/*******************************************************************************
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
 *
 * 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/>.
 *******************************************************************************/
/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
 * Schema.
 * $Id$
 */

package jalview.binding;

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

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

/**
 * Class JalviewModelSequence.
 * 
 * @version $Revision$ $Date$
 */
public class JalviewModelSequence implements java.io.Serializable {


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

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

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

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

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

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

    /**
     * Field _featureSettings.
     */
    private jalview.binding.FeatureSettings _featureSettings;


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

    public JalviewModelSequence() {
        super();
        this._JSeqList = new java.util.Vector();
        this._JGroupList = new java.util.Vector();
        this._viewportList = new java.util.Vector();
        this._userColoursList = new java.util.Vector();
        this._treeList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vJGroup
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addJGroup(
            final jalview.binding.JGroup vJGroup)
    throws java.lang.IndexOutOfBoundsException {
        this._JGroupList.addElement(vJGroup);
    }

    /**
     * 
     * 
     * @param index
     * @param vJGroup
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addJGroup(
            final int index,
            final jalview.binding.JGroup vJGroup)
    throws java.lang.IndexOutOfBoundsException {
        this._JGroupList.add(index, vJGroup);
    }

    /**
     * 
     * 
     * @param vJSeq
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addJSeq(
            final jalview.binding.JSeq vJSeq)
    throws java.lang.IndexOutOfBoundsException {
        this._JSeqList.addElement(vJSeq);
    }

    /**
     * 
     * 
     * @param index
     * @param vJSeq
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addJSeq(
            final int index,
            final jalview.binding.JSeq vJSeq)
    throws java.lang.IndexOutOfBoundsException {
        this._JSeqList.add(index, vJSeq);
    }

    /**
     * 
     * 
     * @param vTree
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addTree(
            final jalview.binding.Tree vTree)
    throws java.lang.IndexOutOfBoundsException {
        this._treeList.addElement(vTree);
    }

    /**
     * 
     * 
     * @param index
     * @param vTree
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addTree(
            final int index,
            final jalview.binding.Tree vTree)
    throws java.lang.IndexOutOfBoundsException {
        this._treeList.add(index, vTree);
    }

    /**
     * 
     * 
     * @param vUserColours
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addUserColours(
            final jalview.binding.UserColours vUserColours)
    throws java.lang.IndexOutOfBoundsException {
        this._userColoursList.addElement(vUserColours);
    }

    /**
     * 
     * 
     * @param index
     * @param vUserColours
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addUserColours(
            final int index,
            final jalview.binding.UserColours vUserColours)
    throws java.lang.IndexOutOfBoundsException {
        this._userColoursList.add(index, vUserColours);
    }

    /**
     * 
     * 
     * @param vViewport
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addViewport(
            final jalview.binding.Viewport vViewport)
    throws java.lang.IndexOutOfBoundsException {
        this._viewportList.addElement(vViewport);
    }

    /**
     * 
     * 
     * @param index
     * @param vViewport
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addViewport(
            final int index,
            final jalview.binding.Viewport vViewport)
    throws java.lang.IndexOutOfBoundsException {
        this._viewportList.add(index, vViewport);
    }

    /**
     * Method enumerateJGroup.
     * 
     * @return an Enumeration over all jalview.binding.JGroup
     * elements
     */
    public java.util.Enumeration enumerateJGroup(
    ) {
        return this._JGroupList.elements();
    }

    /**
     * Method enumerateJSeq.
     * 
     * @return an Enumeration over all jalview.binding.JSeq elements
     */
    public java.util.Enumeration enumerateJSeq(
    ) {
        return this._JSeqList.elements();
    }

    /**
     * Method enumerateTree.
     * 
     * @return an Enumeration over all jalview.binding.Tree elements
     */
    public java.util.Enumeration enumerateTree(
    ) {
        return this._treeList.elements();
    }

    /**
     * Method enumerateUserColours.
     * 
     * @return an Enumeration over all jalview.binding.UserColours
     * elements
     */
    public java.util.Enumeration enumerateUserColours(
    ) {
        return this._userColoursList.elements();
    }

    /**
     * Method enumerateViewport.
     * 
     * @return an Enumeration over all jalview.binding.Viewport
     * elements
     */
    public java.util.Enumeration enumerateViewport(
    ) {
        return this._viewportList.elements();
    }

    /**
     * Returns the value of field 'featureSettings'.
     * 
     * @return the value of field 'FeatureSettings'.
     */
    public jalview.binding.FeatureSettings getFeatureSettings(
    ) {
        return this._featureSettings;
    }

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

    /**
     * Method getJGroup.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 jalview.binding.JGroup[] getJGroup(
    ) {
        jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
        return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
    }

