/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\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
+//---------------------------------/\r
+//- Imported classes and packages -/\r
+//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
*/\r
private boolean _has_order;\r
\r
+ /**\r
+ * Optional minimum colour for graduated feature colour\r
+ */\r
+ private int _mincolour;\r
+\r
+ /**\r
+ * keeps track of state for field: _mincolour\r
+ */\r
+ private boolean _has_mincolour;\r
+\r
+ /**\r
+ * threshold value for graduated feature colour\r
+ */\r
+ private float _threshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshold\r
+ */\r
+ private boolean _has_threshold;\r
+\r
+ /**\r
+ * threshold type for graduated feature colour\r
+ */\r
+ private int _threshstate;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshstate\r
+ */\r
+ private boolean _has_threshstate;\r
+\r
+ /**\r
+ * Field _max.\r
+ */\r
+ private float _max;\r
+\r
+ /**\r
+ * keeps track of state for field: _max\r
+ */\r
+ private boolean _has_max;\r
+\r
+ /**\r
+ * Field _min.\r
+ */\r
+ private float _min;\r
+\r
+ /**\r
+ * keeps track of state for field: _min\r
+ */\r
+ private boolean _has_min;\r
+\r
+ /**\r
+ * Field _colourByLabel.\r
+ */\r
+ private boolean _colourByLabel;\r
+\r
+ /**\r
+ * keeps track of state for field: _colourByLabel\r
+ */\r
+ private boolean _has_colourByLabel;\r
+\r
+ /**\r
+ * Field _autoScale.\r
+ */\r
+ private boolean _autoScale;\r
+\r
+ /**\r
+ * keeps track of state for field: _autoScale\r
+ */\r
+ private boolean _has_autoScale;\r
+\r
// ----------------/\r
// - Constructors -/\r
// ----------------/\r
// -----------/\r
\r
/**\r
- */\r
+ */\r
+ public void deleteAutoScale()\r
+ {\r
+ this._has_autoScale = false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteColour()\r
{\r
this._has_colour = false;\r
}\r
\r
/**\r
- */\r
+ */\r
+ public void deleteColourByLabel()\r
+ {\r
+ this._has_colourByLabel = false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteDisplay()\r
{\r
this._has_display = false;\r
}\r
\r
/**\r
- */\r
+ */\r
+ public void deleteMax()\r
+ {\r
+ this._has_max = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMin()\r
+ {\r
+ this._has_min = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMincolour()\r
+ {\r
+ this._has_mincolour = false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteOrder()\r
{\r
this._has_order = false;\r
}\r
\r
/**\r
+ */\r
+ public void deleteThreshold()\r
+ {\r
+ this._has_threshold = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshstate()\r
+ {\r
+ this._has_threshstate = false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoScale'.\r
+ * \r
+ * @return the value of field 'AutoScale'.\r
+ */\r
+ public boolean getAutoScale()\r
+ {\r
+ return this._autoScale;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'colour'.\r
* \r
* @return the value of field 'Colour'.\r
}\r
\r
/**\r
+ * Returns the value of field 'colourByLabel'.\r
+ * \r
+ * @return the value of field 'ColourByLabel'.\r
+ */\r
+ public boolean getColourByLabel()\r
+ {\r
+ return this._colourByLabel;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'display'.\r
* \r
* @return the value of field 'Display'.\r
}\r
\r
/**\r
+ * Returns the value of field 'max'.\r
+ * \r
+ * @return the value of field 'Max'.\r
+ */\r
+ public float getMax()\r
+ {\r
+ return this._max;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'min'.\r
+ * \r
+ * @return the value of field 'Min'.\r
+ */\r
+ public float getMin()\r
+ {\r
+ return this._min;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mincolour'. The field 'mincolour' has the\r
+ * following description: Optional minimum colour for graduated feature colour\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 'order'.\r
* \r
* @return the value of field 'Order'.\r
}\r
\r
/**\r
+ * Returns the value of field 'threshold'. The field 'threshold' has the\r
+ * following description: threshold value for graduated feature colour\r
+ * \r
+ * @return the value of field 'Threshold'.\r
+ */\r
+ public float getThreshold()\r
+ {\r
+ return this._threshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshstate'. The field 'threshstate' has the\r
+ * following description: threshold type for graduated feature colour\r
+ * \r
+ * @return the value of field 'Threshstate'.\r
+ */\r
+ public int getThreshstate()\r
+ {\r
+ return this._threshstate;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'type'.\r
* \r
* @return the value of field 'Type'.\r
}\r
\r
/**\r
+ * Method hasAutoScale.\r
+ * \r
+ * @return true if at least one AutoScale has been added\r
+ */\r
+ public boolean hasAutoScale()\r
+ {\r
+ return this._has_autoScale;\r
+ }\r
+\r
+ /**\r
* Method hasColour.\r
* \r
* @return true if at least one Colour has been added\r
}\r
\r
/**\r
+ * Method hasColourByLabel.\r
+ * \r
