/*
 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 * 
 * This program 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 2
 * of the License, or (at your option) any later version.
 * 
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.binding;

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

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

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


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

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

    /**
     * Field _aligned.
     */
    private boolean _aligned;

    /**
     * keeps track of state for field: _aligned
     */
    private boolean _has_aligned;

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

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


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

    public SequenceSet() {
        super();
        this._sequenceList = new java.util.Vector();
        this._annotationList = new java.util.Vector();
    }


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

    /**
     * 
     * 
     * @param vAnnotation
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addAnnotation(
            final jalview.binding.Annotation vAnnotation)
    throws java.lang.IndexOutOfBoundsException {
        this._annotationList.addElement(vAnnotation);
    }

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

    /**
     * 
     * 
     * @param vSequence
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addSequence(
            final jalview.binding.Sequence vSequence)
    throws java.lang.IndexOutOfBoundsException {
        this._sequenceList.addElement(vSequence);
    }

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

    /**
     */
    public void deleteAligned(
    ) {
        this._has_aligned= false;
    }

    /**
     * Method enumerateAnnotation.
     * 
     * @return an Enumeration over all jalview.binding.Annotation
     * elements
     */
    public java.util.Enumeration enumerateAnnotation(
    ) {
        return this._annotationList.elements();
    }

    /**
     * Method enumerateSequence.
     * 
     * @return an Enumeration over all jalview.binding.Sequence
     * elements
     */
    public java.util.Enumeration enumerateSequence(
    ) {
        return this._sequenceList.elements();
    }

    /**
     * Returns the value of field 'aligned'.
     * 
     * @return the value of field 'Aligned'.
     */
    public boolean getAligned(
    ) {
        return this._aligned;
    }

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

    /**
     * Method getAnnotation.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.Annotation[] getAnnotation(
    ) {
        jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
        return (jalview.binding.Annotation[]) this._annotationList.toArray(array);
    }

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

    /**
     * Returns the value of field 'gapChar'.
     * 
     * @return the value of field 'GapChar'.
     */
    public java.lang.String getGapChar(
    ) {
        return this._gapChar;
    }

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

    /**
     * Method getSequence.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.Sequence[] getSequence(
    ) {
        jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
        return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
    }

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

    /**
     * Method hasAligned.
     * 
     * @return true if at least one Aligned has been added
     */
    public boolean hasAligned(
    ) {
        return this._has_aligned;
    }

    /**
     * Returns the value of field 'aligned'.
     * 
     * @return the value of field 'Aligned'.
     */
    public boolean isAligned(
    ) {
        return this._aligned;
    }

    /**
     * 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 removeAllAnnotation(
    ) {
        this._annotationList.clear();
    }

    /**
     */
    public void removeAllSequence(
    ) {
        this._sequenceList.clear();
    }

    /**
     * Method removeAnnotation.
     * 
     * @param vAnnotation
     * @return true if the object was removed from the collection.
     */
    public boolean removeAnnotation(
            final jalview.binding.Annotation vAnnotation) {
        boolean removed = _annotationList.remove(vAnnotation);
        return removed;
    }

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

    /**
     * Method removeSequence.
     * 
     * @param vSequence
     * @return true if the object was removed from the collection.
     */
    public boolean removeSequence(
            final jalview.binding.Sequence vSequence) {
        boolean removed = _sequenceList.remove(vSequence);
        return removed;
    }

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

    /**
     * Sets the value of field 'aligned'.
     * 
     * @param aligned the value of field 'aligned'.
     */
    public void setAligned(
            final boolean aligned) {
        this._aligned = aligned;
        this._has_aligned = true;
    }

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

    /**
     * 
     * 
     * @param vAnnotationArray
     */
    public void setAnnotation(
            final jalview.binding.Annotation[] vAnnotationArray) {
        //-- copy array
        _annotationList.clear();
        
        for (int i = 0; i < vAnnotationArray.length; i++) {
                this._annotationList.add(vAnnotationArray[i]);
        }
    }

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

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

    /**
     * 
     * 
     * @param vSequenceArray
     */
    public void setSequence(
            final jalview.binding.Sequence[] vSequenceArray) {
        //-- copy array
        _sequenceList.clear();
        
        for (int i = 0; i < vSequenceArray.length; i++) {
                this._sequenceList.add(vSequenceArray[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.SequenceSet
     */
    public static jalview.binding.SequenceSet unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.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);
    }

}