/*\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 Annotation implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _graph.\r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _graphType.\r
- */\r
- private int _graphType;\r
-\r
- /**\r
- * keeps track of state for field: _graphType\r
- */\r
- private boolean _has_graphType;\r
-\r
- /**\r
- * Field _sequenceRef.\r
- */\r
- private java.lang.String _sequenceRef;\r
-\r
- /**\r
- * Field _groupRef.\r
- */\r
- private java.lang.String _groupRef;\r
-\r
- /**\r
- * Field _graphColour.\r
- */\r
- private int _graphColour;\r
-\r
- /**\r
- * keeps track of state for field: _graphColour\r
- */\r
- private boolean _has_graphColour;\r
-\r
- /**\r
- * Field _graphGroup.\r
- */\r
- private int _graphGroup;\r
-\r
- /**\r
- * keeps track of state for field: _graphGroup\r
- */\r
- private boolean _has_graphGroup;\r
-\r
- /**\r
- * Field _id.\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _scoreOnly.\r
- */\r
- private boolean _scoreOnly = false;\r
-\r
- /**\r
- * keeps track of state for field: _scoreOnly\r
- */\r
- private boolean _has_scoreOnly;\r
-\r
- /**\r
- * Field _score.\r
- */\r
- private double _score;\r
-\r
- /**\r
- * keeps track of state for field: _score\r
- */\r
- private boolean _has_score;\r
-\r
- /**\r
- * Field _visible.\r
- */\r
- private boolean _visible;\r
-\r
- /**\r
- * keeps track of state for field: _visible\r
- */\r
- private boolean _has_visible;\r
-\r
- /**\r
- * Field _centreColLabels.\r
- */\r
- private boolean _centreColLabels;\r
-\r
- /**\r
- * keeps track of state for field: _centreColLabels\r
- */\r
- private boolean _has_centreColLabels;\r
-\r
- /**\r
- * Field _scaleColLabels.\r
- */\r
- private boolean _scaleColLabels;\r
-\r
- /**\r
- * keeps track of state for field: _scaleColLabels\r
- */\r
- private boolean _has_scaleColLabels;\r
-\r
- /**\r
- * Field _showAllColLabels.\r
- */\r
- private boolean _showAllColLabels;\r
-\r
- /**\r
- * keeps track of state for field: _showAllColLabels\r
- */\r
- private boolean _has_showAllColLabels;\r
-\r
- /**\r
- * is an autocalculated annotation row\r
- */\r
- private boolean _autoCalculated = false;\r
-\r
- /**\r
- * keeps track of state for field: _autoCalculated\r
- */\r
- private boolean _has_autoCalculated;\r
-\r
- /**\r
- * Field _annotationElementList.\r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Field _label.\r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Field _description.\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _thresholdLine.\r
- */\r
- private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Annotation() {\r
- super();\r
- this._annotationElementList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vAnnotationElement\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addAnnotationElement(\r
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._annotationElementList.addElement(vAnnotationElement);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addAnnotationElement(\r
- final int index,\r
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._annotationElementList.add(index, vAnnotationElement);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteAutoCalculated(\r
- ) {\r
- this._has_autoCalculated= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteCentreColLabels(\r
- ) {\r
- this._has_centreColLabels= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteGraph(\r
- ) {\r
- this._has_graph= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteGraphColour(\r
- ) {\r
- this._has_graphColour= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteGraphGroup(\r
- ) {\r
- this._has_graphGroup= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteGraphType(\r
- ) {\r
- this._has_graphType= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteScaleColLabels(\r
- ) {\r
- this._has_scaleColLabels= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteScore(\r
- ) {\r
- this._has_score= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteScoreOnly(\r
- ) {\r
- this._has_scoreOnly= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowAllColLabels(\r
- ) {\r
- this._has_showAllColLabels= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteVisible(\r
