/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
 * Schema.
 * $Id$
 */

package uk.ac.vamsas.objects.core;

  //---------------------------------/
 //- Imported classes and packages -/
//---------------------------------/

import java.io.IOException;
import java.io.Reader;
import java.io.Serializable;
import java.io.Writer;
import java.util.Enumeration;
import java.util.Vector;
import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
import org.exolab.castor.xml.ValidationException;
import org.xml.sax.ContentHandler;

/**
 * Store a list of database references
 *  for this sequence record - with optional mapping
 *  from database sequence to the given sequence record 
 * 
 * @version $Revision$ $Date$
 */
public class DbRef extends uk.ac.vamsas.client.Vobject 
implements java.io.Serializable
{


      //--------------------------/
     //- Class/Member Variables -/
    //--------------------------/

    /**
     * TODO Database Naming
     *  Convention: either start using LSID (so
     *  change type to URI) or leave this as an
     *  uncontrolled/unspecified string ID
     *  
     */
    private java.lang.String _source;

    /**
     * Version must be specified -
     *  
     */
    private java.lang.String _version;

    /**
     * TODO: make some specification
     *  of the database field from which this
     *  accessionId is taken from - should that be a
     *  special property of the dbRef object ?
     *  
     */
    private java.lang.String _accessionId;

    /**
     * Primary Key for vamsas object
     *  referencing 
     */
    private java.lang.String _id;

    /**
     * From: Offset to first
     *  position in dataset sequence record that
     *  this database entry maps to To: Offset
     *  to last position in dataset sequence
     *  record that this database entry maps to
     *  Start: Offset to first last position in
     *  database entry that first (or offset)
     *  position in sequence maps to End: Offset
     *  to last position in database entry that
     *  last (offset) position in sequence maps
     *  to 
     */
    private java.util.Vector _mapList;

    /**
     * Field _linkList
     */
    private java.util.Vector _linkList;

    /**
     * Field _propertyList
     */
    private java.util.Vector _propertyList;


      //----------------/
     //- Constructors -/
    //----------------/

    public DbRef() 
     {
        super();
        _mapList = new Vector();
        _linkList = new Vector();
        _propertyList = new Vector();
    } //-- uk.ac.vamsas.objects.core.DbRef()


      //-----------/
     //- Methods -/
    //-----------/

    /**
     * Method addLink
     * 
     * 
     * 
     * @param vLink
     */
    public void addLink(uk.ac.vamsas.objects.core.Link vLink)
        throws java.lang.IndexOutOfBoundsException
    {
        _linkList.addElement(vLink);
    } //-- void addLink(uk.ac.vamsas.objects.core.Link) 

    /**
     * Method addLink
     * 
     * 
     * 
     * @param index
     * @param vLink
     */
    public void addLink(int index, uk.ac.vamsas.objects.core.Link vLink)
        throws java.lang.IndexOutOfBoundsException
    {
        _linkList.insertElementAt(vLink, index);
    } //-- void addLink(int, uk.ac.vamsas.objects.core.Link) 

    /**
     * Method addMap
     * 
     * 
     * 
     * @param vMap
     */
    public void addMap(uk.ac.vamsas.objects.core.Map vMap)
        throws java.lang.IndexOutOfBoundsException
    {
        _mapList.addElement(vMap);
    } //-- void addMap(uk.ac.vamsas.objects.core.Map) 

    /**
     * Method addMap
     * 
     * 
     * 
     * @param index
     * @param vMap
     */
    public void addMap(int index, uk.ac.vamsas.objects.core.Map vMap)
        throws java.lang.IndexOutOfBoundsException
    {
        _mapList.insertElementAt(vMap, index);
    } //-- void addMap(int, uk.ac.vamsas.objects.core.Map) 

    /**
     * Method addProperty
     * 
     * 
     * 
     * @param vProperty
     */
    public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
        throws java.lang.IndexOutOfBoundsException
    {
        _propertyList.addElement(vProperty);
    } //-- void addProperty(uk.ac.vamsas.objects.core.Property) 

    /**
     * Method addProperty
     * 
     * 
     * 
     * @param index
     * @param vProperty
     */
    public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
        throws java.lang.IndexOutOfBoundsException
    {
        _propertyList.insertElementAt(vProperty, index);
    } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property) 

    /**
     * Method enumerateLink
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateLink()
    {
        return _linkList.elements();
    } //-- java.util.Enumeration enumerateLink() 

