourceTerm : OntoTools.ANY;
        this.type = template.type != null ? template.type : typeTerm.getName();
        this.source = template.source != null ? template.source : sourceTerm.getName();
        if (this.type == null) {
            throw new NullPointerException("Either type or typeTerm must have a non-null value");
        }
        if (this.source == null) {
            throw new NullPointerException("Either source or sourceTerm must have a non-null value");
        }
        this.annotation = template.annotation != null ? new SimpleAnnotation(template.annotation) : null;
    }

    public String toString() {
	return "Feature " + getType() + " " +
	    getSource() + " " + getLocation();
    }

    public Feature realizeFeature(FeatureHolder fh, Feature.Template templ)
        throws BioException
    {
	try {
	    RealizingFeatureHolder rfh = (RealizingFeatureHolder) getParent();
	    return rfh.realizeFeature(fh, templ);
	} catch (ClassCastException ex) {
	    throw new BioException("Couldn't propagate feature creation request.");
	}
    }

    public Feature createFeature(Feature.Template temp)
        throws BioException, ChangeVetoException
    {
	Feature f = realizeFeature(this, temp);
	getFeatureHolder().addFeature(f);
	return f;
    }

    public int hashCode() {
	return makeTemplate().hashCode();
    }

    public boolean equals(Object o) {
	if (! (o instanceof Feature)) {
	    return false;
	}

	Feature fo = (Feature) o;
	if (! fo.getSequence().equals(getSequence()))
	    return false;

	return makeTemplate().equals(fo.makeTemplate());
    }

    public FeatureFilter getSchema() {
        return new FeatureFilter.ByParent(new FeatureFilter.ByFeature(this));
    }
}