/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.datamodel;

import jalview.util.CaseInsensitiveString;

import java.util.Collections;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Map.Entry;

public class PDBEntry
{

  /**
   * constant for storing chain code in properties table
   */
  private static final String CHAIN_ID = "chain_code";

  Hashtable<String, Object> properties;

  private String file;

  private String type;

  private String id;

  public enum Type
  {
    PDB, MMCIF, FILE;
    /**
     * case insensitive matching for Type enum
     * 
     * @param value
     * @return
     */
    public static Type getType(String value)
    {
      for (Type t : Type.values())
      {
        if (t.toString().equalsIgnoreCase(value))
        {
          return t;
        }
      }
      return null;
    }

    /**
     * case insensitive equivalence for strings resolving to PDBEntry type
     * 
     * @param t
     * @return
     */
    public boolean matches(String t)
    {
      return (this.toString().equalsIgnoreCase(t));
    }
  }


  /*
   * (non-Javadoc)
   * 
   * @see java.lang.Object#equals(java.lang.Object)
   */
  @Override
  public boolean equals(Object obj)
  {
    if (obj == null || !(obj instanceof PDBEntry))
    {
      return false;
    }
    if (obj == this)
    {
      return true;
    }
    PDBEntry o = (PDBEntry) obj;
    return (type == o.type || (type != null && o.type != null && o.type
            .equals(type)))
            && (id == o.id || (id != null && o.id != null && o.id
                    .equalsIgnoreCase(id)))
            && (properties == o.properties || (properties != null
                    && o.properties != null && properties
                      .equals(o.properties)));

  }

  /**
   * Default constructor
   */
  public PDBEntry()
  {
  }

  /**
   * Constructor given file path and PDB id.
   * 
   * @param filePath
   */
  // public PDBEntry(String filePath, String pdbId)
  // {
  // this.file = filePath;
  // this.id = pdbId;
  // }

  public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
          String filePath)
  {
    this.id = pdbId;
    this.type = type == null ? null : type.toString();
    this.file = filePath;
    setChainCode(chain);
  }

  /**
   * Copy constructor.
   * 
   * @param entry
   */
  public PDBEntry(PDBEntry entry)
  {
    file = entry.file;
    type = entry.type;
    id = entry.id;
    if (entry.properties != null)
    {
      properties = (Hashtable<String, Object>) entry.properties.clone();
    }
  }

  public void setFile(String f)
  {
    this.file = f;
  }

  public String getFile()
  {
    return file;
  }

  public void setType(String t)
  {
    this.type = t;
  }

  public void setType(PDBEntry.Type type)
  {
    this.type = type == null ? null : type.toString();
  }

  public String getType()
  {
    return type;
  }

  public void setId(String id)
  {
    this.id = id;
  }

  public String getId()
  {
    return id;
  }

  public void setProperty(String key, Object value)
  {
    if (this.properties == null)
    {
      this.properties = new Hashtable<String, Object>();
    }
    properties.put(key, value);
  }

  public Object getProperty(String key)
  {
    return properties == null ? null : properties.get(key);
  }

  /**
   * Returns an enumeration of the keys of this object's properties (or an empty
   * enumeration if it has no properties)
   * 
   * @return
   */
  public Enumeration<String> getProperties()
  {
    if (properties == null)
    {
      return Collections.emptyEnumeration();
    }
    return properties.keys();
  }

  /**
   * 
   * @return null or a string for associated chain IDs
   */
  public String getChainCode()
  {
    return (properties == null || properties.get(CHAIN_ID) == null) ? null
            : properties.get(CHAIN_ID).toString();
  }

  /**
   * Sets a non-case-sensitive property for the given chain code. Two PDBEntry
   * objects which differ only in the case of their chain code are considered
   * equal. This avoids duplication of objects in lists of PDB ids.
   * 
   * @param chainCode
   */
  public void setChainCode(String chainCode)
  {
    if (chainCode == null)
    {
      deleteProperty(CHAIN_ID);
    }
    else
    {
      setProperty(CHAIN_ID, new CaseInsensitiveString(chainCode));
    }
  }

  /**
   * Deletes the property with the given key, and returns the deleted value (or
   * null)
   */
  Object deleteProperty(String key)
  {
    Object result = null;
    if (properties != null)
    {
      result = properties.remove(key);
    }
    return result;
  }

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

  /**
   * Getter provided for Castor binding only. Application code should call
   * getProperty() or getProperties() instead.
   * 
   * @deprecated
   * @see #getProperty(String)
   * @see #getProperties()
   * @see jalview.ws.dbsources.Uniprot#getUniprotEntries
   * @return
   */
  @Deprecated
  public Hashtable<String, Object> getProps()
  {
    return properties;
  }

  /**
   * Setter provided for Castor binding only. Application code should call
   * setProperty() instead.
   * 
   * @deprecated
   * @return
   */
  @Deprecated
  public void setProps(Hashtable<String, Object> props)
  {
    properties = props;
  }

  /**
   * update entry with details from another entry concerning the same PDB
   * ID/file spec.
   * 
   * @param newEntry
   * @return true if modifications were made
   */
  public boolean updateFrom(PDBEntry newEntry)
  {
    boolean modified = false;

    if (getFile() == null)
    {
      // update file and type of file
      modified = newEntry.getFile() != null;
      setFile(newEntry.getFile());
    }
    if (newEntry.getType() != null && newEntry.getFile() != null
            && newEntry.getFile().equals(getFile()))
    {
      setType(newEntry.getType());
    }
    if (getChainCode() == null
            || (getChainCode() != null && getChainCode().length() == 0 && newEntry
                    .getChainCode() != null))
    {
      modified |= (getChainCode() == null || !newEntry.getChainCode()
              .equals(getChainCode()));
      setChainCode(newEntry.getChainCode());
    }
    if (newEntry.properties != null)
    {
      for (Entry<String, Object> entry : newEntry.properties.entrySet())
      {
        if (!entry.getValue().equals(getProperty(entry.getKey())))
        {
          modified = true;
        }
        setProperty(entry.getKey(), entry.getValue());
      }
    }
    return modified;
  }
}