/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 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;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
/**
* Class AnnotationElement.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class AnnotationElement extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * position with respect to the coordinate frame defined by a
- * rangeType specification
- */
- private long _position;
-
- /**
- * keeps track of state for field: _position
- */
- private boolean _has_position;
-
- /**
- * true means the annotation element appears between the
- * specified position and the next
- */
- private boolean _after = false;
-
- /**
- * keeps track of state for field: _after
- */
- private boolean _has_after;
-
- /**
- * Primary Key for vamsas object referencing
- */
- private java.lang.String _id;
-
- /**
- * Free text at this position
- */
- private java.lang.String _description;
-
- /**
- * Discrete symbol - possibly graphically represented
- *
- */
- private java.util.Vector _glyphList;
-
- /**
- * Ordered set of float values - an application may treat
- * the values together as a vector with common support for a
- * set of
- * annotation elements - but this is, again, not validated so
- * applications
- * should deal gracefully with varying numbers of dimensions
- *
- */
- private java.util.Vector _valueList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationElement() {
- super();
- this._glyphList = new java.util.Vector();
- this._valueList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vGlyph
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addGlyph(
- final uk.ac.vamsas.objects.core.Glyph vGlyph)
- throws java.lang.IndexOutOfBoundsException {
- this._glyphList.addElement(vGlyph);
- }
-
- /**
- *
- *
- * @param index
- * @param vGlyph
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addGlyph(
- final int index,
- final uk.ac.vamsas.objects.core.Glyph vGlyph)
- throws java.lang.IndexOutOfBoundsException {
- this._glyphList.add(index, vGlyph);
- }
-
- /**
- *
- *
- * @param vValue
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addValue(
- final float vValue)
- throws java.lang.IndexOutOfBoundsException {
- this._valueList.addElement(new java.lang.Float(vValue));
- }
-
- /**
- *
- *
- * @param index
- * @param vValue
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addValue(
- final int index,
- final float vValue)
- throws java.lang.IndexOutOfBoundsException {
- this._valueList.add(index, new java.lang.Float(vValue));
- }
-
- /**
- */
- public void deleteAfter(
- ) {
- this._has_after= false;
- }
-
- /**
- */
- public void deletePosition(
- ) {
- this._has_position= false;
- }
-
- /**
- * Method enumerateGlyph.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Glyph elements
- */
- public java.util.Enumeration enumerateGlyph(
- ) {
- return this._glyphList.elements();
- }
-
- /**
- * Method enumerateValue.
- *
- * @return an Enumeration over all float elements
- */
- public java.util.Enumeration enumerateValue(
- ) {
- return this._valueList.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)
+public class AnnotationElement extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * position with respect to the coordinate frame defined by a rangeType
+ * specification
+ */
+ private long _position;
+
+ /**
+ * keeps track of state for field: _position
+ */
+ private boolean _has_position;
+
+ /**
+ * true means the annotation element appears between the specified position
+ * and the next
+ */
+ private boolean _after = false;
+
+ /**
+ * keeps track of state for field: _after
+ */
+ private boolean _has_after;
+
+ /**
+ * Primary Key for vamsas object referencing
+ */
+ private java.lang.String _id;
+
+ /**
+ * Free text at this position
+ */
+ private java.lang.String _description;
+
+ /**
+ * Discrete symbol - possibly graphically represented
+ *
+ */
+ private java.util.Vector _glyphList;
+
+ /**
+ * Ordered set of float values - an application may treat the values together
+ * as a vector with common support for a set of annotation elements - but this
+ * is, again, not validated so applications should deal gracefully with
+ * varying numbers of dimensions
+ *
+ */
+ private java.util.Vector _valueList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationElement() {
+ super();
+ this._glyphList = new java.util.Vector();
+ this._valueList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vGlyph
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addGlyph(final uk.ac.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException {
+ this._glyphList.addElement(vGlyph);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vGlyph
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addGlyph(final int index,
+ final uk.ac.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException {
+ this._glyphList.add(index, vGlyph);
+ }
+
+ /**
+ *
+ *
+ * @param vValue
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addValue(final float vValue)
+ throws java.lang.IndexOutOfBoundsException {
+ this._valueList.addElement(new java.lang.Float(vValue));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vValue
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addValue(final int index, final float vValue)
+ throws java.lang.IndexOutOfBoundsException {
+ this._valueList.add(index, new java.lang.Float(vValue));
+ }
+
+ /**
+ */
+ public void deleteAfter() {
+ this._has_after = false;
+ }
+
+ /**
+ */
+ public void deletePosition() {
+ this._has_position = false;
+ }
+
+ /**
+ * Method enumerateGlyph.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Glyph elements
+ */
+ public java.util.Enumeration enumerateGlyph() {
+ return this._glyphList.elements();
+ }
+
+ /**
+ * Method enumerateValue.
