/*
 * 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;

/**
 * This is annotation over the coordinate frame
 *  defined by all the columns in the alignment.
 *  
 * 
 * @version $Revision$ $Date$
 */
public class AlignmentAnnotation extends uk.ac.vamsas.objects.core.RangeAnnotation 
implements java.io.Serializable
{


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

    /**
     * TODO: decide if this flag is
     *  redundant - when true it would suggest that
     *  the annotationElement values together form a
     *  graph 
     */
    private boolean _graph;

    /**
     * keeps track of state for field: _graph
     */
    private boolean _has_graph;

    /**
     * annotation is associated with
     *  a range on a particular group of alignment
     *  sequences
     */
    private java.util.Vector _seqrefs;

    /**
     * Field _provenance.
     */
    private uk.ac.vamsas.objects.core.Provenance _provenance;


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

    public AlignmentAnnotation() {
        super();
        this._seqrefs = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vSeqrefs
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSeqrefs(
            final java.lang.Object vSeqrefs)
    throws java.lang.IndexOutOfBoundsException {
        this._seqrefs.addElement(vSeqrefs);
    }

    /**
     * 
     * 
     * @param index
     * @param vSeqrefs
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSeqrefs(
            final int index,
            final java.lang.Object vSeqrefs)
    throws java.lang.IndexOutOfBoundsException {
        this._seqrefs.add(index, vSeqrefs);
    }

    /**
     */
    public void deleteGraph(
    ) {
        this._has_graph= false;
    }

    /**
     * Method enumerateSeqrefs.
     * 
     * @return an Enumeration over all java.lang.Object elements
     */
    public java.util.Enumeration enumerateSeqrefs(
    ) {
        return this._seqrefs.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 AlignmentAnnotation) {
        
            AlignmentAnnotation temp = (AlignmentAnnotation)obj;
            boolean thcycle;
            boolean tmcycle;
            if (this._graph != temp._graph)
                return false;
            if (this._has_graph != temp._has_graph)
                return false;
            if (this._seqrefs != null) {
                if (temp._seqrefs == null) return false;
                if (this._seqrefs != temp._seqrefs) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._seqrefs);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._seqrefs);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._seqrefs.equals(temp._seqrefs)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);
                    }
                }
            } else if (temp._seqrefs != null)
                return false;
            if (this._provenance != null) {
                if (temp._provenance == null) return false;
                if (this._provenance != temp._provenance) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._provenance.equals(temp._provenance)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
                    }
                }
            } else if (temp._provenance != null)
                return false;
            return true;
        }
        return false;
    }

    /**
     * Returns the value of field 'graph'. The field 'graph' has
     * the following description: TODO: decide if this flag is
     *  redundant - when true it would suggest that
     *  the annotationElement values together form a
     *  graph 
     * 
     * @return the value of field 'Graph'.
     */
    public boolean getGraph(
    ) {
        return this._graph;
    }

    /**
     * Returns the value of field 'provenance'.
     * 
     * @return the value of field 'Provenance'.
     */
    public uk.ac.vamsas.objects.core.Provenance getProvenance(
    ) {
        return this._provenance;
    }

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

    /**
     * Method getSeqrefs.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 java.lang.Object[] getSeqrefs(
    ) {
        java.lang.Object[] array = new java.lang.Object[0];
        return (java.lang.Object[]) this._seqrefs.toArray(array);
    }

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

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

    /**
     * Method hasGraph.
     * 
     * @return true if at least one Graph has been added
     */
    public boolean hasGraph(
    ) {
        return this._has_graph;
    }

    /**
     * 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;
        result = 37 * result + (_graph?0:1);
        if (_seqrefs != null
            && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) {
           result = 37 * result + _seqrefs.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs);
        }
        if (_provenance != null
            && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
           result = 37 * result + _provenance.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
        }
        
        return result;
    }

    /**
     * Returns the value of field 'graph'. The field 'graph' has
     * the following description: TODO: decide if this flag is
     *  redundant - when true it would suggest that
     *  the annotationElement values together form a
     *  graph 
     * 
     * @return the value of field 'Graph'.
     */
    public boolean isGraph(
    ) {
        return this._graph;
    }

    /**
     * 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 removeAllSeqrefs(
    ) {
        this._seqrefs.clear();
    }

    /**
     * Method removeSeqrefs.
     * 
     * @param vSeqrefs
     * @return true if the object was removed from the collection.
     */
    public boolean removeSeqrefs(
            final java.lang.Object vSeqrefs) {
        boolean removed = _seqrefs.remove(vSeqrefs);
        return removed;
    }

    /**
     * Method removeSeqrefsAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public java.lang.Object removeSeqrefsAt(
            final int index) {
        java.lang.Object obj = this._seqrefs.remove(index);
        return obj;
    }

    /**
     * Sets the value of field 'graph'. The field 'graph' has the
     * following description: TODO: decide if this flag is
     *  redundant - when true it would suggest that
     *  the annotationElement values together form a
     *  graph 
     * 
     * @param graph the value of field 'graph'.
     */
    public void setGraph(
            final boolean graph) {
        this._graph = graph;
        this._has_graph = true;
    }

    /**
     * Sets the value of field 'provenance'.
     * 
     * @param provenance the value of field 'provenance'.
     */
    public void setProvenance(
            final uk.ac.vamsas.objects.core.Provenance provenance) {
        this._provenance = provenance;
    }

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

    /**
     * 
     * 
     * @param vSeqrefsArray
     */
    public void setSeqrefs(
            final java.lang.Object[] vSeqrefsArray) {
        //-- copy array
        _seqrefs.clear();
        
        for (int i = 0; i < vSeqrefsArray.length; i++) {
                this._seqrefs.add(vSeqrefsArray[i]);
        }
    }

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

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

    /**
     * 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.RangeType
     */
    public static uk.ac.vamsas.objects.core.RangeType unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentAnnotation.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);
    }

}