    /**
     * Method enumerateMap
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateMap()
    {
        return _mapList.elements();
    } //-- java.util.Enumeration enumerateMap() 

    /**
     * Method enumerateProperty
     * 
     * 
     * 
     * @return Enumeration
     */
    public java.util.Enumeration enumerateProperty()
    {
        return _propertyList.elements();
    } //-- java.util.Enumeration enumerateProperty() 

    /**
     * Note: hashCode() has not been overriden
     * 
     * @param obj
     * @return boolean
     */
    public boolean equals(java.lang.Object obj)
    {
        if ( this == obj )
            return true;
        
        if (super.equals(obj)==false)
            return false;
        
        if (obj instanceof DbRef) {
        
            DbRef temp = (DbRef)obj;
            if (this._source != null) {
                if (temp._source == null) return false;
                else if (!(this._source.equals(temp._source))) 
                    return false;
            }
            else if (temp._source != null)
                return false;
            if (this._version != null) {
                if (temp._version == null) return false;
                else if (!(this._version.equals(temp._version))) 
                    return false;
            }
            else if (temp._version != null)
                return false;
            if (this._accessionId != null) {
                if (temp._accessionId == null) return false;
                else if (!(this._accessionId.equals(temp._accessionId))) 
                    return false;
            }
            else if (temp._accessionId != null)
                return false;
            if (this._id != null) {
                if (temp._id == null) return false;
                else if (!(this._id.equals(temp._id))) 
                    return false;
            }
            else if (temp._id != null)
                return false;
            if (this._mapList != null) {
                if (temp._mapList == null) return false;
                else if (!(this._mapList.equals(temp._mapList))) 
                    return false;
            }
            else if (temp._mapList != null)
                return false;
            if (this._linkList != null) {
                if (temp._linkList == null) return false;
                else if (!(this._linkList.equals(temp._linkList))) 
                    return false;
            }
            else if (temp._linkList != null)
                return false;
            if (this._propertyList != null) {
                if (temp._propertyList == null) return false;
                else if (!(this._propertyList.equals(temp._propertyList))) 
                    return false;
            }
            else if (temp._propertyList != null)
                return false;
            return true;
        }
        return false;
    } //-- boolean equals(java.lang.Object) 

    /**
     * Returns the value of field 'accessionId'. The field
     * 'accessionId' has the following description: TODO: make some
     * specification
     *  of the database field from which this
     *  accessionId is taken from - should that be a
     *  special property of the dbRef object ?
     *  
     * 
     * @return String
     * @return the value of field 'accessionId'.
     */
    public java.lang.String getAccessionId()
    {
        return this._accessionId;
    } //-- java.lang.String getAccessionId() 

    /**
     * Returns the value of field 'id'. The field 'id' has the
     * following description: Primary Key for vamsas object
     *  referencing 
     * 
     * @return String
     * @return the value of field 'id'.
     */
    public java.lang.String getId()
    {
        return this._id;
    } //-- java.lang.String getId() 

    /**
     * Method getLink
     * 
     * 
     * 
     * @param index
     * @return Link
     */
    public uk.ac.vamsas.objects.core.Link getLink(int index)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _linkList.size())) {
            throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
        }
        
        return (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
    } //-- uk.ac.vamsas.objects.core.Link getLink(int) 

    /**
     * Method getLink
     * 
     * 
     * 
     * @return Link
     */
    public uk.ac.vamsas.objects.core.Link[] getLink()
    {
        int size = _linkList.size();
        uk.ac.vamsas.objects.core.Link[] mArray = new uk.ac.vamsas.objects.core.Link[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (uk.ac.vamsas.objects.core.Link) _linkList.elementAt(index);
        }
        return mArray;
    } //-- uk.ac.vamsas.objects.core.Link[] getLink() 

    /**
     * Method getLinkCount
     * 
     * 
     * 
     * @return int
     */
    public int getLinkCount()
    {
        return _linkList.size();
    } //-- int getLinkCount() 

    /**
     * Method getMap
     * 
     * 
     * 
     * @param index
     * @return Map
     */
    public uk.ac.vamsas.objects.core.Map getMap(int index)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _mapList.size())) {
            throw new IndexOutOfBoundsException("getMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
        }
        
        return (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index);
    } //-- uk.ac.vamsas.objects.core.Map getMap(int) 