+ *
+ * @return an Enumeration over all float elements
+ */
+ public java.util.Enumeration enumerateValue() {
+ return this._valueList.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 AnnotationElement) {
+
+ AnnotationElement temp = (AnnotationElement) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._position != temp._position)
+ return false;
+ if (this._has_position != temp._has_position)
+ return false;
+ if (this._after != temp._after)
+ return false;
+ if (this._has_after != temp._has_after)
+ return false;
+ if (this._id != null) {
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
return false;
-
- if (obj instanceof AnnotationElement) {
-
- AnnotationElement temp = (AnnotationElement)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._position != temp._position)
- return false;
- if (this._has_position != temp._has_position)
- return false;
- if (this._after != temp._after)
- return false;
- if (this._has_after != temp._has_after)
- return false;
- if (this._id != null) {
- if (temp._id == null) return false;
- if (this._id != temp._id) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- if (this._description != temp._description) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._description);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._description);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._description); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); };
- return false;
- }
- if (!thcycle) {
- if (!this._description.equals(temp._description)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
- }
- }
- } else if (temp._description != null)
- return false;
- if (this._glyphList != null) {
- if (temp._glyphList == null) return false;
- if (this._glyphList != temp._glyphList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._glyphList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._glyphList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList); };
- return false;
- }
- if (!thcycle) {
- if (!this._glyphList.equals(temp._glyphList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
- }
- }
- } else if (temp._glyphList != null)
- return false;
- if (this._valueList != null) {
- if (temp._valueList == null) return false;
- if (this._valueList != temp._valueList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._valueList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._valueList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList); };
- return false;
- }
- if (!thcycle) {
- if (!this._valueList.equals(temp._valueList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
- }
- }
- } else if (temp._valueList != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
}
+ } else if (temp._id != null)
return false;
- }
-
- /**
- * Returns the value of field 'after'. The field 'after' has
- * the following description: true means the annotation element
- * appears between the
- * specified position and the next
- *
- * @return the value of field 'After'.
- */
- public boolean getAfter(
- ) {
- return this._after;
- }
-
- /**
- * Returns the value of field 'description'. The field
- * 'description' has the following description: Free text at
- * this position
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Method getGlyph.
- *
- * @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.Glyph at
- * the given index
- */
- public uk.ac.vamsas.objects.core.Glyph getGlyph(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._glyphList.size()) {
- throw new IndexOutOfBoundsException("getGlyph: Index value '" + index + "' not in range [0.." + (this._glyphList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Glyph) _glyphList.get(index);
- }
-
- /**
- * Method getGlyph.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.Glyph[] getGlyph(
- ) {
- uk.ac.vamsas.objects.core.Glyph[] array = new uk.ac.vamsas.objects.core.Glyph[0];
- return (uk.ac.vamsas.objects.core.Glyph[]) this._glyphList.toArray(array);
- }
-
- /**
- * Method getGlyphAsReference.Returns a reference to
- * '_glyphList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getGlyphAsReference(
- ) {
- return this._glyphList;
- }
-
- /**
- * Method getGlyphCount.
