X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbinding%2FAnnotationElement.java;h=d133fe0af2ce1a682e597756fbb2d9f9f8030fd0;hb=89077cf6f65c82f9004592a0b4d3bde391163286;hp=211810dcb59a9c7078b4fc32e25d035a4a501908;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
index 211810d..d133fe0 100755
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -1,325 +1,291 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.binding;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * 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();
- } //-- jalview.binding.AnnotationElement()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method deletePosition
- *
- */
- public void deletePosition()
- {
- this._has_position= false;
- } //-- void deletePosition()
-
- /**
- * Method deleteValue
- *
- */
- public void deleteValue()
- {
- this._has_value= false;
- } //-- void deleteValue()
-
- /**
- * Returns the value of field 'description'.
- *
- * @return String
- * @return the value of field 'description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- } //-- java.lang.String getDescription()
-
- /**
- * Returns the value of field 'displayCharacter'.
- *
- * @return String
- * @return the value of field 'displayCharacter'.
- */
- public java.lang.String getDisplayCharacter()
- {
- return this._displayCharacter;
- } //-- java.lang.String getDisplayCharacter()
-
- /**
- * Returns the value of field 'position'.
- *
- * @return int
- * @return the value of field 'position'.
- */
- public int getPosition()
- {
- return this._position;
- } //-- int getPosition()
-
- /**
- * Returns the value of field 'secondaryStructure'.
- *
- * @return String
- * @return the value of field 'secondaryStructure'.
- */
- public java.lang.String getSecondaryStructure()
- {
- return this._secondaryStructure;
- } //-- java.lang.String getSecondaryStructure()
-
- /**
- * Returns the value of field 'value'.
- *
- * @return float
- * @return the value of field 'value'.
- */
- public float getValue()
- {
- return this._value;
- } //-- float getValue()
-
- /**
- * Method hasPosition
- *
- *
- *
- * @return boolean
- */
- public boolean hasPosition()
- {
- return this._has_position;
- } //-- boolean hasPosition()
-
- /**
- * Method hasValue
- *
- *
- *
- * @return boolean
- */
- public boolean hasValue()
- {
- return this._has_value;
- } //-- boolean hasValue()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(java.lang.String description)
- {
- this._description = description;
- } //-- void setDescription(java.lang.String)
-
- /**
- * Sets the value of field 'displayCharacter'.
- *
- * @param displayCharacter the value of field 'displayCharacter'
- */
- public void setDisplayCharacter(java.lang.String displayCharacter)
- {
- this._displayCharacter = displayCharacter;
- } //-- void setDisplayCharacter(java.lang.String)
-
- /**
- * Sets the value of field 'position'.
- *
- * @param position the value of field 'position'.
- */
- public void setPosition(int position)
- {
- this._position = position;
- this._has_position = true;
- } //-- void setPosition(int)
-
- /**
- * Sets the value of field 'secondaryStructure'.
- *
- * @param secondaryStructure the value of field
- * 'secondaryStructure'.
- */
- public void setSecondaryStructure(java.lang.String secondaryStructure)
- {
- this._secondaryStructure = secondaryStructure;
- } //-- void setSecondaryStructure(java.lang.String)
-
- /**
- * Sets the value of field 'value'.
- *
- * @param value the value of field 'value'.
- */
- public void setValue(float value)
- {
- this._value = value;
- this._has_value = true;
- } //-- void setValue(float)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*
+ * This class was automatically generated with
+ * Castor 1.1, 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);
+ }
+
+}