- ) {\r
- this._has_visible= false;\r
- }\r
-\r
- /**\r
- * Method enumerateAnnotationElement.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.AnnotationElement elements\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement(\r
- ) {\r
- return this._annotationElementList.elements();\r
- }\r
-\r
- /**\r
- * Method getAnnotationElement.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.AnnotationElement at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._annotationElementList.size()) {\r
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index);\r
- }\r
-\r
- /**\r
- * Method getAnnotationElement.Returns the contents of the\r
- * collection in an Array. <p>Note: Just in case the\r
- * collection contents are changing in another thread, we pass\r
- * a 0-length Array of the correct type into the API call. \r
- * This way we <i>know</i> that the Array returned is of\r
- * exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement(\r
- ) {\r
- jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];\r
- return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAnnotationElementCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAnnotationElementCount(\r
- ) {\r
- return this._annotationElementList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'autoCalculated'. The field\r
- * 'autoCalculated' has the following description: is an\r
- * autocalculated annotation row\r
- * \r
- * @return the value of field 'AutoCalculated'.\r
- */\r
- public boolean getAutoCalculated(\r
- ) {\r
- return this._autoCalculated;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'centreColLabels'.\r
- * \r
- * @return the value of field 'CentreColLabels'.\r
- */\r
- public boolean getCentreColLabels(\r
- ) {\r
- return this._centreColLabels;\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 'graph'.\r
- * \r
- * @return the value of field 'Graph'.\r
- */\r
- public boolean getGraph(\r
- ) {\r
- return this._graph;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'graphColour'.\r
- * \r
- * @return the value of field 'GraphColour'.\r
- */\r
- public int getGraphColour(\r
- ) {\r
- return this._graphColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'graphGroup'.\r
- * \r
- * @return the value of field 'GraphGroup'.\r
- */\r
- public int getGraphGroup(\r
- ) {\r
- return this._graphGroup;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'graphType'.\r
- * \r
- * @return the value of field 'GraphType'.\r
- */\r
- public int getGraphType(\r
- ) {\r
- return this._graphType;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'groupRef'.\r
- * \r
- * @return the value of field 'GroupRef'.\r
- */\r
- public java.lang.String getGroupRef(\r
- ) {\r
- return this._groupRef;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return the value of field 'Id'.\r
- */\r
- public java.lang.String getId(\r
- ) {\r
- return this._id;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'label'.\r
- * \r
- * @return the value of field 'Label'.\r
- */\r
- public java.lang.String getLabel(\r
- ) {\r
- return this._label;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'scaleColLabels'.\r
- * \r
- * @return the value of field 'ScaleColLabels'.\r
- */\r
- public boolean getScaleColLabels(\r
- ) {\r
- return this._scaleColLabels;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'score'.\r
- * \r
- * @return the value of field 'Score'.\r
- */\r
- public double getScore(\r
- ) {\r
- return this._score;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'scoreOnly'.\r
- * \r
- * @return the value of field 'ScoreOnly'.\r
- */\r
- public boolean getScoreOnly(\r
- ) {\r
- return this._scoreOnly;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequenceRef'.\r
- * \r
- * @return the value of field 'SequenceRef'.\r
- */\r
- public java.lang.String getSequenceRef(\r
- ) {\r
- return this._sequenceRef;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showAllColLabels'.\r
- * \r
- * @return the value of field 'ShowAllColLabels'.\r
- */\r
- public boolean getShowAllColLabels(\r
- ) {\r
- return this._showAllColLabels;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'thresholdLine'.\r
- * \r
- * @return the value of field 'ThresholdLine'.\r
