X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FAnnotationElement.java;h=45cb5c7c0a039a66904c49cb0eaaff18dac34f66;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=a53f1eeeb8e6f4bc1232c1b34052cb3a93ad1419;hpb=ac12127b5cf22bb34b6042e543d506894164a94c;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/AnnotationElement.java b/src/uk/ac/vamsas/objects/core/AnnotationElement.java index a53f1ee..45cb5c7 100644 --- a/src/uk/ac/vamsas/objects/core/AnnotationElement.java +++ b/src/uk/ac/vamsas/objects/core/AnnotationElement.java @@ -1,14 +1,28 @@ /* - * This class was automatically generated with - * Castor 1.1, 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 . */ - package uk.ac.vamsas.objects.core; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -17,771 +31,829 @@ import org.exolab.castor.xml.Unmarshaller; /** * 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; - 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; - else if (!(this._id.equals(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; } - else if (temp._id != null) - return false; - if (this._description != null) { - if (temp._description == null) return false; - else if (!(this._description.equals(temp._description))) - 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); } - else if (temp._description != null) - return false; - if (this._glyphList != null) { - if (temp._glyphList == null) return false; - else if (!(this._glyphList.equals(temp._glyphList))) - return false; + ; + if (!tmcycle) { + org.castor.util.CycleBreaker + .releaseCycleHandle(temp._description); } - else if (temp._glyphList != null) - return false; - if (this._valueList != null) { - if (temp._valueList == null) return false; - else if (!(this._valueList.equals(temp._valueList))) - return false; + ; + 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; } - else if (temp._valueList != null) - return false; - return true; + org.castor.util.CycleBreaker.releaseCycleHandle(this._description); + org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); + } } + } else if (temp._description != 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.

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 know - * 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. - *

- * The following steps came from Effective Java Programming - * Language Guide 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) { - result = 37 * result + _id.hashCode(); - } - if (_description != null) { - result = 37 * result + _description.hashCode(); - } - if (_glyphList != null) { - result = 37 * result + _glyphList.hashCode(); - } - if (_valueList != null) { - result = 37 * result + _valueList.hashCode(); - } - - 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._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); + } } - 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])); + } 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. + *

+ * 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 + * know 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. + *

+ * The following steps came from Effective Java Programming Language + * Guide 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); + } }