/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
 * Schema.
 * $Id$
 */

package uk.ac.vamsas.objects.core;

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

import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;

/**
 * Class Sequence.
 * 
 * @version $Revision$ $Date$
 */
public class Sequence extends uk.ac.vamsas.objects.core.SequenceType 
implements java.io.Serializable
{


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

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

    /**
     * symbol class for sequence
     *  
     */
    private java.lang.String _dictionary;

    /**
     * Store a list of database references
     *  for this sequence record - with optional mapping
     *  from database sequence to the given sequence record 
     */
    private java.util.Vector _dbRefList;

    /**
     * explicitly named cross reference to
     *  other objects in the document. 
     */
    private java.util.Vector _vxrefList;


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

    public Sequence() {
        super();
        this._dbRefList = new java.util.Vector();
        this._vxrefList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vDbRef
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addDbRef(
            final uk.ac.vamsas.objects.core.DbRef vDbRef)
    throws java.lang.IndexOutOfBoundsException {
        this._dbRefList.addElement(vDbRef);
    }

    /**
     * 
     * 
     * @param index
     * @param vDbRef
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addDbRef(
            final int index,
            final uk.ac.vamsas.objects.core.DbRef vDbRef)
    throws java.lang.IndexOutOfBoundsException {
        this._dbRefList.add(index, vDbRef);
    }

    /**
     * 
     * 
     * @param vVxref
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addVxref(
            final uk.ac.vamsas.objects.core.Vxref vVxref)
    throws java.lang.IndexOutOfBoundsException {
        this._vxrefList.addElement(vVxref);
    }

    /**
     * 
     * 
     * @param index
     * @param vVxref
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addVxref(
            final int index,
            final uk.ac.vamsas.objects.core.Vxref vVxref)
    throws java.lang.IndexOutOfBoundsException {
        this._vxrefList.add(index, vVxref);
    }

    /**
     * Method enumerateDbRef.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.DbRef elements
     */
    public java.util.Enumeration enumerateDbRef(
    ) {
        return this._dbRefList.elements();
    }

    /**
     * Method enumerateVxref.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Vxref elements
     */
    public java.util.Enumeration enumerateVxref(
    ) {
        return this._vxrefList.elements();
    }

    /**
     * Overrides the java.lang.Object.equals method.
     * 
     * @param obj
     * @return true if the objects are equal.
     */
    public boolean equals(
            final java.lang.Object obj) {
        if ( this == obj )
            return true;
        
        if (super.equals(obj)==false)
            return false;
        
        if (obj instanceof Sequence) {
        
            Sequence temp = (Sequence)obj;
            boolean thcycle;
            boolean tmcycle;
            if (this._id != null) {
                if (temp._id == null) return false;
                if (this._id != temp._id) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._id.equals(temp._id)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
                    }
                }
            } else if (temp._id != null)
                return false;
            if (this._dictionary != null) {
                if (temp._dictionary == null) return false;
                if (this._dictionary != temp._dictionary) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dictionary);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dictionary);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._dictionary.equals(temp._dictionary)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
                    }
                }
            } else if (temp._dictionary != null)
                return false;
            if (this._dbRefList != null) {
                if (temp._dbRefList == null) return false;
                if (this._dbRefList != temp._dbRefList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dbRefList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dbRefList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._dbRefList.equals(temp._dbRefList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
                    }
                }
            } else if (temp._dbRefList != null)
                return false;
            if (this._vxrefList != null) {
                if (temp._vxrefList == null) return false;
                if (this._vxrefList != temp._vxrefList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._vxrefList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._vxrefList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._vxrefList.equals(temp._vxrefList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
                    }
                }
            } else if (temp._vxrefList != null)
                return false;
            return true;
        }
        return false;
    }

    /**
     * Method getDbRef.
     * 
     * @param index
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     * @return the value of the uk.ac.vamsas.objects.core.DbRef at
     * the given index
     */
    public uk.ac.vamsas.objects.core.DbRef getDbRef(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._dbRefList.size()) {
            throw new IndexOutOfBoundsException("getDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.get(index);
    }

    /**
     * Method getDbRef.Returns the contents of the collection in an
     * Array.  <p>Note:  Just in case the collection contents are
     * changing in another thread, we pass a 0-length Array of the
     * correct type into the API call.  This way we <i>know</i>
     * that the Array returned is of exactly the correct length.
     * 
     * @return this collection as an Array
     */
    public uk.ac.vamsas.objects.core.DbRef[] getDbRef(
    ) {
        uk.ac.vamsas.objects.core.DbRef[] array = new uk.ac.vamsas.objects.core.DbRef[0];
        return (uk.ac.vamsas.objects.core.DbRef[]) this._dbRefList.toArray(array);
    }

