/*******************************************************************************
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, 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 JGroup.
 * 
 * @version $Revision$ $Date$
 */
public class JGroup implements java.io.Serializable {


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

    /**
     * Field _start.
     */
    private int _start;

    /**
     * keeps track of state for field: _start
     */
    private boolean _has_start;

    /**
     * Field _end.
     */
    private int _end;

    /**
     * keeps track of state for field: _end
     */
    private boolean _has_end;

    /**
     * Field _name.
     */
    private java.lang.String _name;

    /**
     * Field _colour.
     */
    private java.lang.String _colour;

    /**
     * Field _consThreshold.
     */
    private int _consThreshold;

    /**
     * keeps track of state for field: _consThreshold
     */
    private boolean _has_consThreshold;

    /**
     * Field _pidThreshold.
     */
    private int _pidThreshold;

    /**
     * keeps track of state for field: _pidThreshold
     */
    private boolean _has_pidThreshold;

    /**
     * Field _outlineColour.
     */
    private int _outlineColour;

    /**
     * keeps track of state for field: _outlineColour
     */
    private boolean _has_outlineColour;

    /**
     * Field _displayBoxes.
     */
    private boolean _displayBoxes;

    /**
     * keeps track of state for field: _displayBoxes
     */
    private boolean _has_displayBoxes;

    /**
     * Field _displayText.
     */
    private boolean _displayText;

    /**
     * keeps track of state for field: _displayText
     */
    private boolean _has_displayText;

    /**
     * Field _colourText.
     */
    private boolean _colourText;

    /**
     * keeps track of state for field: _colourText
     */
    private boolean _has_colourText;

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


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

    public JGroup() {
        super();
        this._seqList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vSeq
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSeq(
            final int vSeq)
    throws java.lang.IndexOutOfBoundsException {
        this._seqList.addElement(new java.lang.Integer(vSeq));
    }

    /**
     * 
     * 
     * @param index
     * @param vSeq
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSeq(
            final int index,
            final int vSeq)
    throws java.lang.IndexOutOfBoundsException {
        this._seqList.add(index, new java.lang.Integer(vSeq));
    }

    /**
     */
    public void deleteColourText(
    ) {
        this._has_colourText= false;
    }

    /**
     */
    public void deleteConsThreshold(
    ) {
        this._has_consThreshold= false;
    }

    /**
     */
    public void deleteDisplayBoxes(
    ) {
        this._has_displayBoxes= false;
    }

    /**
     */
    public void deleteDisplayText(
    ) {
        this._has_displayText= false;
    }

    /**
     */
    public void deleteEnd(
    ) {
        this._has_end= false;
    }

    /**
     */
    public void deleteOutlineColour(
    ) {
        this._has_outlineColour= false;
    }

    /**
     */
    public void deletePidThreshold(
    ) {
        this._has_pidThreshold= false;
    }

    /**
     */
    public void deleteStart(
    ) {
        this._has_start= false;
    }

    /**
     * Method enumerateSeq.
     * 
     * @return an Enumeration over all int elements
     */
    public java.util.Enumeration enumerateSeq(
    ) {
        return this._seqList.elements();
    }

    /**
     * Returns the value of field 'colour'.
     * 
     * @return the value of field 'Colour'.
     */
    public java.lang.String getColour(
    ) {
        return this._colour;
    }

    /**
     * Returns the value of field 'colourText'.
     * 
     * @return the value of field 'ColourText'.
     */
    public boolean getColourText(
    ) {
        return this._colourText;
    }

    /**
     * Returns the value of field 'consThreshold'.
     * 
     * @return the value of field 'ConsThreshold'.
     */
    public int getConsThreshold(
    ) {
        return this._consThreshold;
    }

    /**
     * Returns the value of field 'displayBoxes'.
     * 
     * @return the value of field 'DisplayBoxes'.
     */
    public boolean getDisplayBoxes(
    ) {
        return this._displayBoxes;
    }

    /**
     * Returns the value of field 'displayText'.
     * 
     * @return the value of field 'DisplayText'.
     */
    public boolean getDisplayText(
    ) {
        return this._displayText;
    }

    /**
     * Returns the value of field 'end'.
     * 
     * @return the value of field 'End'.
     */
    public int getEnd(
    ) {
        return this._end;
    }

    /**
     * Returns the value of field 'name'.
     * 
     * @return the value of field 'Name'.
     */
    public java.lang.String getName(
    ) {
        return this._name;
    }

    /**
     * Returns the value of field 'outlineColour'.
     * 
     * @return the value of field 'OutlineColour'.
     */
    public int getOutlineColour(
    ) {
        return this._outlineColour;
    }

    /**
     * Returns the value of field 'pidThreshold'.
     * 
     * @return the value of field 'PidThreshold'.
     */
    public int getPidThreshold(
    ) {
        return this._pidThreshold;
    }

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

    /**
     * Method getSeq.Returns the contents of the collection in an
     * Array.  
     * 
     * @return this collection as an Array
     */
    public int[] getSeq(
    ) {
        int size = this._seqList.size();
        int[] array = new int[size];
        java.util.Iterator iter = _seqList.iterator();
        for (int index = 0; index < size; index++) {
            array[index] = ((java.lang.Integer) iter.next()).intValue();
        }
        return array;
    }