- */\r
- public jalview.schemabinding.version2.ThresholdLine getThresholdLine(\r
- ) {\r
- return this._thresholdLine;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'visible'.\r
- * \r
- * @return the value of field 'Visible'.\r
- */\r
- public boolean getVisible(\r
- ) {\r
- return this._visible;\r
- }\r
-\r
- /**\r
- * Method hasAutoCalculated.\r
- * \r
- * @return true if at least one AutoCalculated has been added\r
- */\r
- public boolean hasAutoCalculated(\r
- ) {\r
- return this._has_autoCalculated;\r
- }\r
-\r
- /**\r
- * Method hasCentreColLabels.\r
- * \r
- * @return true if at least one CentreColLabels has been added\r
- */\r
- public boolean hasCentreColLabels(\r
- ) {\r
- return this._has_centreColLabels;\r
- }\r
-\r
- /**\r
- * Method hasGraph.\r
- * \r
- * @return true if at least one Graph has been added\r
- */\r
- public boolean hasGraph(\r
- ) {\r
- return this._has_graph;\r
- }\r
-\r
- /**\r
- * Method hasGraphColour.\r
- * \r
- * @return true if at least one GraphColour has been added\r
- */\r
- public boolean hasGraphColour(\r
- ) {\r
- return this._has_graphColour;\r
- }\r
-\r
- /**\r
- * Method hasGraphGroup.\r
- * \r
- * @return true if at least one GraphGroup has been added\r
- */\r
- public boolean hasGraphGroup(\r
- ) {\r
- return this._has_graphGroup;\r
- }\r
-\r
- /**\r
- * Method hasGraphType.\r
- * \r
- * @return true if at least one GraphType has been added\r
- */\r
- public boolean hasGraphType(\r
- ) {\r
- return this._has_graphType;\r
- }\r
-\r
- /**\r
- * Method hasScaleColLabels.\r
- * \r
- * @return true if at least one ScaleColLabels has been added\r
- */\r
- public boolean hasScaleColLabels(\r
- ) {\r
- return this._has_scaleColLabels;\r
- }\r
-\r
- /**\r
- * Method hasScore.\r
- * \r
- * @return true if at least one Score has been added\r
- */\r
- public boolean hasScore(\r
- ) {\r
- return this._has_score;\r
- }\r
-\r
- /**\r
- * Method hasScoreOnly.\r
- * \r
- * @return true if at least one ScoreOnly has been added\r
- */\r
- public boolean hasScoreOnly(\r
- ) {\r
- return this._has_scoreOnly;\r
- }\r
-\r
- /**\r
- * Method hasShowAllColLabels.\r
- * \r
- * @return true if at least one ShowAllColLabels has been added\r
- */\r
- public boolean hasShowAllColLabels(\r
- ) {\r
- return this._has_showAllColLabels;\r
- }\r
-\r
- /**\r
- * Method hasVisible.\r
- * \r
- * @return true if at least one Visible has been added\r
- */\r
- public boolean hasVisible(\r
- ) {\r
- return this._has_visible;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'autoCalculated'. The field\r
- * 'autoCalculated' has the following description: is an\r
- * autocalculated annotation row\r
- * \r
- * @return the value of field 'AutoCalculated'.\r
- */\r
- public boolean isAutoCalculated(\r
- ) {\r
- return this._autoCalculated;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'centreColLabels'.\r
- * \r
- * @return the value of field 'CentreColLabels'.\r
- */\r
- public boolean isCentreColLabels(\r
- ) {\r
- return this._centreColLabels;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'graph'.\r
- * \r
- * @return the value of field 'Graph'.\r
- */\r
- public boolean isGraph(\r
- ) {\r
- return this._graph;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'scaleColLabels'.\r
- * \r
- * @return the value of field 'ScaleColLabels'.\r
- */\r
- public boolean isScaleColLabels(\r
- ) {\r
- return this._scaleColLabels;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'scoreOnly'.\r
- * \r
- * @return the value of field 'ScoreOnly'.\r
- */\r
- public boolean isScoreOnly(\r
- ) {\r
- return this._scoreOnly;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showAllColLabels'.\r
- * \r
- * @return the value of field 'ShowAllColLabels'.\r
- */\r
- public boolean isShowAllColLabels(\r
- ) {\r
- return this._showAllColLabels;\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
- * Returns the value of field 'visible'.\r
- * \r
- * @return the value of field 'Visible'.\r
- */\r
- public boolean isVisible(\r
- ) {\r
- return this._visible;\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
- */\r
- public void removeAllAnnotationElement(\r
- ) {\r
- this._annotationElementList.clear();\r
- }\r
-\r
