-/*\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 file is part of Jalview.\r
- * \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
- * 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
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class AnnotationColours.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AnnotationColours implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _aboveThreshold.\r
- */\r
- private int _aboveThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _aboveThreshold\r
- */\r
- private boolean _has_aboveThreshold;\r
-\r
- /**\r
- * Field _annotation.\r
- */\r
- private java.lang.String _annotation;\r
-\r
- /**\r
- * Field _minColour.\r
- */\r
- private int _minColour;\r
-\r
- /**\r
- * keeps track of state for field: _minColour\r
- */\r
- private boolean _has_minColour;\r
-\r
- /**\r
- * Field _maxColour.\r
- */\r
- private int _maxColour;\r
-\r
- /**\r
- * keeps track of state for field: _maxColour\r
- */\r
- private boolean _has_maxColour;\r
-\r
- /**\r
- * Field _colourScheme.\r
- */\r
- private java.lang.String _colourScheme;\r
-\r
- /**\r
- * Field _threshold.\r
- */\r
- private float _threshold;\r
-\r
- /**\r
- * keeps track of state for field: _threshold\r
- */\r
- private boolean _has_threshold;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AnnotationColours()\r
- {\r
- super();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- */\r
- public void deleteAboveThreshold()\r
- {\r
- this._has_aboveThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMaxColour()\r
- {\r
- this._has_maxColour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMinColour()\r
- {\r
- this._has_minColour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold = false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'aboveThreshold'.\r
- * \r
- * @return the value of field 'AboveThreshold'.\r
- */\r
- public int getAboveThreshold()\r
- {\r
- return this._aboveThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'annotation'.\r
- * \r
- * @return the value of field 'Annotation'.\r
- */\r
- public java.lang.String getAnnotation()\r
- {\r
- return this._annotation;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourScheme'.\r
- * \r
- * @return the value of field 'ColourScheme'.\r
- */\r
- public java.lang.String getColourScheme()\r
- {\r
- return this._colourScheme;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'maxColour'.\r
- * \r
- * @return the value of field 'MaxColour'.\r
- */\r
- public int getMaxColour()\r
- {\r
- return this._maxColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'minColour'.\r
- * \r
- * @return the value of field 'MinColour'.\r
- */\r
- public int getMinColour()\r
- {\r
- return this._minColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'threshold'.\r
- * \r
- * @return the value of field 'Threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\r
- }\r
-\r
- /**\r
- * Method hasAboveThreshold.\r
- * \r
- * @return true if at least one AboveThreshold has been added\r
- */\r
- public boolean hasAboveThreshold()\r
- {\r
- return this._has_aboveThreshold;\r
- }\r
-\r
- /**\r
- * Method hasMaxColour.\r
- * \r
- * @return true if at least one MaxColour has been added\r
- */\r
- public boolean hasMaxColour()\r
- {\r
- return this._has_maxColour;\r
- }\r
-\r
- /**\r
- * Method hasMinColour.\r
- * \r
- * @return true if at least one MinColour has been added\r
- */\r
- public boolean hasMinColour()\r
- {\r
- return this._has_minColour;\r
- }\r
-\r
- /**\r
- * Method hasThreshold.\r
- * \r
- * @return true if at least one Threshold has been added\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\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 'aboveThreshold'.\r
- * \r
- * @param aboveThreshold\r
- * the value of field 'aboveThreshold'.\r
- */\r
- public void setAboveThreshold(final int aboveThreshold)\r
- {\r
- this._aboveThreshold = aboveThreshold;\r
- this._has_aboveThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'annotation'.\r
- * \r
- * @param annotation\r
- * the value of field 'annotation'.\r
- */\r
- public void setAnnotation(final java.lang.String annotation)\r
- {\r
- this._annotation = annotation;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colourScheme'.\r
- * \r
- * @param colourScheme\r
- * the value of field 'colourScheme'.\r
- */\r
- public void setColourScheme(final java.lang.String colourScheme)\r
- {\r
- this._colourScheme = colourScheme;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'maxColour'.\r
- * \r
- * @param maxColour\r
- * the value of field 'maxColour'.\r
- */\r
- public void setMaxColour(final int maxColour)\r
- {\r
- this._maxColour = maxColour;\r
- this._has_maxColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'minColour'.\r
- * \r
- * @param minColour\r
- * the value of field 'minColour'.\r
- */\r
- public void setMinColour(final int minColour)\r
- {\r
- this._minColour = minColour;\r
- this._has_minColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'threshold'.\r
- * \r
- * @param threshold\r
- * the value of field 'threshold'.\r
- */\r
- public void setThreshold(final float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = 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.AnnotationColours\r
- */\r
- public static jalview.schemabinding.version2.AnnotationColours 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.AnnotationColours) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.AnnotationColours.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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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 AnnotationColours.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AnnotationColours extends AnnotationColourScheme implements
+ java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColours()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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.AnnotationColourScheme
+ */
+ public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.AnnotationColours.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