-/*\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 Setting.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Setting implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _type.\r
- */\r
- private java.lang.String _type;\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 _display.\r
- */\r
- private boolean _display;\r
-\r
- /**\r
- * keeps track of state for field: _display\r
- */\r
- private boolean _has_display;\r
-\r
- /**\r
- * Field _order.\r
- */\r
- private float _order;\r
-\r
- /**\r
- * keeps track of state for field: _order\r
- */\r
- private boolean _has_order;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Setting()\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 deleteDisplay()\r
- {\r
- this._has_display = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteOrder()\r
- {\r
- this._has_order = 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 'display'.\r
- * \r
- * @return the value of field 'Display'.\r
- */\r
- public boolean getDisplay()\r
- {\r
- return this._display;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'order'.\r
- * \r
- * @return the value of field 'Order'.\r
- */\r
- public float getOrder()\r
- {\r
- return this._order;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return the value of field 'Type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\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 hasDisplay.\r
- * \r
- * @return true if at least one Display has been added\r
- */\r
- public boolean hasDisplay()\r
- {\r
- return this._has_display;\r
- }\r
-\r
- /**\r
- * Method hasOrder.\r
- * \r
- * @return true if at least one Order has been added\r
- */\r
- public boolean hasOrder()\r
- {\r
- return this._has_order;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'display'.\r
- * \r
- * @return the value of field 'Display'.\r
- */\r
- public boolean isDisplay()\r
- {\r
- return this._display;\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 'display'.\r
- * \r
- * @param display\r
- * the value of field 'display'.\r
- */\r
- public void setDisplay(final boolean display)\r
- {\r
- this._display = display;\r
- this._has_display = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'order'.\r
- * \r
- * @param order\r
- * the value of field 'order'.\r
- */\r
- public void setOrder(final float order)\r
- {\r
- this._order = order;\r
- this._has_order = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type\r
- * the value of field 'type'.\r
- */\r
- public void setType(final java.lang.String type)\r
- {\r
- this._type = type;\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.Settin\r
- */\r
- public static jalview.schemabinding.version2.Setting 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.Setting) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Setting.class, 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 2.8.2b1)
+ * 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 Setting.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Setting implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _display.
+ */
+ private boolean _display;
+
+ /**
+ * keeps track of state for field: _display
+ */
+ private boolean _has_display;
+
+ /**
+ * Field _order.
+ */
+ private float _order;
+
+ /**
+ * keeps track of state for field: _order
+ */
+ private boolean _has_order;
+
+ /**
+ * Optional minimum colour for graduated feature colour
+ *
+ */
+ private int _mincolour;
+
+ /**
+ * keeps track of state for field: _mincolour
+ */
+ private boolean _has_mincolour;
+
+ /**
+ * threshold value for graduated feature colour
+ *
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * threshold type for graduated feature colour
+ *
+ */
+ private int _threshstate;
+
+ /**
+ * keeps track of state for field: _threshstate
+ */
+ private boolean _has_threshstate;
+
+ /**
+ * Field _max.
+ */
+ private float _max;
+
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
+
+ /**
+ * Field _min.
+ */
+ private float _min;
+
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
+
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Setting()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAutoScale()
+ {
+ this._has_autoScale = false;
+ }
+
+ /**
+ */
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel()
+ {
+ this._has_colourByLabel = false;
+ }
+
+ /**
+ */
+ public void deleteDisplay()
+ {
+ this._has_display = false;
+ }
+
+ /**
+ */
+ public void deleteMax()
+ {
+ this._has_max = false;
+ }
+
+ /**
+ */
+ public void deleteMin()
+ {
+ this._has_min = false;
+ }
+
+ /**
+ */
+ public void deleteMincolour()
+ {
+ this._has_mincolour = false;
+ }
+
+ /**
+ */
+ public void deleteOrder()
+ {
+ this._has_order = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ */
+ public void deleteThreshstate()
+ {
+ this._has_threshstate = false;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean getDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax()
+ {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin()
+ {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'mincolour'. The field 'mincolour' has the
+ * following description: Optional minimum colour for graduated feature colour
+ *
+ *
+ * @return the value of field 'Mincolour'.
+ */
+ public int getMincolour()
+ {
+ return this._mincolour;
+ }
+
+ /**
+ * Returns the value of field 'order'.
+ *
+ * @return the value of field 'Order'.
+ */
+ public float getOrder()
+ {
+ return this._order;
+ }
+
+ /**
+ * Returns the value of field 'threshold'. The field 'threshold' has the
+ * following description: threshold value for graduated feature colour
+ *
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Returns the value of field 'threshstate'. The field 'threshstate' has the
+ * following description: threshold type for graduated feature colour
+ *
+ *
+ * @return the value of field 'Threshstate'.
+ */
+ public int getThreshstate()
+ {
+ return this._threshstate;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale()
+ {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour()
+ {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel()
+ {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasDisplay.
+ *
+ * @return true if at least one Display has been added
+ */
+ public boolean hasDisplay()
+ {
+ return this._has_display;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax()
+ {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin()
+ {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasMincolour.
+ *
+ * @return true if at least one Mincolour has been added
+ */
+ public boolean hasMincolour()
+ {
+ return this._has_mincolour;
+ }
+
+ /**
+ * Method hasOrder.
+ *
+ * @return true if at least one Order has been added
+ */
+ public boolean hasOrder()
+ {
+ return this._has_order;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasThreshstate.
+ *
+ * @return true if at least one Threshstate has been added
+ */
+ public boolean hasThreshstate()
+ {
+ return this._has_threshstate;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean isDisplay()
+ {
+ return this._display;
+ }
+
+ /**
+ * 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 'autoScale'.
+ *
+ * @param autoScale
+ * the value of field 'autoScale'.
+ */
+ public void setAutoScale(final boolean autoScale)
+ {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * 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 'colourByLabel'.
+ *
+ * @param colourByLabel
+ * the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(final boolean colourByLabel)
+ {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'display'.
+ *
+ * @param display
+ * the value of field 'display'.
+ */
+ public void setDisplay(final boolean display)
+ {
+ this._display = display;
+ this._has_display = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max
+ * the value of field 'max'.
+ */
+ public void setMax(final float max)
+ {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min
+ * the value of field 'min'.
+ */
+ public void setMin(final float min)
+ {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'mincolour'. The field 'mincolour' has the
+ * following description: Optional minimum colour for graduated feature colour
+ *
+ *
+ * @param mincolour
+ * the value of field 'mincolour'.
+ */
+ public void setMincolour(final int mincolour)
+ {
+ this._mincolour = mincolour;
+ this._has_mincolour = true;
+ }
+
+ /**
+ * Sets the value of field 'order'.
+ *
+ * @param order
+ * the value of field 'order'.
+ */
+ public void setOrder(final float order)
+ {
+ this._order = order;
+ this._has_order = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'. The field 'threshold' has the
+ * following description: threshold value for graduated feature colour
+ *
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Sets the value of field 'threshstate'. The field 'threshstate' has the
+ * following description: threshold type for graduated feature colour
+ *
+ *
+ * @param threshstate
+ * the value of field 'threshstate'.
+ */
+ public void setThreshstate(final int threshstate)
+ {
+ this._threshstate = threshstate;
+ this._has_threshstate = true;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type
+ * the value of field 'type'.
+ */
+ public void setType(final java.lang.String type)
+ {
+ this._type = type;
+ }
+
+ /**
+ * 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.Settin
+ */
+ public static jalview.schemabinding.version2.Setting unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.Setting.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