    /**
     * Method getMap
     * 
     * 
     * 
     * @return Map
     */
    public uk.ac.vamsas.objects.core.Map[] getMap()
    {
        int size = _mapList.size();
        uk.ac.vamsas.objects.core.Map[] mArray = new uk.ac.vamsas.objects.core.Map[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (uk.ac.vamsas.objects.core.Map) _mapList.elementAt(index);
        }
        return mArray;
    } //-- uk.ac.vamsas.objects.core.Map[] getMap() 

    /**
     * Method getMapCount
     * 
     * 
     * 
     * @return int
     */
    public int getMapCount()
    {
        return _mapList.size();
    } //-- int getMapCount() 

    /**
     * Method getProperty
     * 
     * 
     * 
     * @param index
     * @return Property
     */
    public uk.ac.vamsas.objects.core.Property getProperty(int index)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _propertyList.size())) {
            throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
        }
        
        return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
    } //-- uk.ac.vamsas.objects.core.Property getProperty(int) 

    /**
     * Method getProperty
     * 
     * 
     * 
     * @return Property
     */
    public uk.ac.vamsas.objects.core.Property[] getProperty()
    {
        int size = _propertyList.size();
        uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
        for (int index = 0; index < size; index++) {
            mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
        }
        return mArray;
    } //-- uk.ac.vamsas.objects.core.Property[] getProperty() 

    /**
     * Method getPropertyCount
     * 
     * 
     * 
     * @return int
     */
    public int getPropertyCount()
    {
        return _propertyList.size();
    } //-- int getPropertyCount() 

    /**
     * Returns the value of field 'source'. The field 'source' has
     * the following description: TODO Database Naming
     *  Convention: either start using LSID (so
     *  change type to URI) or leave this as an
     *  uncontrolled/unspecified string ID
     *  
     * 
     * @return String
     * @return the value of field 'source'.
     */
    public java.lang.String getSource()
    {
        return this._source;
    } //-- java.lang.String getSource() 

    /**
     * Returns the value of field 'version'. The field 'version'
     * has the following description: Version must be specified -
     *  
     * 
     * @return String
     * @return the value of field 'version'.
     */
    public java.lang.String getVersion()
    {
        return this._version;
    } //-- java.lang.String getVersion() 

    /**
     * Method isValid
     * 
     * 
     * 
     * @return boolean
     */
    public boolean isValid()
    {
        try {
            validate();
        }
        catch (org.exolab.castor.xml.ValidationException vex) {
            return false;
        }
        return true;
    } //-- boolean isValid() 

    /**
     * Method marshal
     * 
     * 
     * 
     * @param out
     */
    public void marshal(java.io.Writer out)
        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
    {
        
        Marshaller.marshal(this, out);
    } //-- void marshal(java.io.Writer) 

    /**
     * Method marshal
     * 
     * 
     * 
     * @param handler
     */
    public void marshal(org.xml.sax.ContentHandler handler)
        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
    {
        
        Marshaller.marshal(this, handler);
    } //-- void marshal(org.xml.sax.ContentHandler) 

    /**
     * Method removeAllLink
     * 
     */
    public void removeAllLink()
    {
        _linkList.removeAllElements();
    } //-- void removeAllLink() 

    /**
     * Method removeAllMap
     * 
     */
    public void removeAllMap()
    {
        _mapList.removeAllElements();
    } //-- void removeAllMap() 

    /**
     * Method removeAllProperty
     * 
     */
    public void removeAllProperty()
    {
        _propertyList.removeAllElements();
    } //-- void removeAllProperty() 

    /**
     * Method removeLink
     * 
     * 
     * 
     * @param index
     * @return Link
     */
    public uk.ac.vamsas.objects.core.Link removeLink(int index)
    {
        java.lang.Object obj = _linkList.elementAt(index);
        _linkList.removeElementAt(index);
        return (uk.ac.vamsas.objects.core.Link) obj;
    } //-- uk.ac.vamsas.objects.core.Link removeLink(int) 

    /**
     * Method removeMap
     * 
     * 
     * 
     * @param index
     * @return Map
     */
    public uk.ac.vamsas.objects.core.Map removeMap(int index)
    {
        java.lang.Object obj = _mapList.elementAt(index);
        _mapList.removeElementAt(index);
        return (uk.ac.vamsas.objects.core.Map) obj;
    } //-- uk.ac.vamsas.objects.core.Map removeMap(int) 

    /**
     * Method removeProperty
     * 
     * 
     * 
     * @param index
     * @return Property
     */
    public uk.ac.vamsas.objects.core.Property removeProperty(int index)
    {
        java.lang.Object obj = _propertyList.elementAt(index);
        _propertyList.removeElementAt(index);
        return (uk.ac.vamsas.objects.core.Property) obj;
    } //-- uk.ac.vamsas.objects.core.Property removeProperty(int) 