- /**\r
- * Method removeAnnotationElement.\r
- * \r
- * @param vAnnotationElement\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAnnotationElement(\r
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) {\r
- boolean removed = _annotationElementList.remove(vAnnotationElement);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAnnotationElementAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(\r
- final int index) {\r
- java.lang.Object obj = this._annotationElementList.remove(index);\r
- return (jalview.schemabinding.version2.AnnotationElement) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setAnnotationElement(\r
- final int index,\r
- final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._annotationElementList.size()) {\r
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");\r
- }\r
- \r
- this._annotationElementList.set(index, vAnnotationElement);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAnnotationElementArray\r
- */\r
- public void setAnnotationElement(\r
- final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) {\r
- //-- copy array\r
- _annotationElementList.clear();\r
- \r
- for (int i = 0; i < vAnnotationElementArray.length; i++) {\r
- this._annotationElementList.add(vAnnotationElementArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'autoCalculated'. The field\r
- * 'autoCalculated' has the following description: is an\r
- * autocalculated annotation row\r
- * \r
- * @param autoCalculated the value of field 'autoCalculated'.\r
- */\r
- public void setAutoCalculated(\r
- final boolean autoCalculated) {\r
- this._autoCalculated = autoCalculated;\r
- this._has_autoCalculated = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'centreColLabels'.\r
- * \r
- * @param centreColLabels the value of field 'centreColLabels'.\r
- */\r
- public void setCentreColLabels(\r
- final boolean centreColLabels) {\r
- this._centreColLabels = centreColLabels;\r
- this._has_centreColLabels = 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 'graph'.\r
- * \r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(\r
- final boolean graph) {\r
- this._graph = graph;\r
- this._has_graph = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'graphColour'.\r
- * \r
- * @param graphColour the value of field 'graphColour'.\r
- */\r
- public void setGraphColour(\r
- final int graphColour) {\r
- this._graphColour = graphColour;\r
- this._has_graphColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'graphGroup'.\r
- * \r
- * @param graphGroup the value of field 'graphGroup'.\r
- */\r
- public void setGraphGroup(\r
- final int graphGroup) {\r
- this._graphGroup = graphGroup;\r
- this._has_graphGroup = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'graphType'.\r
- * \r
- * @param graphType the value of field 'graphType'.\r
- */\r
- public void setGraphType(\r
- final int graphType) {\r
- this._graphType = graphType;\r
- this._has_graphType = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'groupRef'.\r
- * \r
- * @param groupRef the value of field 'groupRef'.\r
- */\r
- public void setGroupRef(\r
- final java.lang.String groupRef) {\r
- this._groupRef = groupRef;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(\r
- final java.lang.String id) {\r
- this._id = id;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'label'.\r
- * \r
- * @param label the value of field 'label'.\r
- */\r
- public void setLabel(\r
- final java.lang.String label) {\r
- this._label = label;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'scaleColLabels'.\r
- * \r
- * @param scaleColLabels the value of field 'scaleColLabels'.\r
- */\r
- public void setScaleColLabels(\r
- final boolean scaleColLabels) {\r
- this._scaleColLabels = scaleColLabels;\r
- this._has_scaleColLabels = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'score'.\r
- * \r
- * @param score the value of field 'score'.\r
- */\r
- public void setScore(\r
- final double score) {\r
- this._score = score;\r
- this._has_score = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'scoreOnly'.\r
- * \r
- * @param scoreOnly the value of field 'scoreOnly'.\r
- */\r
- public void setScoreOnly(\r
- final boolean scoreOnly) {\r
- this._scoreOnly = scoreOnly;\r
