/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\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 _colour.\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\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
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- */\r
- public void deleteColour(\r
- ) {\r
- this._has_colour= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deletePosition(\r
- ) {\r
- this._has_position= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteValue(\r
- ) {\r
- this._has_value= false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public int getColour(\r
- ) {\r
- return this._colour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return the value of field 'Description'.\r
- */\r
- public java.lang.String getDescription(\r
- ) {\r
- return this._description;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayCharacter'.\r
- * \r
- * @return the value of field 'DisplayCharacter'.\r
- */\r
- public java.lang.String getDisplayCharacter(\r
- ) {\r
- return this._displayCharacter;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'position'.\r
- * \r
- * @return the value of field 'Position'.\r
- */\r
- public int getPosition(\r
- ) {\r
- return this._position;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'secondaryStructure'.\r
- * \r
- * @return the value of field 'SecondaryStructure'.\r
- */\r
- public java.lang.String getSecondaryStructure(\r
- ) {\r
- return this._secondaryStructure;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return the value of field 'Value'.\r
- */\r
- public float getValue(\r
- ) {\r
- return this._value;\r
- }\r
-\r
- /**\r
- * Method hasColour.\r
- * \r
- * @return true if at least one Colour has been added\r
- */\r
- public boolean hasColour(\r
- ) {\r
- return this._has_colour;\r
- }\r
-\r
- /**\r
- * Method hasPosition.\r
- * \r
- * @return true if at least one Position has been added\r
- */\r
- public boolean hasPosition(\r
- ) {\r
- return this._has_position;\r
- }\r
-\r
- /**\r
- * Method hasValue.\r
- * \r
- * @return true if at least one Value has been added\r
- */\r
- public boolean hasValue(\r
- ) {\r
- return this._has_value;\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid(\r
- ) {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour the value of field 'colour'.\r
- */\r
- public void setColour(\r
- final int colour) {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'description'.\r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(\r
- final java.lang.String description) {\r
- this._description = description;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'displayCharacter'.\r
- * \r
- * @param displayCharacter the value of field 'displayCharacter'\r
- */\r
- public void setDisplayCharacter(\r
- final java.lang.String displayCharacter) {\r
- this._displayCharacter = displayCharacter;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'position'.\r
- * \r
- * @param position the value of field 'position'.\r
- */\r
- public void setPosition(\r
- final int position) {\r
- this._position = position;\r
- this._has_position = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'secondaryStructure'.\r
- * \r
- * @param secondaryStructure the value of field\r
- * 'secondaryStructure'.\r
- */\r
- public void setSecondaryStructure(\r
- final java.lang.String secondaryStructure) {\r
- this._secondaryStructure = secondaryStructure;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value the value of field 'value'.\r
- */\r
- public void setValue(\r
- final float value) {\r
- this._value = value;\r
- this._has_value = true;\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @return the unmarshaled\r
- * jalview.schemabinding.version2.AnnotationElement\r
- */\r
- public static jalview.schemabinding.version2.AnnotationElement unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\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 _colour.\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
+ */\r
+ private boolean _has_colour;\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
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public AnnotationElement()\r
+ {\r
+ super();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteColour()\r
+ {\r
+ this._has_colour = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePosition()\r
+ {\r
+ this._has_position = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteValue()\r
+ {\r
+ this._has_value = false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return the value of field 'Colour'.\r
+ */\r
+ public int getColour()\r
+ {\r
+ return this._colour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'description'.\r
+ * \r
+ * @return the value of field 'Description'.\r
+ */\r
+ public java.lang.String getDescription()\r
+ {\r
+ return this._description;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayCharacter'.\r
+ * \r
+ * @return the value of field 'DisplayCharacter'.\r
+ */\r
+ public java.lang.String getDisplayCharacter()\r
+ {\r
+ return this._displayCharacter;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'position'.\r
+ * \r
+ * @return the value of field 'Position'.\r
+ */\r
+ public int getPosition()\r
+ {\r
+ return this._position;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'secondaryStructure'.\r
+ * \r
+ * @return the value of field 'SecondaryStructure'.\r
+ */\r
+ public java.lang.String getSecondaryStructure()\r
+ {\r
+ return this._secondaryStructure;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'value'.\r
+ * \r
+ * @return the value of field 'Value'.\r
+ */\r
+ public float getValue()\r
+ {\r
+ return this._value;\r
+ }\r
+\r
+ /**\r
+ * Method hasColour.\r
+ * \r
+ * @return true if at least one Colour has been added\r
+ */\r
+ public boolean hasColour()\r
+ {\r
+ return this._has_colour;\r
+ }\r
+\r
+ /**\r
+ * Method hasPosition.\r
+ * \r
+ * @return true if at least one Position has been added\r
+ */\r
+ public boolean hasPosition()\r
+ {\r
+ return this._has_position;\r
+ }\r
+\r
+ /**\r
+ * Method hasValue.\r
+ * \r
+ * @return true if at least one Value has been added\r
+ */\r
+ public boolean hasValue()\r
+ {\r
+ return this._has_value;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try\r
+ {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex)\r
+ {\r
+ return false;\r
}\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException,\r
+ org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour\r
+ * the value of field 'colour'.\r
+ */\r
+ public void setColour(final int colour)\r
+ {\r
+ this._colour = colour;\r
+ this._has_colour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'description'.\r
+ * \r
+ * @param description\r
+ * the value of field 'description'.\r
+ */\r
+ public void setDescription(final java.lang.String description)\r
+ {\r
+ this._description = description;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'displayCharacter'.\r
+ * \r
+ * @param displayCharacter\r
+ * the value of field 'displayCharacter'\r
+ */\r
+ public void setDisplayCharacter(final java.lang.String displayCharacter)\r
+ {\r
+ this._displayCharacter = displayCharacter;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'position'.\r
+ * \r
+ * @param position\r
+ * the value of field 'position'.\r
+ */\r
+ public void setPosition(final int position)\r
+ {\r
+ this._position = position;\r
+ this._has_position = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'secondaryStructure'.\r
+ * \r
+ * @param secondaryStructure\r
+ * the value of field 'secondaryStructure'.\r
+ */\r
+ public void setSecondaryStructure(\r
+ final java.lang.String secondaryStructure)\r
+ {\r
+ this._secondaryStructure = secondaryStructure;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'value'.\r
+ * \r
+ * @param value\r
+ * the value of field 'value'.\r
+ */\r
+ public void setValue(final float value)\r
+ {\r
+ this._value = value;\r
+ this._has_value = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.AnnotationElement\r
+ */\r
+ public static jalview.schemabinding.version2.AnnotationElement unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller\r
+ .unmarshal(\r
+ jalview.schemabinding.version2.AnnotationElement.class,\r
+ reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void validate() 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
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff