-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, 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
- * \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
- * \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
- */\r
-package jalview.schemabinding.version2;\r
-\r
-// ---------------------------------/\r
-// - Imported classes and packages -/\r
-// ---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\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 _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\r
- * 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\r
- * 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\r
- * 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\r
- * 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- 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 _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * 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 deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deletePosition()
+ {
+ this._has_position = false;
+ }
+
+ /**
+ */
+ public void deleteValue()
+ {
+ this._has_value = false;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * 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 hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * 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 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final int colour)
+ {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * 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.schemabinding.version2.AnnotationElement
+ */
+ public static jalview.schemabinding.version2.AnnotationElement unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff