/*******************************************************************************
* 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 .
*******************************************************************************/
/*
* This class was automatically generated with
* Castor 1.1, 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);
}
}