/*
 * 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.symbol;

import java.io.Serializable;
import java.util.AbstractList;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;

import org.biojava.bio.Annotation;
import org.biojava.bio.BioException;
import org.biojava.bio.BioRuntimeException;
import org.biojava.bio.seq.io.SymbolTokenization;
import org.biojava.utils.AbstractChangeable;
import org.biojava.utils.ChangeEvent;
import org.biojava.utils.ChangeForwarder;
import org.biojava.utils.ChangeSupport;
import org.biojava.utils.ChangeType;
import org.biojava.utils.ChangeVetoException;

/**
 * <p>
 * Abstract helper implementation of the SymbolList core interface.
 * To produce a concrete SymbolList implementation, you need only
 * implement the <code>getAlphabet</code>, <code>length</code> and
 * <code>symbolAt</code> methods.  Iterators and sublists are
 * handled for you automatically.
 * </p>
 *
 * <p>
 * This class makes many custom SymbolList implementations
 * very quick to implement.
 * See org.biojava.bio.seq.tools.ComplementSymbolList
 * for an example of this.
 * </p>
 *
 * <p>
 * To make a mutable SymbolList, override the implementation of edit to perform
 * the apropreate edit. If your implementation of SymbolList is a view onto an
 * underlying SymbolList, then you must forward any apropreate edit requests
 * to that list, and forward all events from the underlying list to your
 * listeners.
 * </p>
 *
 * @author     Thomas Down
 * @author     Matthew Pocock
 */

public abstract class AbstractSymbolList
extends AbstractChangeable
implements SymbolList {
  protected AbstractSymbolList() {
  }

  public Iterator iterator() {
    return new SymbolIterator(1, length());
  }

  public SymbolList subList(int start, int end)
  {
      if (start < 1 || end > length()) {
          throw new IndexOutOfBoundsException(
                  "Sublist index out of bounds " + length() + ":" + start + "," + end
          );
      }

      if (end < start) {
        throw new IllegalArgumentException(
            "end must not be lower than start: start=" + start + ", end=" + end
        );
      }
      return new SubList(start, end);
  }

  public List toList() {
    return new ListView(this);
  }

  public String seqString() {
      try {
          SymbolTokenization toke = getAlphabet().getTokenization("default");
          return toke.tokenizeSymbolList(this);
      } catch (BioException ex) {
          throw new BioRuntimeException("Couldn't tokenize sequence", ex);
      }
  }

  public String subStr(int start, int end) {
      return subList(start, end).seqString();
  }

  public void edit(Edit edit) throws IllegalAlphabetException, ChangeVetoException {
    throw new ChangeVetoException(
      "AbstractSymbolList is immutable"
    );
  }

  /**
   * Provides logical equality for two SymbolLists that share the same list
   * of canonical symbols
   */
  public boolean equals(Object o){
    if(this == o) return true;//just for optimality
    if(o == null) return false;
    if(!(o instanceof SymbolList)) return false;
    return compare(this, (SymbolList)o);
  }

  private volatile int hashCode = 0; //for caching purposes
  public int hashCode(){
    if(hashCode == 0){
      int result = 17;
      for(Iterator i = iterator(); i.hasNext();){
        result = 37*result + i.next().hashCode();
      }
      hashCode = result;
    }
    return hashCode;
  }

  public String toString() {
    return super.toString() + " length: " + length();
  }

  private boolean compare(SymbolList sl1, SymbolList sl2){
    if (!sl1.getAlphabet().equals(sl2.getAlphabet())) {
        return false;
    }
      
    if (sl1.length() != sl2.length()) {
      return false;
    }

    Iterator si1 = sl1.iterator();
    Iterator si2 = sl2.iterator();
    while (si1.hasNext()) {
      if (! (si1.next() == si2.next())) {
         return false;
      }
    }
    return true;
  }

  /**
   * <p>
   * An Iterator over each Symbol in a range of a SymbolList.
   * </p>
   *
   * <p>
   * Objects of this type are returned by
   * <code>AbstractSymbolList.iterator</code>.
   * </p>
   *
   * @author     Thomas Down
   */

  private class SymbolIterator implements Iterator, Serializable {
    private int max;
    private int pos;

    /**
     * Construct a SymbolIterator object that will return the symbols from
     * min to max inclusive.
     *
     * @param  min  the first index to return
     * @param  max  the last index to return
     */

    public SymbolIterator(int min, int max) {
      this.max = max;
      pos = min;
    }

    protected SymbolIterator() {
    }

    public boolean hasNext() {
      return (pos <= max);
    }

    public Object next() {
      if (pos > max) {
        throw new NoSuchElementException();
      }
      return symbolAt(pos++);
    }

    public void remove() {
      throw new UnsupportedOperationException();
    }
  }