    /**
     * Method getDbRefAsReference.Returns a reference to
     * '_dbRefList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getDbRefAsReference(
    ) {
        return this._dbRefList;
    }

    /**
     * Method getDbRefCount.
     * 
     * @return the size of this collection
     */
    public int getDbRefCount(
    ) {
        return this._dbRefList.size();
    }

    /**
     * Returns the value of field 'dictionary'. The field
     * 'dictionary' has the following description: symbol class for
     * sequence
     *  
     * 
     * @return the value of field 'Dictionary'.
     */
    public java.lang.String getDictionary(
    ) {
        return this._dictionary;
    }

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

    /**
     * Method getVxref.
     * 
     * @param index
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     * @return the value of the uk.ac.vamsas.objects.core.Vxref at
     * the given index
     */
    public uk.ac.vamsas.objects.core.Vxref getVxref(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._vxrefList.size()) {
            throw new IndexOutOfBoundsException("getVxref: Index value '" + index + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.Vxref) _vxrefList.get(index);
    }

    /**
     * Method getVxref.Returns the contents of the collection in an
     * Array.  <p>Note:  Just in case the collection contents are
     * changing in another thread, we pass a 0-length Array of the
     * correct type into the API call.  This way we <i>know</i>
     * that the Array returned is of exactly the correct length.
     * 
     * @return this collection as an Array
     */
    public uk.ac.vamsas.objects.core.Vxref[] getVxref(
    ) {
        uk.ac.vamsas.objects.core.Vxref[] array = new uk.ac.vamsas.objects.core.Vxref[0];
        return (uk.ac.vamsas.objects.core.Vxref[]) this._vxrefList.toArray(array);
    }

    /**
     * Method getVxrefAsReference.Returns a reference to
     * '_vxrefList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getVxrefAsReference(
    ) {
        return this._vxrefList;
    }

    /**
     * Method getVxrefCount.
     * 
     * @return the size of this collection
     */
    public int getVxrefCount(
    ) {
        return this._vxrefList.size();
    }

    /**
     * Overrides the java.lang.Object.hashCode method.
     * <p>
     * The following steps came from <b>Effective Java Programming
     * Language Guide</b> by Joshua Bloch, Chapter 3
     * 
     * @return a hash code value for the object.
     */
    public int hashCode(
    ) {
        int result = super.hashCode();
        
        long tmp;
        if (_id != null
            && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
           result = 37 * result + _id.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_id);
        }
        if (_dictionary != null
            && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) {
           result = 37 * result + _dictionary.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary);
        }
        if (_dbRefList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) {
           result = 37 * result + _dbRefList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList);
        }
        if (_vxrefList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) {
           result = 37 * result + _vxrefList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList);
        }
        
        return result;
    }

    /**
     * Method isValid.
     * 
     * @return true if this object is valid according to the schema
     */
    public boolean isValid(
    ) {
        try {
            validate();
        } catch (org.exolab.castor.xml.ValidationException vex) {
            return false;
        }
        return true;
    }

    /**
     * 
     * 
     * @param out
     * @throws org.exolab.castor.xml.MarshalException if object is
     * null or if any SAXException is thrown during marshaling
     * @throws org.exolab.castor.xml.ValidationException if this
     * object is an invalid instance according to the schema
     */
    public void marshal(
            final java.io.Writer out)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        Marshaller.marshal(this, out);
    }

    /**
     * 
     * 
     * @param handler
     * @throws java.io.IOException if an IOException occurs during
     * marshaling
     * @throws org.exolab.castor.xml.ValidationException if this
     * object is an invalid instance according to the schema
     * @throws org.exolab.castor.xml.MarshalException if object is
     * null or if any SAXException is thrown during marshaling
     */
    public void marshal(
            final org.xml.sax.ContentHandler handler)
    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        Marshaller.marshal(this, handler);
    }

    /**
     */
    public void removeAllDbRef(
    ) {
        this._dbRefList.clear();
    }

    /**
     */
    public void removeAllVxref(
    ) {
        this._vxrefList.clear();
    }

    /**
     * Method removeDbRef.
     * 
     * @param vDbRef
     * @return true if the object was removed from the collection.
     */
    public boolean removeDbRef(
            final uk.ac.vamsas.objects.core.DbRef vDbRef) {
        boolean removed = _dbRefList.remove(vDbRef);
        return removed;
    }