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

    /**
     * Returns the value of field 'start'.
     * 
     * @return the value of field 'Start'.
     */
    public int getStart(
    ) {
        return this._start;
    }

    /**
     * Method hasColourText.
     * 
     * @return true if at least one ColourText has been added
     */
    public boolean hasColourText(
    ) {
        return this._has_colourText;
    }

    /**
     * Method hasConsThreshold.
     * 
     * @return true if at least one ConsThreshold has been added
     */
    public boolean hasConsThreshold(
    ) {
        return this._has_consThreshold;
    }

    /**
     * Method hasDisplayBoxes.
     * 
     * @return true if at least one DisplayBoxes has been added
     */
    public boolean hasDisplayBoxes(
    ) {
        return this._has_displayBoxes;
    }

    /**
     * Method hasDisplayText.
     * 
     * @return true if at least one DisplayText has been added
     */
    public boolean hasDisplayText(
    ) {
        return this._has_displayText;
    }

    /**
     * Method hasEnd.
     * 
     * @return true if at least one End has been added
     */
    public boolean hasEnd(
    ) {
        return this._has_end;
    }

    /**
     * Method hasOutlineColour.
     * 
     * @return true if at least one OutlineColour has been added
     */
    public boolean hasOutlineColour(
    ) {
        return this._has_outlineColour;
    }

    /**
     * Method hasPidThreshold.
     * 
     * @return true if at least one PidThreshold has been added
     */
    public boolean hasPidThreshold(
    ) {
        return this._has_pidThreshold;
    }

    /**
     * Method hasStart.
     * 
     * @return true if at least one Start has been added
     */
    public boolean hasStart(
    ) {
        return this._has_start;
    }

    /**
     * Returns the value of field 'colourText'.
     * 
     * @return the value of field 'ColourText'.
     */
    public boolean isColourText(
    ) {
        return this._colourText;
    }

    /**
     * Returns the value of field 'displayBoxes'.
     * 
     * @return the value of field 'DisplayBoxes'.
     */
    public boolean isDisplayBoxes(
    ) {
        return this._displayBoxes;
    }

    /**
     * Returns the value of field 'displayText'.
     * 
     * @return the value of field 'DisplayText'.
     */
    public boolean isDisplayText(
    ) {
        return this._displayText;
    }

    /**
     * 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 removeAllSeq(
    ) {
        this._seqList.clear();
    }

    /**
     * Method removeSeq.
     * 
     * @param vSeq
     * @return true if the object was removed from the collection.
     */
    public boolean removeSeq(
            final int vSeq) {
        boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
        return removed;
    }

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

    /**
     * Sets the value of field 'colour'.
     * 
     * @param colour the value of field 'colour'.
     */
    public void setColour(
            final java.lang.String colour) {
        this._colour = colour;
    }

    /**
     * Sets the value of field 'colourText'.
     * 
     * @param colourText the value of field 'colourText'.
     */
    public void setColourText(
            final boolean colourText) {
        this._colourText = colourText;
        this._has_colourText = true;
    }

    /**
     * Sets the value of field 'consThreshold'.
     * 
     * @param consThreshold the value of field 'consThreshold'.
     */
    public void setConsThreshold(
            final int consThreshold) {
        this._consThreshold = consThreshold;
        this._has_consThreshold = true;
    }

    /**
     * Sets the value of field 'displayBoxes'.
     * 
     * @param displayBoxes the value of field 'displayBoxes'.
     */
    public void setDisplayBoxes(
            final boolean displayBoxes) {
        this._displayBoxes = displayBoxes;
        this._has_displayBoxes = true;
    }

    /**
     * Sets the value of field 'displayText'.
     * 
     * @param displayText the value of field 'displayText'.
     */
    public void setDisplayText(
            final boolean displayText) {
        this._displayText = displayText;
        this._has_displayText = true;
    }

    /**
     * Sets the value of field 'end'.
     * 
     * @param end the value of field 'end'.
     */
    public void setEnd(
            final int end) {
        this._end = end;
        this._has_end = true;
    }

    /**
     * Sets the value of field 'name'.
     * 
     * @param name the value of field 'name'.
     */
    public void setName(
            final java.lang.String name) {
        this._name = name;
    }

    /**
     * Sets the value of field 'outlineColour'.
     * 
     * @param outlineColour the value of field 'outlineColour'.
     */
    public void setOutlineColour(
            final int outlineColour) {
        this._outlineColour = outlineColour;
        this._has_outlineColour = true;
    }

    /**
     * Sets the value of field 'pidThreshold'.
     * 
     * @param pidThreshold the value of field 'pidThreshold'.
     */
    public void setPidThreshold(
            final int pidThreshold) {
        this._pidThreshold = pidThreshold;
        this._has_pidThreshold = true;
    }

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

    /**
     * 
     * 
     * @param vSeqArray
     */
    public void setSeq(
            final int[] vSeqArray) {
        //-- copy array
        _seqList.clear();
        
        for (int i = 0; i < vSeqArray.length; i++) {
                this._seqList.add(new java.lang.Integer(vSeqArray[i]));
        }
    }

    /**
     * Sets the value of field 'start'.
     * 
     * @param start the value of field 'start'.
     */
    public void setStart(
            final int start) {
        this._start = start;
        this._has_start = true;
    }

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

}
