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/*
* This file is part of the Vamsas Client version 0.2.
* Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
* Andrew Waterhouse and Dominik Lindner.
*
* Earlier versions have also been incorporated into Jalview version 2.4
* since 2008, and TOPALi version 2 since 2007.
*
* The Vamsas Client is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The Vamsas Client 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
*/
package uk.ac.vamsas.objects.core;
/**
* Specify an ordered set of positions and/or regions on the principle dimension
* of some associated vamsas object Keeping to jaxb-1.0 specification for the
* moment - this choice should become a substitution group when we use jaxb-2.0
* capable bindings
*
*
* @version $Revision$ $Date$
*/
public abstract class RangeType extends uk.ac.vamsas.client.Vobject implements
java.io.Serializable {
// --------------------------/
// - Class/Member Variables -/
// --------------------------/
/**
* Internal choice value storage
*/
private java.lang.Object _choiceValue;
/**
* a position within the associated object's coordinate system
*
*/
private java.util.Vector _posList;
/**
* a region from start to end, with flag for inclusivity of terminii
*/
private java.util.Vector _segList;
// ----------------/
// - Constructors -/
// ----------------/
public RangeType() {
super();
this._posList = new java.util.Vector();
this._segList = new java.util.Vector();
}
// -----------/
// - Methods -/
// -----------/
/**
*
*
* @param vPos
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addPos(final uk.ac.vamsas.objects.core.Pos vPos)
throws java.lang.IndexOutOfBoundsException {
this._posList.addElement(vPos);
}
/**
*
*
* @param index
* @param vPos
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addPos(final int index, final uk.ac.vamsas.objects.core.Pos vPos)
throws java.lang.IndexOutOfBoundsException {
this._posList.add(index, vPos);
}
/**
*
*
* @param vSeg
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addSeg(final uk.ac.vamsas.objects.core.Seg vSeg)
throws java.lang.IndexOutOfBoundsException {
this._segList.addElement(vSeg);
}
/**
*
*
* @param index
* @param vSeg
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void addSeg(final int index, final uk.ac.vamsas.objects.core.Seg vSeg)
throws java.lang.IndexOutOfBoundsException {
this._segList.add(index, vSeg);
}
/**
* Method enumeratePos.
*
* @return an Enumeration over all uk.ac.vamsas.objects.core.Pos elements
*/
public java.util.Enumeration enumeratePos() {
return this._posList.elements();
}
/**
* Method enumerateSeg.
*
* @return an Enumeration over all uk.ac.vamsas.objects.core.Seg elements
*/
public java.util.Enumeration enumerateSeg() {
return this._segList.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 RangeType) {
RangeType temp = (RangeType) obj;
boolean thcycle;
boolean tmcycle;
if (this._choiceValue != null) {
if (temp._choiceValue == null)
return false;
if (this._choiceValue != temp._choiceValue) {
thcycle = org.castor.core.util.CycleBreaker
.startingToCycle(this._choiceValue);
tmcycle = org.castor.core.util.CycleBreaker
.startingToCycle(temp._choiceValue);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._choiceValue);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._choiceValue);
}
;
return false;
}
if (!thcycle) {
if (!this._choiceValue.equals(temp._choiceValue)) {
org.castor.core.util.CycleBreaker
.releaseCycleHandle(this._choiceValue);
org.castor.core.util.CycleBreaker
.releaseCycleHandle(temp._choiceValue);
return false;
}
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._choiceValue);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._choiceValue);
}
}
} else if (temp._choiceValue != null)
return false;
if (this._posList != null) {
if (temp._posList == null)
return false;
if (this._posList != temp._posList) {
thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._posList);
tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._posList);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._posList);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._posList);
}
;
return false;
}
if (!thcycle) {
if (!this._posList.equals(temp._posList)) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._posList);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._posList);
return false;
}
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._posList);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._posList);
}
}
} else if (temp._posList != null)
return false;
if (this._segList != null) {
if (temp._segList == null)
return false;
if (this._segList != temp._segList) {
thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._segList);
tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._segList);
if (thcycle != tmcycle) {
if (!thcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._segList);
}
;
if (!tmcycle) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._segList);
}
;
return false;
}
if (!thcycle) {
if (!this._segList.equals(temp._segList)) {
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._segList);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._segList);
return false;
}
org.castor.core.util.CycleBreaker.releaseCycleHandle(this._segList);
org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._segList);
}
}
} else if (temp._segList != null)
return false;
return true;
}
return false;
}
/**
* Returns the value of field 'choiceValue'. The field 'choiceValue' has the
* following description: Internal choice value storage
*
* @return the value of field 'ChoiceValue'.
*/
public java.lang.Object getChoiceValue() {
return this._choiceValue;
}
/**
* Method getPos.
*
* @param index
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
* @return the value of the uk.ac.vamsas.objects.core.Pos at the given index
*/
public uk.ac.vamsas.objects.core.Pos getPos(final int index)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._posList.size()) {
throw new IndexOutOfBoundsException("getPos: Index value '" + index
+ "' not in range [0.." + (this._posList.size() - 1) + "]");
}
return (uk.ac.vamsas.objects.core.Pos) _posList.get(index);
}
/**
* Method getPos.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 uk.ac.vamsas.objects.core.Pos[] getPos() {
uk.ac.vamsas.objects.core.Pos[] array = new uk.ac.vamsas.objects.core.Pos[0];
return (uk.ac.vamsas.objects.core.Pos[]) this._posList.toArray(array);
}
/**
* Method getPosAsReference.Returns a reference to '_posList'. No type
* checking is performed on any modifications to the Vector.