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

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

    /**
     * Method getJSeq.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 jalview.binding.JSeq[] getJSeq(
    ) {
        jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
        return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
    }

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

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

    /**
     * Method getTree.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 jalview.binding.Tree[] getTree(
    ) {
        jalview.binding.Tree[] array = new jalview.binding.Tree[0];
        return (jalview.binding.Tree[]) this._treeList.toArray(array);
    }

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

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

    /**
     * Method getUserColours.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 jalview.binding.UserColours[] getUserColours(
    ) {
        jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
        return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
    }

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

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

    /**
     * Method getViewport.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 jalview.binding.Viewport[] getViewport(
    ) {
        jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
        return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
    }

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

    /**
     * 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 removeAllJGroup(
    ) {
        this._JGroupList.clear();
    }

    /**
     */
    public void removeAllJSeq(
    ) {
        this._JSeqList.clear();
    }

    /**
     */
    public void removeAllTree(
    ) {
        this._treeList.clear();
    }

    /**
     */
    public void removeAllUserColours(
    ) {
        this._userColoursList.clear();
    }

    /**
     */
    public void removeAllViewport(
    ) {
        this._viewportList.clear();
    }

    /**
     * Method removeJGroup.
     * 
     * @param vJGroup
     * @return true if the object was removed from the collection.
     */
    public boolean removeJGroup(
            final jalview.binding.JGroup vJGroup) {
        boolean removed = _JGroupList.remove(vJGroup);
        return removed;
    }

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

    /**
     * Method removeJSeq.
     * 
     * @param vJSeq
     * @return true if the object was removed from the collection.
     */
    public boolean removeJSeq(
            final jalview.binding.JSeq vJSeq) {
        boolean removed = _JSeqList.remove(vJSeq);
        return removed;
    }

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

    /**
     * Method removeTree.
     * 
     * @param vTree
     * @return true if the object was removed from the collection.
     */
    public boolean removeTree(
            final jalview.binding.Tree vTree) {
        boolean removed = _treeList.remove(vTree);
        return removed;
    }

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

    /**
     * Method removeUserColours.
     * 
     * @param vUserColours
     * @return true if the object was removed from the collection.
     */
    public boolean removeUserColours(
            final jalview.binding.UserColours vUserColours) {
        boolean removed = _userColoursList.remove(vUserColours);
        return removed;
    }

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

    /**
     * Method removeViewport.
     * 
     * @param vViewport
     * @return true if the object was removed from the collection.
     */
    public boolean removeViewport(
            final jalview.binding.Viewport vViewport) {
        boolean removed = _viewportList.remove(vViewport);
        return removed;
    }

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

    /**
     * Sets the value of field 'featureSettings'.
     * 
     * @param featureSettings the value of field 'featureSettings'.
     */
    public void setFeatureSettings(
            final jalview.binding.FeatureSettings featureSettings) {
        this._featureSettings = featureSettings;
    }

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

    /**
     * 
     * 
     * @param vJGroupArray
     */
    public void setJGroup(
            final jalview.binding.JGroup[] vJGroupArray) {
        //-- copy array
        _JGroupList.clear();
        
        for (int i = 0; i < vJGroupArray.length; i++) {
                this._JGroupList.add(vJGroupArray[i]);
        }
    }

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

    /**
     * 
     * 
     * @param vJSeqArray
     */
    public void setJSeq(
            final jalview.binding.JSeq[] vJSeqArray) {
        //-- copy array
        _JSeqList.clear();
        
        for (int i = 0; i < vJSeqArray.length; i++) {
                this._JSeqList.add(vJSeqArray[i]);
        }
    }

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

    /**
     * 
     * 
     * @param vTreeArray
     */
    public void setTree(
            final jalview.binding.Tree[] vTreeArray) {
        //-- copy array
        _treeList.clear();
        
        for (int i = 0; i < vTreeArray.length; i++) {
                this._treeList.add(vTreeArray[i]);
        }
    }

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

    /**
     * 
     * 
     * @param vUserColoursArray
     */
    public void setUserColours(
            final jalview.binding.UserColours[] vUserColoursArray) {
        //-- copy array
        _userColoursList.clear();
        
        for (int i = 0; i < vUserColoursArray.length; i++) {
                this._userColoursList.add(vUserColoursArray[i]);
        }
    }

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

    /**
     * 
     * 
     * @param vViewportArray
     */
    public void setViewport(
            final jalview.binding.Viewport[] vViewportArray) {
        //-- copy array
        _viewportList.clear();
        
        for (int i = 0; i < vViewportArray.length; i++) {
                this._viewportList.add(vViewportArray[i]);
        }
    }

    /**
     * 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 jalview.binding.JalviewModelSequence
     */
    public static jalview.binding.JalviewModelSequence unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.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);
    }

}