- *
- * @return the size of this collection
- */
- public int getGlyphCount(
- ) {
- return this._glyphList.size();
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'position'. The field 'position'
- * has the following description: position with respect to the
- * coordinate frame defined by a
- * rangeType specification
- *
- * @return the value of field 'Position'.
- */
- public long getPosition(
- ) {
- return this._position;
- }
-
- /**
- * Method getValue.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the float at the given index
- */
- public float getValue(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._valueList.size()) {
- throw new IndexOutOfBoundsException("getValue: Index value '" + index + "' not in range [0.." + (this._valueList.size() - 1) + "]");
- }
-
- return ((java.lang.Float) _valueList.get(index)).floatValue();
- }
-
- /**
- * Method getValue.Returns the contents of the collection in an
- * Array.
- *
- * @return this collection as an Array
- */
- public float[] getValue(
- ) {
- int size = this._valueList.size();
- float[] array = new float[size];
- java.util.Iterator iter = _valueList.iterator();
- for (int index = 0; index < size; index++) {
- array[index] = ((java.lang.Float) iter.next()).floatValue();
- }
- return array;
- }
-
- /**
- * Method getValueAsReference.Returns a reference to
- * '_valueList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getValueAsReference(
- ) {
- return this._valueList;
- }
-
- /**
- * Method getValueCount.
- *
- * @return the size of this collection
- */
- public int getValueCount(
- ) {
- return this._valueList.size();
- }
-
- /**
- * Method hasAfter.
- *
- * @return true if at least one After has been added
- */
- public boolean hasAfter(
- ) {
- return this._has_after;
- }
-
- /**
- * Method hasPosition.
- *
- * @return true if at least one Position has been added
- */
- public boolean hasPosition(
- ) {
- return this._has_position;
- }
-
- /**
- * 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;
- result = 37 * result + (int)(_position^(_position>>>32));
- result = 37 * result + (_after?0:1);
- if (_id != null
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_description != null
- && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
- result = 37 * result + _description.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_description);
- }
- if (_glyphList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_glyphList)) {
- result = 37 * result + _glyphList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_glyphList);
- }
- if (_valueList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_valueList)) {
- result = 37 * result + _valueList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_valueList);
- }
-
- return result;
- }
-
- /**
- * Returns the value of field 'after'. The field 'after' has
- * the following description: true means the annotation element
- * appears between the
- * specified position and the next
- *
- * @return the value of field 'After'.
- */
- public boolean isAfter(
- ) {
- return this._after;
- }
-
- /**
- * 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) {
+ if (this._description != null) {
+ if (temp._description == null)
+ return false;
+ if (this._description != temp._description) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._description);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._description);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._description.equals(temp._description)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
+ }
}
- 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 removeAllGlyph(
- ) {
- this._glyphList.clear();
- }
-
- /**
- */
- public void removeAllValue(
- ) {
- this._valueList.clear();
- }
-
- /**
- * Method removeGlyph.
- *
- * @param vGlyph
- * @return true if the object was removed from the collection.
- */
- public boolean removeGlyph(
- final uk.ac.vamsas.objects.core.Glyph vGlyph) {
- boolean removed = _glyphList.remove(vGlyph);
- return removed;
- }
-
- /**
- * Method removeGlyphAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Glyph removeGlyphAt(
- final int index) {
- java.lang.Object obj = this._glyphList.remove(index);
- return (uk.ac.vamsas.objects.core.Glyph) obj;
- }
-
- /**
- * Method removeValue.
- *
- * @param vValue
- * @return true if the object was removed from the collection.
- */
- public boolean removeValue(
- final float vValue) {
- boolean removed = _valueList.remove(new java.lang.Float(vValue));
- return removed;
- }
-
- /**
- * Method removeValueAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public float removeValueAt(
- final int index) {
- java.lang.Object obj = this._valueList.remove(index);
- return ((java.lang.Float) obj).floatValue();
- }
-
- /**
- * Sets the value of field 'after'. The field 'after' has the
- * following description: true means the annotation element
- * appears between the
- * specified position and the next
- *
- * @param after the value of field 'after'.