    /**
     * Method removeDbRefAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.DbRef removeDbRefAt(
            final int index) {
        java.lang.Object obj = this._dbRefList.remove(index);
        return (uk.ac.vamsas.objects.core.DbRef) obj;
    }

    /**
     * Method removeVxref.
     * 
     * @param vVxref
     * @return true if the object was removed from the collection.
     */
    public boolean removeVxref(
            final uk.ac.vamsas.objects.core.Vxref vVxref) {
        boolean removed = _vxrefList.remove(vVxref);
        return removed;
    }

    /**
     * Method removeVxrefAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.Vxref removeVxrefAt(
            final int index) {
        java.lang.Object obj = this._vxrefList.remove(index);
        return (uk.ac.vamsas.objects.core.Vxref) obj;
    }

    /**
     * 
     * 
     * @param index
     * @param vDbRef
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setDbRef(
            final int index,
            final uk.ac.vamsas.objects.core.DbRef vDbRef)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._dbRefList.size()) {
            throw new IndexOutOfBoundsException("setDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]");
        }
        
        this._dbRefList.set(index, vDbRef);
    }

    /**
     * 
     * 
     * @param vDbRefArray
     */
    public void setDbRef(
            final uk.ac.vamsas.objects.core.DbRef[] vDbRefArray) {
        //-- copy array
        _dbRefList.clear();
        
        for (int i = 0; i < vDbRefArray.length; i++) {
                this._dbRefList.add(vDbRefArray[i]);
        }
    }

    /**
     * Sets the value of '_dbRefList' by copying the given Vector.
     * All elements will be checked for type safety.
     * 
     * @param vDbRefList the Vector to copy.
     */
    public void setDbRef(
            final java.util.Vector vDbRefList) {
        // copy vector
        this._dbRefList.clear();
        
        this._dbRefList.addAll(vDbRefList);
    }

    /**
     * Sets the value of '_dbRefList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param dbRefVector the Vector to set.
     */
    public void setDbRefAsReference(
            final java.util.Vector dbRefVector) {
        this._dbRefList = dbRefVector;
    }

    /**
     * Sets the value of field 'dictionary'. The field 'dictionary'
     * has the following description: symbol class for sequence
     *  
     * 
     * @param dictionary the value of field 'dictionary'.
     */
    public void setDictionary(
            final java.lang.String dictionary) {
        this._dictionary = dictionary;
    }

    /**
     * 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(
            final java.lang.String id) {
        this._id = id;
    }

    /**
     * 
     * 
     * @param index
     * @param vVxref
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setVxref(
            final int index,
            final uk.ac.vamsas.objects.core.Vxref vVxref)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._vxrefList.size()) {
            throw new IndexOutOfBoundsException("setVxref: Index value '" + index + "' not in range [0.." + (this._vxrefList.size() - 1) + "]");
        }
        
        this._vxrefList.set(index, vVxref);
    }

    /**
     * 
     * 
     * @param vVxrefArray
     */
    public void setVxref(
            final uk.ac.vamsas.objects.core.Vxref[] vVxrefArray) {
        //-- copy array
        _vxrefList.clear();
        
        for (int i = 0; i < vVxrefArray.length; i++) {
                this._vxrefList.add(vVxrefArray[i]);
        }
    }

    /**
     * Sets the value of '_vxrefList' by copying the given Vector.
     * All elements will be checked for type safety.
     * 
     * @param vVxrefList the Vector to copy.
     */
    public void setVxref(
            final java.util.Vector vVxrefList) {
        // copy vector
        this._vxrefList.clear();
        
        this._vxrefList.addAll(vVxrefList);
    }

    /**
     * Sets the value of '_vxrefList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param vxrefVector the Vector to set.
     */
    public void setVxrefAsReference(
            final java.util.Vector vxrefVector) {
        this._vxrefList = vxrefVector;
    }

    /**
     * Method unmarshal.
     * 
     * @param reader
     * @throws org.exolab.castor.xml.MarshalException if object is
     * null or if any SAXException is thrown during marshaling
     * @throws org.exolab.castor.xml.ValidationException if this
     * object is an invalid instance according to the schema
     * @return the unmarshaled uk.ac.vamsas.objects.core.SequenceTyp
     */
    public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Sequence.class, reader);
    }

    /**
     * 
     * 
     * @throws org.exolab.castor.xml.ValidationException if this
     * object is an invalid instance according to the schema
     */
    public void validate(
    )
    throws org.exolab.castor.xml.ValidationException {
        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
        validator.validate(this);
    }

}