-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.binding;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class AnnotationElement.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AnnotationElement implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _position\r
- */\r
- private int _position;\r
-\r
- /**\r
- * keeps track of state for field: _position\r
- */\r
- private boolean _has_position;\r
-\r
- /**\r
- * Field _displayCharacter\r
- */\r
- private java.lang.String _displayCharacter;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _secondaryStructure\r
- */\r
- private java.lang.String _secondaryStructure;\r
-\r
- /**\r
- * Field _value\r
- */\r
- private float _value;\r
-\r
- /**\r
- * keeps track of state for field: _value\r
- */\r
- private boolean _has_value;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AnnotationElement() {\r
- super();\r
- } //-- jalview.binding.AnnotationElement()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deletePosition\r
- * \r
- */\r
- public void deletePosition()\r
- {\r
- this._has_position= false;\r
- } //-- void deletePosition() \r
-\r
- /**\r
- * Method deleteValue\r
- * \r
- */\r
- public void deleteValue()\r
- {\r
- this._has_value= false;\r
- } //-- void deleteValue() \r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \r
-\r
- /**\r
- * Returns the value of field 'displayCharacter'.\r
- * \r
- * @return String\r
- * @return the value of field 'displayCharacter'.\r
- */\r
- public java.lang.String getDisplayCharacter()\r
- {\r
- return this._displayCharacter;\r
- } //-- java.lang.String getDisplayCharacter() \r
-\r
- /**\r
- * Returns the value of field 'position'.\r
- * \r
- * @return int\r
- * @return the value of field 'position'.\r
- */\r
- public int getPosition()\r
- {\r
- return this._position;\r
- } //-- int getPosition() \r
-\r
- /**\r
- * Returns the value of field 'secondaryStructure'.\r
- * \r
- * @return String\r
- * @return the value of field 'secondaryStructure'.\r
- */\r
- public java.lang.String getSecondaryStructure()\r
- {\r
- return this._secondaryStructure;\r
- } //-- java.lang.String getSecondaryStructure() \r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return float\r
- * @return the value of field 'value'.\r
- */\r
- public float getValue()\r
- {\r
- return this._value;\r
- } //-- float getValue() \r
-\r
- /**\r
- * Method hasPosition\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasPosition()\r
- {\r
- return this._has_position;\r
- } //-- boolean hasPosition() \r
-\r
- /**\r
- * Method hasValue\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasValue()\r
- {\r
- return this._has_value;\r
- } //-- boolean hasValue() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'description'.\r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description)\r
- {\r
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'displayCharacter'.\r
- * \r
- * @param displayCharacter the value of field 'displayCharacter'\r
- */\r
- public void setDisplayCharacter(java.lang.String displayCharacter)\r
- {\r
- this._displayCharacter = displayCharacter;\r
- } //-- void setDisplayCharacter(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'position'.\r
- * \r
- * @param position the value of field 'position'.\r
- */\r
- public void setPosition(int position)\r
- {\r
- this._position = position;\r
- this._has_position = true;\r
- } //-- void setPosition(int) \r
-\r
- /**\r
- * Sets the value of field 'secondaryStructure'.\r
- * \r
- * @param secondaryStructure the value of field\r
- * 'secondaryStructure'.\r
- */\r
- public void setSecondaryStructure(java.lang.String secondaryStructure)\r
- {\r
- this._secondaryStructure = secondaryStructure;\r
- } //-- void setSecondaryStructure(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value the value of field 'value'.\r
- */\r
- public void setValue(float value)\r
- {\r
- this._value = value;\r
- this._has_value = true;\r
- } //-- void setValue(float) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+/*******************************************************************************
+ * 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 <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class AnnotationElement.
+ *
+ * @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 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 validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}