- */
- public void setAfter(
- final boolean after) {
- this._after = after;
- this._has_after = true;
- }
-
- /**
- * Sets the value of field 'description'. The field
- * 'description' has the following description: Free text at
- * this position
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- *
- *
- * @param index
- * @param vGlyph
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setGlyph(
- final int index,
- final uk.ac.vamsas.objects.core.Glyph vGlyph)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._glyphList.size()) {
- throw new IndexOutOfBoundsException("setGlyph: Index value '" + index + "' not in range [0.." + (this._glyphList.size() - 1) + "]");
- }
-
- this._glyphList.set(index, vGlyph);
- }
-
- /**
- *
- *
- * @param vGlyphArray
- */
- public void setGlyph(
- final uk.ac.vamsas.objects.core.Glyph[] vGlyphArray) {
- //-- copy array
- _glyphList.clear();
-
- for (int i = 0; i < vGlyphArray.length; i++) {
- this._glyphList.add(vGlyphArray[i]);
- }
- }
-
- /**
- * Sets the value of '_glyphList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vGlyphList the Vector to copy.
- */
- public void setGlyph(
- final java.util.Vector vGlyphList) {
- // copy vector
- this._glyphList.clear();
-
- this._glyphList.addAll(vGlyphList);
- }
-
- /**
- * Sets the value of '_glyphList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param glyphVector the Vector to set.
- */
- public void setGlyphAsReference(
- final java.util.Vector glyphVector) {
- this._glyphList = glyphVector;
- }
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'position'. The field 'position' has
- * the following description: position with respect to the
- * coordinate frame defined by a
- * rangeType specification
- *
- * @param position the value of field 'position'.
- */
- public void setPosition(
- final long position) {
- this._position = position;
- this._has_position = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vValue
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setValue(
- final int index,
- final float vValue)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._valueList.size()) {
- throw new IndexOutOfBoundsException("setValue: Index value '" + index + "' not in range [0.." + (this._valueList.size() - 1) + "]");
+ } else if (temp._description != null)
+ return false;
+ if (this._glyphList != null) {
+ if (temp._glyphList == null)
+ return false;
+ if (this._glyphList != temp._glyphList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._glyphList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._glyphList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._glyphList.equals(temp._glyphList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
+ }
}
-
- this._valueList.set(index, new java.lang.Float(vValue));
- }
-
- /**
- *
- *
- * @param vValueArray
- */
- public void setValue(
- final float[] vValueArray) {
- //-- copy array
- _valueList.clear();
-
- for (int i = 0; i < vValueArray.length; i++) {
- this._valueList.add(new java.lang.Float(vValueArray[i]));
+ } else if (temp._glyphList != null)
+ return false;
+ if (this._valueList != null) {
+ if (temp._valueList == null)
+ return false;
+ if (this._valueList != temp._valueList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._valueList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._valueList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._valueList.equals(temp._valueList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
+ }
}
- }
-
- /**
- * Sets the value of '_valueList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vValueList the Vector to copy.
- */
- public void setValue(
- final java.util.Vector vValueList) {
- // copy vector
- this._valueList.clear();
-
- this._valueList.addAll(vValueList);
- }
-
- /**
- * Sets the value of '_valueList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param valueVector the Vector to set.
- */
- public void setValueAsReference(
- final java.util.Vector valueVector) {
- this._valueList = valueVector;
- }
-
- /**
- * 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
- * uk.ac.vamsas.objects.core.AnnotationElement
- */
- public static uk.ac.vamsas.objects.core.AnnotationElement unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.AnnotationElement) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AnnotationElement.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);
- }
+ } else if (temp._valueList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the value of field 'after'. The field 'after' has the following
+ * description: true means the annotation element appears between the
+ * specified position and the next
+ *
+ * @return the value of field 'After'.
+ */
+ public boolean getAfter() {
+ return this._after;
+ }
+
+ /**
+ * Returns the value of field 'description'. The field 'description' has the
+ * following description: Free text at this position
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription() {
+ return this._description;
+ }
+
+ /**
+ * Method getGlyph.