*
* @return a reference to the Vector backing this class
*/
public java.util.Vector getPosAsReference() {
return this._posList;
}
/**
* Method getPosCount.
*
* @return the size of this collection
*/
public int getPosCount() {
return this._posList.size();
}
/**
* Method getSeg.
*
* @param index
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
* @return the value of the uk.ac.vamsas.objects.core.Seg at the given index
*/
public uk.ac.vamsas.objects.core.Seg getSeg(final int index)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._segList.size()) {
throw new IndexOutOfBoundsException("getSeg: Index value '" + index
+ "' not in range [0.." + (this._segList.size() - 1) + "]");
}
return (uk.ac.vamsas.objects.core.Seg) _segList.get(index);
}
/**
* Method getSeg.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 uk.ac.vamsas.objects.core.Seg[] getSeg() {
uk.ac.vamsas.objects.core.Seg[] array = new uk.ac.vamsas.objects.core.Seg[0];
return (uk.ac.vamsas.objects.core.Seg[]) this._segList.toArray(array);
}
/**
* Method getSegAsReference.Returns a reference to '_segList'. No type
* checking is performed on any modifications to the Vector.
*
* @return a reference to the Vector backing this class
*/
public java.util.Vector getSegAsReference() {
return this._segList;
}
/**
* Method getSegCount.
*
* @return the size of this collection
*/
public int getSegCount() {
return this._segList.size();
}
/**
* 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;
if (_choiceValue != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_choiceValue)) {
result = 37 * result + _choiceValue.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_choiceValue);
}
if (_posList != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_posList)) {
result = 37 * result + _posList.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_posList);
}
if (_segList != null
&& !org.castor.core.util.CycleBreaker.startingToCycle(_segList)) {
result = 37 * result + _segList.hashCode();
org.castor.core.util.CycleBreaker.releaseCycleHandle(_segList);
}
return result;
}
/**
* 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;
}
/**
*/
public void removeAllPos() {
this._posList.clear();
}
/**
*/
public void removeAllSeg() {
this._segList.clear();
}
/**
* Method removePos.
*
* @param vPos
* @return true if the object was removed from the collection.
*/
public boolean removePos(final uk.ac.vamsas.objects.core.Pos vPos) {
boolean removed = _posList.remove(vPos);
return removed;
}
/**
* Method removePosAt.
*
* @param index
* @return the element removed from the collection
*/
public uk.ac.vamsas.objects.core.Pos removePosAt(final int index) {
java.lang.Object obj = this._posList.remove(index);
return (uk.ac.vamsas.objects.core.Pos) obj;
}
/**
* Method removeSeg.
*
* @param vSeg
* @return true if the object was removed from the collection.
*/
public boolean removeSeg(final uk.ac.vamsas.objects.core.Seg vSeg) {
boolean removed = _segList.remove(vSeg);
return removed;
}
/**
* Method removeSegAt.
*
* @param index
* @return the element removed from the collection
*/
public uk.ac.vamsas.objects.core.Seg removeSegAt(final int index) {
java.lang.Object obj = this._segList.remove(index);
return (uk.ac.vamsas.objects.core.Seg) obj;
}
/**
*
*
* @param index
* @param vPos
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void setPos(final int index, final uk.ac.vamsas.objects.core.Pos vPos)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._posList.size()) {
throw new IndexOutOfBoundsException("setPos: Index value '" + index
+ "' not in range [0.." + (this._posList.size() - 1) + "]");
}
this._posList.set(index, vPos);
}
/**
*
*
* @param vPosArray
*/
public void setPos(final uk.ac.vamsas.objects.core.Pos[] vPosArray) {
// -- copy array
_posList.clear();
for (int i = 0; i < vPosArray.length; i++) {
this._posList.add(vPosArray[i]);
}
}
/**
* Sets the value of '_posList' by copying the given Vector. All elements will
* be checked for type safety.
*
* @param vPosList
* the Vector to copy.
*/
public void setPos(final java.util.Vector vPosList) {
// copy vector
this._posList.clear();
this._posList.addAll(vPosList);
}
/**
* Sets the value of '_posList' by setting it to the given Vector. No type
* checking is performed.
*
* @deprecated
*
* @param posVector
* the Vector to set.
*/
public void setPosAsReference(final java.util.Vector posVector) {
this._posList = posVector;
}
/**
*
*
* @param index
* @param vSeg
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
public void setSeg(final int index, final uk.ac.vamsas.objects.core.Seg vSeg)
throws java.lang.IndexOutOfBoundsException {
// check bounds for index
if (index < 0 || index >= this._segList.size()) {
throw new IndexOutOfBoundsException("setSeg: Index value '" + index
+ "' not in range [0.." + (this._segList.size() - 1) + "]");
}
this._segList.set(index, vSeg);
}
/**
*
*
* @param vSegArray
*/
public void setSeg(final uk.ac.vamsas.objects.core.Seg[] vSegArray) {
// -- copy array
_segList.clear();
for (int i = 0; i < vSegArray.length; i++) {
this._segList.add(vSegArray[i]);
}
}
/**
* Sets the value of '_segList' by copying the given Vector. All elements will
* be checked for type safety.
*
* @param vSegList
* the Vector to copy.
*/
public void setSeg(final java.util.Vector vSegList) {
// copy vector
this._segList.clear();
this._segList.addAll(vSegList);
}
/**
* Sets the value of '_segList' by setting it to the given Vector. No type
* checking is performed.
*
* @deprecated
*
* @param segVector
* the Vector to set.
*/
public void setSegAsReference(final java.util.Vector segVector) {
this._segList = segVector;
}
/**
*
*
* @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);
}
}
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