- this._has_scoreOnly = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'sequenceRef'.\r
- * \r
- * @param sequenceRef the value of field 'sequenceRef'.\r
- */\r
- public void setSequenceRef(\r
- final java.lang.String sequenceRef) {\r
- this._sequenceRef = sequenceRef;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showAllColLabels'.\r
- * \r
- * @param showAllColLabels the value of field 'showAllColLabels'\r
- */\r
- public void setShowAllColLabels(\r
- final boolean showAllColLabels) {\r
- this._showAllColLabels = showAllColLabels;\r
- this._has_showAllColLabels = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'thresholdLine'.\r
- * \r
- * @param thresholdLine the value of field 'thresholdLine'.\r
- */\r
- public void setThresholdLine(\r
- final jalview.schemabinding.version2.ThresholdLine thresholdLine) {\r
- this._thresholdLine = thresholdLine;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'visible'.\r
- * \r
- * @param visible the value of field 'visible'.\r
- */\r
- public void setVisible(\r
- final boolean visible) {\r
- this._visible = visible;\r
- this._has_visible = 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.Annotation\r
- */\r
- public static jalview.schemabinding.version2.Annotation unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.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
- }\r
+public class Annotation implements java.io.Serializable\r
+{\r
+\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
+\r
+ /**\r
+ * Field _graph.\r
+ */\r
+ private boolean _graph;\r
+\r
+ /**\r
+ * keeps track of state for field: _graph\r
+ */\r
+ private boolean _has_graph;\r
+\r
+ /**\r
+ * Field _graphType.\r
+ */\r
+ private int _graphType;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphType\r
+ */\r
+ private boolean _has_graphType;\r
+\r
+ /**\r
+ * Field _sequenceRef.\r
+ */\r
+ private java.lang.String _sequenceRef;\r
+\r
+ /**\r
+ * Field _groupRef.\r
+ */\r
+ private java.lang.String _groupRef;\r
+\r
+ /**\r
+ * Field _graphColour.\r
+ */\r
+ private int _graphColour;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphColour\r
+ */\r
+ private boolean _has_graphColour;\r
+\r
+ /**\r
+ * Field _graphGroup.\r
+ */\r
+ private int _graphGroup;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphGroup\r
+ */\r
+ private boolean _has_graphGroup;\r
+\r
+ /**\r
+ * Field _id.\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _scoreOnly.\r
+ */\r
+ private boolean _scoreOnly = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _scoreOnly\r
+ */\r
+ private boolean _has_scoreOnly;\r
+\r
+ /**\r
+ * Field _score.\r
+ */\r
+ private double _score;\r
+\r
+ /**\r
+ * keeps track of state for field: _score\r
+ */\r
+ private boolean _has_score;\r
+\r
+ /**\r
+ * Field _visible.\r
+ */\r
+ private boolean _visible;\r
+\r
+ /**\r
+ * keeps track of state for field: _visible\r
+ */\r
+ private boolean _has_visible;\r
+\r
+ /**\r
+ * Field _centreColLabels.\r
+ */\r
+ private boolean _centreColLabels;\r
+\r
+ /**\r
+ * keeps track of state for field: _centreColLabels\r
+ */\r
+ private boolean _has_centreColLabels;\r
+\r
+ /**\r
+ * Field _scaleColLabels.\r
+ */\r
+ private boolean _scaleColLabels;\r
+\r
+ /**\r
+ * keeps track of state for field: _scaleColLabels\r
+ */\r
+ private boolean _has_scaleColLabels;\r
+\r
+ /**\r
+ * Field _showAllColLabels.\r
+ */\r
+ private boolean _showAllColLabels;\r
+\r
+ /**\r
+ * keeps track of state for field: _showAllColLabels\r
+ */\r
+ private boolean _has_showAllColLabels;\r
+\r
+ /**\r
+ * is an autocalculated annotation row\r
+ */\r
+ private boolean _autoCalculated = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _autoCalculated\r
+ */\r
+ private boolean _has_autoCalculated;\r
+\r
+ /**\r
+ * Field _annotationElementList.\r
+ */\r
+ private java.util.Vector _annotationElementList;\r
+\r
+ /**\r
+ * Field _label.\r
+ */\r
+ private java.lang.String _label;\r
+\r
+ /**\r
+ * Field _description.\r
+ */\r
+ private java.lang.String _description;\r
+\r
+ /**\r
+ * Field _thresholdLine.\r
+ */\r
+ private jalview.schemabinding.version2.ThresholdLine _thresholdLine;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public Annotation()\r