+ *
+ * @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.Glyph at the given index
+ */
+ public uk.ac.vamsas.objects.core.Glyph getGlyph(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._glyphList.size()) {
+ throw new IndexOutOfBoundsException("getGlyph: Index value '" + index
+ + "' not in range [0.." + (this._glyphList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Glyph) _glyphList.get(index);
+ }
+
+ /**
+ * Method getGlyph.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.Glyph[] getGlyph() {
+ uk.ac.vamsas.objects.core.Glyph[] array = new uk.ac.vamsas.objects.core.Glyph[0];
+ return (uk.ac.vamsas.objects.core.Glyph[]) this._glyphList.toArray(array);
+ }
+
+ /**
+ * Method getGlyphAsReference.Returns a reference to '_glyphList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getGlyphAsReference() {
+ return this._glyphList;
+ }
+
+ /**
+ * Method getGlyphCount.
+ *
+ * @return the size of this collection
+ */
+ public int getGlyphCount() {
+ return this._glyphList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Primary Key for vamsas object referencing
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId() {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'position'. The field 'position' has the
+ * following description: position with respect to the coordinate frame
+ * defined by a rangeType specification
+ *
+ * @return the value of field 'Position'.
+ */
+ public long getPosition() {
+ return this._position;
+ }
+
+ /**
+ * Method getValue.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the float at the given index
+ */
+ public float getValue(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._valueList.size()) {
+ throw new IndexOutOfBoundsException("getValue: Index value '" + index
+ + "' not in range [0.." + (this._valueList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Float) _valueList.get(index)).floatValue();
+ }
+
+ /**
+ * Method getValue.Returns the contents of the collection in an Array.
+ *
+ * @return this collection as an Array
+ */
+ public float[] getValue() {
+ int size = this._valueList.size();
+ float[] array = new float[size];
+ java.util.Iterator iter = _valueList.iterator();
+ for (int index = 0; index < size; index++) {
+ array[index] = ((java.lang.Float) iter.next()).floatValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getValueAsReference.Returns a reference to '_valueList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getValueAsReference() {
+ return this._valueList;
+ }
+
+ /**
+ * Method getValueCount.
+ *
+ * @return the size of this collection
+ */
+ public int getValueCount() {
+ return this._valueList.size();
+ }
+
+ /**
+ * Method hasAfter.
+ *
+ * @return true if at least one After has been added
+ */
+ public boolean hasAfter() {
+ return this._has_after;
+ }
+
+ /**
+ * Method hasPosition.
+ *
+ * @return true if at least one Position has been added
+ */
+ public boolean hasPosition() {
+ return this._has_position;
+ }
+
+ /**
+ * 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;
+ result = 37 * result + (int) (_position ^ (_position >>> 32));
+ result = 37 * result + (_after ? 0 : 1);
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_description != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
+ result = 37 * result + _description.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_description);
+ }
+ if (_glyphList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_glyphList)) {
+ result = 37 * result + _glyphList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_glyphList);
+ }
+ if (_valueList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_valueList)) {
+ result = 37 * result + _valueList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_valueList);
+ }
+
+ return result;
+ }
+
+ /**
+ * Returns the value of field 'after'. The field 'after' has the following
+ * description: true means the annotation element appears between the
+ * specified position and the next
+ *
+ * @return the value of field 'After'.
+ */
+ public boolean isAfter() {
+ return this._after;
+ }
+
+ /**
+ * 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 removeAllGlyph() {
+ this._glyphList.clear();
+ }
+
+ /**
+ */
+ public void removeAllValue() {
+ this._valueList.clear();
+ }
+
+ /**
+ * Method removeGlyph.
+ *
+ * @param vGlyph
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeGlyph(final uk.ac.vamsas.objects.core.Glyph vGlyph) {
+ boolean removed = _glyphList.remove(vGlyph);
+ return removed;
+ }
+
+ /**
+ * Method removeGlyphAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Glyph removeGlyphAt(final int index) {
+ java.lang.Object obj = this._glyphList.remove(index);
+ return (uk.ac.vamsas.objects.core.Glyph) obj;
+ }
+
+ /**
+ * Method removeValue.
