X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotationElement.java;h=8b018c5ac424358e4d523043d3dfe0379a11b11b;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=bc9571ebcc3c7613442df22986cae9835ffd952b;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java old mode 100755 new mode 100644 index bc9571e..8b018c5 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -1,24 +1,31 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * +/******************************************************************************* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + *******************************************************************************/ +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,287 +36,273 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class AnnotationElement implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _position. - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * Field _displayCharacter. - */ - private java.lang.String _displayCharacter; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _secondaryStructure. - */ - private java.lang.String _secondaryStructure; - - /** - * Field _value. - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationElement() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** +public class AnnotationElement implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _position. + */ + private int _position; + + /** + * keeps track of state for field: _position + */ + private boolean _has_position; + + /** + * Field _displayCharacter. + */ + private java.lang.String _displayCharacter; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _secondaryStructure. + */ + private java.lang.String _secondaryStructure; + + /** + * Field _value. */ - public void deletePosition() - { - this._has_position = false; - } + private float _value; + + /** + * keeps track of state for field: _value + */ + private boolean _has_value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationElement() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deletePosition( + ) { + this._has_position= false; + } + + /** + */ + public void deleteValue( + ) { + this._has_value= false; + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'displayCharacter'. + * + * @return the value of field 'DisplayCharacter'. + */ + public java.lang.String getDisplayCharacter( + ) { + return this._displayCharacter; + } + + /** + * Returns the value of field 'position'. + * + * @return the value of field 'Position'. + */ + public int getPosition( + ) { + return this._position; + } + + /** + * Returns the value of field 'secondaryStructure'. + * + * @return the value of field 'SecondaryStructure'. + */ + public java.lang.String getSecondaryStructure( + ) { + return this._secondaryStructure; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public float getValue( + ) { + return this._value; + } + + /** + * Method hasPosition. + * + * @return true if at least one Position has been added + */ + public boolean hasPosition( + ) { + return this._has_position; + } + + /** + * Method hasValue. + * + * @return true if at least one Value has been added + */ + public boolean hasValue( + ) { + return this._has_value; + } + + /** + * 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); + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'displayCharacter'. + * + * @param displayCharacter the value of field 'displayCharacter' + */ + public void setDisplayCharacter( + final java.lang.String displayCharacter) { + this._displayCharacter = displayCharacter; + } + + /** + * Sets the value of field 'position'. + * + * @param position the value of field 'position'. + */ + public void setPosition( + final int position) { + this._position = position; + this._has_position = true; + } + + /** + * Sets the value of field 'secondaryStructure'. + * + * @param secondaryStructure the value of field + * 'secondaryStructure'. + */ + public void setSecondaryStructure( + final java.lang.String secondaryStructure) { + this._secondaryStructure = secondaryStructure; + } + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue( + final float value) { + this._value = value; + this._has_value = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.AnnotationElement + */ + public static jalview.binding.AnnotationElement unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader); + } - /** + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema */ - public void deleteValue() - { - this._has_value = false; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'displayCharacter'. - * - * @return the value of field 'DisplayCharacter'. - */ - public java.lang.String getDisplayCharacter() - { - return this._displayCharacter; - } - - /** - * Returns the value of field 'position'. - * - * @return the value of field 'Position'. - */ - public int getPosition() - { - return this._position; - } - - /** - * Returns the value of field 'secondaryStructure'. - * - * @return the value of field 'SecondaryStructure'. - */ - public java.lang.String getSecondaryStructure() - { - return this._secondaryStructure; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue() - { - return this._value; - } - - /** - * Method hasPosition. - * - * @return true if at least one Position has been added - */ - public boolean hasPosition() - { - return this._has_position; - } - - /** - * Method hasValue. - * - * @return true if at least one Value has been added - */ - public boolean hasValue() - { - return this._has_value; - } - - /** - * 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; + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); } - 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); - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'displayCharacter'. - * - * @param displayCharacter - * the value of field 'displayCharacter' - */ - public void setDisplayCharacter(final java.lang.String displayCharacter) - { - this._displayCharacter = displayCharacter; - } - - /** - * Sets the value of field 'position'. - * - * @param position - * the value of field 'position'. - */ - public void setPosition(final int position) - { - this._position = position; - this._has_position = true; - } - - /** - * Sets the value of field 'secondaryStructure'. - * - * @param secondaryStructure - * the value of field 'secondaryStructure'. - */ - public void setSecondaryStructure( - final java.lang.String secondaryStructure) - { - this._secondaryStructure = secondaryStructure; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final float value) - { - this._value = value; - this._has_value = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.AnnotationElement - */ - public static jalview.binding.AnnotationElement unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal( - jalview.binding.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); - } }