/*
 * 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 AlignmentSequence.
 * 
 * @version $Revision$ $Date$
 */
public class AlignmentSequence 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;

    /**
     * Dataset Sequence from which
     *  this alignment sequence is taken from
     *  
     */
    private java.lang.Object _refid;

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


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

    public AlignmentSequence() {
        super();
        this._alignmentSequenceAnnotationList = new java.util.Vector();
    }


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

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

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

    /**
     * Method enumerateAlignmentSequenceAnnotation.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation element
     */
    public java.util.Enumeration enumerateAlignmentSequenceAnnotation(
    ) {
        return this._alignmentSequenceAnnotationList.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 AlignmentSequence) {
        
            AlignmentSequence temp = (AlignmentSequence)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._refid != null) {
                if (temp._refid == null) return false;
                if (this._refid != temp._refid) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._refid);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._refid);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._refid); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._refid.equals(temp._refid)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
                    }
                }
            } else if (temp._refid != null)
                return false;
            if (this._alignmentSequenceAnnotationList != null) {
                if (temp._alignmentSequenceAnnotationList == null) return false;
                if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._alignmentSequenceAnnotationList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._alignmentSequenceAnnotationList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList);
                    }
                }
            } else if (temp._alignmentSequenceAnnotationList != null)
                return false;
            return true;
        }
        return false;
    }

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

    /**
     * Method getAlignmentSequenceAnnotation.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.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation(
    ) {
        uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
        return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList.toArray(array);
    }

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

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

    /**
     * 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;
    }

    /**
     * Returns the value of field 'refid'. The field 'refid' has
     * the following description: Dataset Sequence from which
     *  this alignment sequence is taken from
     *  
     * 
     * @return the value of field 'Refid'.
     */
    public java.lang.Object getRefid(
    ) {
        return this._refid;
    }

    /**
     * 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 (_refid != null
            && !org.castor.util.CycleBreaker.startingToCycle(_refid)) {
           result = 37 * result + _refid.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_refid);
        }
        if (_alignmentSequenceAnnotationList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_alignmentSequenceAnnotationList)) {
           result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceAnnotationList);
        }
        
        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);
    }

    /**
     * Method removeAlignmentSequenceAnnotation.
     * 
     * @param vAlignmentSequenceAnnotation
     * @return true if the object was removed from the collection.
     */
    public boolean removeAlignmentSequenceAnnotation(
            final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) {
        boolean removed = _alignmentSequenceAnnotationList.remove(vAlignmentSequenceAnnotation);
        return removed;
    }

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

    /**
     */
    public void removeAllAlignmentSequenceAnnotation(
    ) {
        this._alignmentSequenceAnnotationList.clear();
    }

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

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

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

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

    /**
     * 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;
    }

    /**
     * Sets the value of field 'refid'. The field 'refid' has the
     * following description: Dataset Sequence from which
     *  this alignment sequence is taken from
     *  
     * 
     * @param refid the value of field 'refid'.
     */
    public void setRefid(
            final java.lang.Object refid) {
        this._refid = refid;
    }

    /**
     * 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.AlignmentSequence.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);
    }

}