/*
 *                    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.Iterator;
import java.util.List;

import org.biojava.bio.Annotation;
import org.biojava.bio.BioError;
import org.biojava.bio.SimpleAnnotation;

/**
 * A basic implementation of Symbol.
 *
 * If you wish to construct new Symbols, you should normally do so via utility methods
 * on <code>AlphabetManager</code>.
 *
 * This may be a useful base class for custom implementations.
 *
 * @author Matthew Pocock
 * @author Greg Cox
 */
class SimpleSymbol
  extends
    AbstractSymbol
  implements
    Symbol,
    Serializable
{
  private final Annotation annotation;
  protected Alphabet matches;

  protected SimpleSymbol(Annotation annotation)
  {
    this.annotation = new SimpleAnnotation(annotation);
  }

  public SimpleSymbol(
    Annotation annotation,
    Alphabet matches
  ) {
    this(annotation);
    if(matches == null) {
      throw new NullPointerException(
        "Can't construct SimpleSymbol with a null matches alphabet"
      );
    } else {
      this.matches = matches;
    }
  }

  public Annotation getAnnotation() {
    return annotation;
  }

  public Alphabet getMatches() {
    if(matches == null) {
      matches = createMatches();
    }
    return matches;
  }

  protected Alphabet createMatches() {
    throw new BioError(
      "Assertion Failure: Matches alphabet is null in " + this
    );
  }

  public String getName() {
    // basis symbol name is a join of the names of each aymbol it spans
    if (this instanceof BasisSymbol) {
      List l = ((BasisSymbol) this).getSymbols();
      if (l.size() > 1) {
        StringBuffer sb = new StringBuffer();
        sb.append('(');
        Iterator si = l.iterator();
        if(si.hasNext()) {
          Symbol sym = (Symbol) si.next();
          sb.append(sym.getName());
        }
        while(si.hasNext()) {
          Symbol sym = (Symbol) si.next();
          sb.append(' ');
          sb.append(sym.getName());
        }
        sb.append(')');
        return sb.substring(0);
      }
    }

    // not a basis symbol - let's name it by they symbols it contains.
    Alphabet a = getMatches();
    if (a instanceof FiniteAlphabet) {
      FiniteAlphabet fa = (FiniteAlphabet) a;

      StringBuffer sb = new StringBuffer();
      sb.append('[');
      Iterator si = fa.iterator();
      if(si.hasNext()) {
        Symbol sym = (Symbol) si.next();
        sb.append(sym.getName());
      }
      while(si.hasNext()) {
        Symbol sym = (Symbol) si.next();
        sb.append(' ');
        sb.append(sym.getName());
      }
      sb.append(']');
      return sb.substring(0);
    }

    // an infinite alphabet - pants!
    return "Infinite";
  }
}