+ * @return true if at least one ColourByLabel has been added\r
+ */\r
+ public boolean hasColourByLabel()\r
+ {\r
+ return this._has_colourByLabel;\r
+ }\r
+\r
+ /**\r
* Method hasDisplay.\r
* \r
* @return true if at least one Display has been added\r
}\r
\r
/**\r
+ * Method hasMax.\r
+ * \r
+ * @return true if at least one Max has been added\r
+ */\r
+ public boolean hasMax()\r
+ {\r
+ return this._has_max;\r
+ }\r
+\r
+ /**\r
+ * Method hasMin.\r
+ * \r
+ * @return true if at least one Min has been added\r
+ */\r
+ public boolean hasMin()\r
+ {\r
+ return this._has_min;\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 hasOrder.\r
* \r
* @return true if at least one Order has been added\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 hasThreshstate.\r
+ * \r
+ * @return true if at least one Threshstate has been added\r
+ */\r
+ public boolean hasThreshstate()\r
+ {\r
+ return this._has_threshstate;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoScale'.\r
+ * \r
+ * @return the value of field 'AutoScale'.\r
+ */\r
+ public boolean isAutoScale()\r
+ {\r
+ return this._autoScale;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourByLabel'.\r
+ * \r
+ * @return the value of field 'ColourByLabel'.\r
+ */\r
+ public boolean isColourByLabel()\r
+ {\r
+ return this._colourByLabel;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'display'.\r
* \r
* @return the value of field 'Display'.\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
+ * 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
+ * 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
* \r
* @param handler\r
* @throws java.io.IOException\r
- * if an IOException occurs during marshaling\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
+ * 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
+ * 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
}\r
\r
/**\r
+ * Sets the value of field 'autoScale'.\r
+ * \r
+ * @param autoScale\r
+ * the value of field 'autoScale'.\r
+ */\r
+ public void setAutoScale(final boolean autoScale)\r
+ {\r
+ this._autoScale = autoScale;\r
+ this._has_autoScale = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour\r
- * the value of field 'colour'.\r
+ * the value of field 'colour'.\r
*/\r
public void setColour(final int colour)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'colourByLabel'.\r
+ * \r
+ * @param colourByLabel\r
+ * the value of field 'colourByLabel'.\r
+ */\r
+ public void setColourByLabel(final boolean colourByLabel)\r
+ {\r
+ this._colourByLabel = colourByLabel;\r
+ this._has_colourByLabel = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'display'.\r
* \r
* @param display\r
- * the value of field 'display'.\r
+ * the value of field 'display'.\r
*/\r
public void setDisplay(final boolean display)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'max'.\r
+ * \r
+ * @param max\r
+ * the value of field 'max'.\r
+ */\r
+ public void setMax(final float max)\r
+ {\r
+ this._max = max;\r
+ this._has_max = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'min'.\r
+ * \r
+ * @param min\r
+ * the value of field 'min'.\r
+ */\r
+ public void setMin(final float min)\r
+ {\r
+ this._min = min;\r
+ this._has_min = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mincolour'. The field 'mincolour' has the\r
+ * following description: Optional minimum colour for graduated feature colour\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 'order'.\r
* \r
* @param order\r
- * the value of field 'order'.\r
+ * the value of field 'order'.\r
*/\r
public void setOrder(final float order)\r
{\r
}\r
\r
/**\r
+ * Sets the value of field 'threshold'. The field 'threshold' has the\r
+ * following description: threshold value for graduated feature colour\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
+ * Sets the value of field 'threshstate'. The field 'threshstate' has the\r
+ * following description: threshold type for graduated feature colour\r
+ * \r
+ * @param threshstate\r
+ * the value of field 'threshstate'.\r
+ */\r
+ public void setThreshstate(final int threshstate)\r
+ {\r
+ this._threshstate = threshstate;\r
+ this._has_threshstate = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'type'.\r
* \r
* @param type\r
- * the value of field 'type'.\r
+ * the value of field 'type'.\r
*/\r
public void setType(final java.lang.String type)\r
{\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
+ * 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
+ * if this object is an invalid instance according to the schema\r
* @return the unmarshaled jalview.schemabinding.version2.Settin\r
*/\r
public static jalview.schemabinding.version2.Setting unmarshal(\r
* \r
* \r
* @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\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
git://source.jalview.org / jalview.git / blobdiff