+ *
+ * @param vValue
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeValue(final float vValue) {
+ boolean removed = _valueList.remove(new java.lang.Float(vValue));
+ return removed;
+ }
+
+ /**
+ * Method removeValueAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public float removeValueAt(final int index) {
+ java.lang.Object obj = this._valueList.remove(index);
+ return ((java.lang.Float) obj).floatValue();
+ }
+
+ /**
+ * Sets the value of field 'after'. The field 'after' has the following
+ * description: true means the annotation element appears between the
+ * specified position and the next
+ *
+ * @param after
+ * the value of field 'after'.
+ */
+ public void setAfter(final boolean after) {
+ this._after = after;
+ this._has_after = true;
+ }
+
+ /**
+ * Sets the value of field 'description'. The field 'description' has the
+ * following description: Free text at this position
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vGlyph
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setGlyph(final int index,
+ final uk.ac.vamsas.objects.core.Glyph vGlyph)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._glyphList.size()) {
+ throw new IndexOutOfBoundsException("setGlyph: Index value '" + index
+ + "' not in range [0.." + (this._glyphList.size() - 1) + "]");
+ }
+
+ this._glyphList.set(index, vGlyph);
+ }
+
+ /**
+ *
+ *
+ * @param vGlyphArray
+ */
+ public void setGlyph(final uk.ac.vamsas.objects.core.Glyph[] vGlyphArray) {
+ // -- copy array
+ _glyphList.clear();
+
+ for (int i = 0; i < vGlyphArray.length; i++) {
+ this._glyphList.add(vGlyphArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_glyphList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vGlyphList
+ * the Vector to copy.
+ */
+ public void setGlyph(final java.util.Vector vGlyphList) {
+ // copy vector
+ this._glyphList.clear();
+
+ this._glyphList.addAll(vGlyphList);
+ }
+
+ /**
+ * Sets the value of '_glyphList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param glyphVector
+ * the Vector to set.
+ */
+ public void setGlyphAsReference(final java.util.Vector glyphVector) {
+ this._glyphList = glyphVector;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Primary Key for vamsas object referencing
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'position'. The field 'position' has the following
+ * description: position with respect to the coordinate frame defined by a
+ * rangeType specification
+ *
+ * @param position
+ * the value of field 'position'.
+ */
+ public void setPosition(final long position) {
+ this._position = position;
+ this._has_position = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vValue
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setValue(final int index, final float vValue)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._valueList.size()) {
+ throw new IndexOutOfBoundsException("setValue: Index value '" + index
+ + "' not in range [0.." + (this._valueList.size() - 1) + "]");
+ }
+
+ this._valueList.set(index, new java.lang.Float(vValue));
+ }
+
+ /**
+ *
+ *
+ * @param vValueArray
+ */
+ public void setValue(final float[] vValueArray) {
+ // -- copy array
+ _valueList.clear();
+
+ for (int i = 0; i < vValueArray.length; i++) {
+ this._valueList.add(new java.lang.Float(vValueArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of '_valueList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vValueList
+ * the Vector to copy.
+ */
+ public void setValue(final java.util.Vector vValueList) {
+ // copy vector
+ this._valueList.clear();
+
+ this._valueList.addAll(vValueList);
+ }
+
+ /**
+ * Sets the value of '_valueList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param valueVector
+ * the Vector to set.
+ */
+ public void setValueAsReference(final java.util.Vector valueVector) {
+ this._valueList = valueVector;
+ }
+
+ /**
+ * 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 uk.ac.vamsas.objects.core.AnnotationElement
+ */
+ public static uk.ac.vamsas.objects.core.AnnotationElement unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.AnnotationElement) Unmarshaller
+ .unmarshal(uk.ac.vamsas.objects.core.AnnotationElement.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);
+ }
}
git://source.jalview.org / vamsas.git / blobdiff