  /**
   * <p>
   * Implements a list view of a SymbolList.
   * </p>
   *
   * <p>
   * Objects of this type are instantiated by
   * <code>AbstractSymbolList.subList</code>.
   * </p>
   *
   * @author     Thomas Down
   * @author     Matthew Pocock
   */

  private class SubList
  extends AbstractChangeable
  implements SymbolList, Serializable {
    private int start, end;

    private transient EditTranslater editTranslater = null;
    private transient ChangeForwarder annotationForwarder = null;

    public SubList(int start, int end) {
      this.start = start;
      this.end = end;
    }

    public Alphabet getAlphabet() {
      return AbstractSymbolList.this.getAlphabet();
    }

    public Iterator iterator() {
      return new SymbolIterator(start, end);
    }

    public int length() {
      return end - start + 1;
    }

    public Symbol symbolAt(int pos) {
      if (pos < 1 || pos > length()) {
        throw new IndexOutOfBoundsException(
            "Symbol index out of bounds " + length() + ":" + pos
            );
      }
      return AbstractSymbolList.this.symbolAt(pos + start - 1);
    }

    public SymbolList subList(int sstart, int send) {
      if (sstart < 1 || send > length()) {
        throw new IndexOutOfBoundsException(
            "Sublist index out of bounds " + length() + ":" + sstart + "," + send
            );
      }

      if (send < sstart) {
        throw new IndexOutOfBoundsException(
            "Requested end must not be lower than start: start=" + sstart + ", end=" + send
            );
      }

      return new SubList(sstart + start - 1, send + start - 1);
    }


      public String seqString() {
          try {
              SymbolTokenization toke = getAlphabet().getTokenization("token");
              return toke.tokenizeSymbolList(this);
          } catch (BioException ex) {
              throw new BioRuntimeException("Couldn't tokenize sequence", ex);
          }
      }

      public String subStr(int start, int end) {
          return subList(start, end).seqString();
      }

    public List toList() {
      return new ListView(this);
    }

    // fixme: doesn't do range checking on edit object
    public void edit(Edit edit) throws IllegalAlphabetException, ChangeVetoException {
      AbstractSymbolList.this.edit(new Edit(
        edit.pos + this.start - 1, edit.length, edit.replacement
      ));
    }

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

      if(
        (SymbolList.EDIT.isMatchingType(changeType) || changeType.isMatchingType(SymbolList.EDIT)) &&
        (editTranslater == null)
      ) {
        editTranslater = new EditTranslater(this, cs, start, end);
        AbstractSymbolList.this.addChangeListener(editTranslater, SymbolList.EDIT);
      }

      if(
        ((changeType == null) || (changeType == Annotation.PROPERTY)) &&
        (annotationForwarder == null)
      ) {
        annotationForwarder =
                new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY);
        AbstractSymbolList.this.addChangeListener(annotationForwarder, Annotation.PROPERTY);
      }

      return cs;
    }

    /**
     * Provides logical equality for two SymbolLists that share the same list
     * of canonical symbols
     */
    public boolean equals(Object o){
      if(this == o) return true;//just for optimality
      if(o == null) return false;
      if(!(o instanceof SymbolList)) return false;
      return compare(this, (SymbolList)o);
    }

    private volatile int hashCode = 0; //for caching purposes
    public int hashCode(){
      if(hashCode == 0){
        int result = 17;
        for(Iterator i = iterator(); i.hasNext();){
          result = 37*result + i.next().hashCode();
        }
        hashCode = result;
      }
      return hashCode;
    }

    public String toString() {
      return super.toString() +
             " start: " + start +
             " end: " + end /*(+
             " parent: " + AbstractSymbolList.this.toString() [causes infinite loop -- odd] */;
    }
  }

  /**
   * <p>
   * Implements a list view of a SymbolList.
   * </p>
   *
   * <p>
   * Objects of this type are instantiated by
   * <code>AbstractSymbolList.asList</code>.
   * </p>
   *
   * @author     Thomas Down
   */

  private static class ListView extends AbstractList implements Serializable {
    private SymbolList rl;

    /**
     * Build a new ListView to view a SymbolList as a list.
     *
     * @param  symList  the SymbolList to view
     */

    ListView(SymbolList symList) {
      this.rl = symList;
    }

    public Object get(int pos) {
      return rl.symbolAt(pos + 1);
    }

    public int size() {
      return rl.length();
    }
  }


  /**
   * This adapter screens all edit events to see if they overlap with a window
   * of interest. If they do, then a new edit event is built for the overlapping
   * region and pased on to all listeners.
   *
   * @author Matthew Pocock
   */
  public class EditScreener extends ChangeForwarder {
    protected final int min;
    protected final int max;

    public EditScreener(
      Object source, ChangeSupport cs,
      int min, int max
    ) {
      super(source, cs);
      this.min = min;
      this.max = max;
    }

    protected ChangeEvent generateEvent(ChangeEvent ce) {
      ChangeType ct = ce.getType();
      if(ct == SymbolList.EDIT) {
        Object change = ce.getChange();
        if( (change != null) && (change instanceof Edit) ) {
          Edit edit = (Edit) change;
          int start = edit.pos;
          int end = start + edit.length - 1; // inclusive
          if( (start <= max) && (end >= min) ) {
            // they overlap
            return new ChangeEvent(
              getSource(),
              ct,
              edit,
              null,
              ce
            );
          }
        }
      }
      return null;
    }
  }

  /**
   * This translates edit events that fall within a window into window co-ordinates.
   *
   * @author Matthew Pocock
   */
  public class EditTranslater extends EditScreener {
    public EditTranslater(
      Object source, ChangeSupport cs,
      int min, int max
    ) {
      super(source, cs, min, max);
    }

    protected ChangeEvent generateEvent(ChangeEvent ce) {
      ce = super.generateEvent(ce);
      if(ce != null) {
        Edit edit = (Edit) ce.getChange();
        return new ChangeEvent(
          ce.getSource(),
          ce.getType(),
          new Edit(edit.pos - min, edit.length, edit.replacement),
          null,
          ce.getChainedEvent()
        );
      }
      return null;
    }
  }
}