    /**
     * Sets the value of field 'accessionId'. The field
     * 'accessionId' has the following description: TODO: make some
     * specification
     *  of the database field from which this
     *  accessionId is taken from - should that be a
     *  special property of the dbRef object ?
     *  
     * 
     * @param accessionId the value of field 'accessionId'.
     */
    public void setAccessionId(java.lang.String accessionId)
    {
        this._accessionId = accessionId;
    } //-- void setAccessionId(java.lang.String) 

    /**
     * Sets the value of field 'id'. The field 'id' has the
     * following description: Primary Key for vamsas object
     *  referencing 
     * 
     * @param id the value of field 'id'.
     */
    public void setId(java.lang.String id)
    {
        this._id = id;
    } //-- void setId(java.lang.String) 

    /**
     * Method setLink
     * 
     * 
     * 
     * @param index
     * @param vLink
     */
    public void setLink(int index, uk.ac.vamsas.objects.core.Link vLink)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _linkList.size())) {
            throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");
        }
        _linkList.setElementAt(vLink, index);
    } //-- void setLink(int, uk.ac.vamsas.objects.core.Link) 

    /**
     * Method setLink
     * 
     * 
     * 
     * @param linkArray
     */
    public void setLink(uk.ac.vamsas.objects.core.Link[] linkArray)
    {
        //-- copy array
        _linkList.removeAllElements();
        for (int i = 0; i < linkArray.length; i++) {
            _linkList.addElement(linkArray[i]);
        }
    } //-- void setLink(uk.ac.vamsas.objects.core.Link) 

    /**
     * Method setMap
     * 
     * 
     * 
     * @param index
     * @param vMap
     */
    public void setMap(int index, uk.ac.vamsas.objects.core.Map vMap)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _mapList.size())) {
            throw new IndexOutOfBoundsException("setMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]");
        }
        _mapList.setElementAt(vMap, index);
    } //-- void setMap(int, uk.ac.vamsas.objects.core.Map) 

    /**
     * Method setMap
     * 
     * 
     * 
     * @param mapArray
     */
    public void setMap(uk.ac.vamsas.objects.core.Map[] mapArray)
    {
        //-- copy array
        _mapList.removeAllElements();
        for (int i = 0; i < mapArray.length; i++) {
            _mapList.addElement(mapArray[i]);
        }
    } //-- void setMap(uk.ac.vamsas.objects.core.Map) 

    /**
     * Method setProperty
     * 
     * 
     * 
     * @param index
     * @param vProperty
     */
    public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
        throws java.lang.IndexOutOfBoundsException
    {
        //-- check bounds for index
        if ((index < 0) || (index > _propertyList.size())) {
            throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
        }
        _propertyList.setElementAt(vProperty, index);
    } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property) 

    /**
     * Method setProperty
     * 
     * 
     * 
     * @param propertyArray
     */
    public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
    {
        //-- copy array
        _propertyList.removeAllElements();
        for (int i = 0; i < propertyArray.length; i++) {
            _propertyList.addElement(propertyArray[i]);
        }
    } //-- void setProperty(uk.ac.vamsas.objects.core.Property) 

    /**
     * Sets the value of field 'source'. The field 'source' has the
     * following description: TODO Database Naming
     *  Convention: either start using LSID (so
     *  change type to URI) or leave this as an
     *  uncontrolled/unspecified string ID
     *  
     * 
     * @param source the value of field 'source'.
     */
    public void setSource(java.lang.String source)
    {
        this._source = source;
    } //-- void setSource(java.lang.String) 

    /**
     * Sets the value of field 'version'. The field 'version' has
     * the following description: Version must be specified -
     *  
     * 
     * @param version the value of field 'version'.
     */
    public void setVersion(java.lang.String version)
    {
        this._version = version;
    } //-- void setVersion(java.lang.String) 

    /**
     * Method unmarshal
     * 
     * 
     * 
     * @param reader
     * @return DbRef
     */
    public static uk.ac.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader)
        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
    {
        return (uk.ac.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DbRef.class, reader);
    } //-- uk.ac.vamsas.objects.core.DbRef unmarshal(java.io.Reader) 

    /**
     * Method validate
     * 
     */
    public void validate()
        throws org.exolab.castor.xml.ValidationException
    {
        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
        validator.validate(this);
    } //-- void validate() 

}