+ {\r
+ super();\r
+ this._annotationElementList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotationElement(\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._annotationElementList.addElement(vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotationElement(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._annotationElementList.add(index, vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteAutoCalculated()\r
+ {\r
+ this._has_autoCalculated = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteCentreColLabels()\r
+ {\r
+ this._has_centreColLabels = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraph()\r
+ {\r
+ this._has_graph = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraphColour()\r
+ {\r
+ this._has_graphColour = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraphGroup()\r
+ {\r
+ this._has_graphGroup = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraphType()\r
+ {\r
+ this._has_graphType = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteScaleColLabels()\r
+ {\r
+ this._has_scaleColLabels = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteScore()\r
+ {\r
+ this._has_score = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteScoreOnly()\r
+ {\r
+ this._has_scoreOnly = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowAllColLabels()\r
+ {\r
+ this._has_showAllColLabels = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteVisible()\r
+ {\r
+ this._has_visible = false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAnnotationElement.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AnnotationElement elements\r
+ */\r
+ public java.util.Enumeration enumerateAnnotationElement()\r
+ {\r
+ return this._annotationElementList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.AnnotationElement\r
+ * at the given index\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException(\r
+ "getAnnotationElement: Index value '" + index\r
+ + "' not in range [0.."\r
+ + (this._annotationElementList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElement.Returns the contents of the collection in an\r
+ * Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()\r
+ {\r
+ jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];\r
+ return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationElementCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAnnotationElementCount()\r
+ {\r
+ return this._annotationElementList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has\r
+ * the following description: is an autocalculated annotation row\r
+ * \r
+ * @return the value of field 'AutoCalculated'.\r
+ */\r
+ public boolean getAutoCalculated()\r
+ {\r
+ return this._autoCalculated;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'centreColLabels'.\r
+ * \r
+ * @return the value of field 'CentreColLabels'.\r
+ */\r
+ public boolean getCentreColLabels()\r
+ {\r
+ return this._centreColLabels;\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 'graph'.\r
+ * \r
+ * @return the value of field 'Graph'.\r
+ */\r
+ public boolean getGraph()\r
+ {\r
+ return this._graph;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graphColour'.\r
+ * \r
+ * @return the value of field 'GraphColour'.\r
+ */\r
+ public int getGraphColour()\r
+ {\r
+ return this._graphColour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graphGroup'.\r
+ * \r
+ * @return the value of field 'GraphGroup'.\r
+ */\r
+ public int getGraphGroup()\r
+ {\r
+ return this._graphGroup;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graphType'.\r
+ * \r
+ * @return the value of field 'GraphType'.\r
+ */\r
+ public int getGraphType()\r
+ {\r
+ return this._graphType;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'groupRef'.\r
+ * \r
+ * @return the value of field 'GroupRef'.\r
+ */\r
+ public java.lang.String getGroupRef()\r
+ {\r
+ return this._groupRef;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'.\r
+ * \r
+ * @return the value of field 'Id'.\r
+ */\r
+ public java.lang.String getId()\r
+ {\r
+ return this._id;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'label'.\r
+ * \r
+ * @return the value of field 'Label'.\r
+ */\r
+ public java.lang.String getLabel()\r
+ {\r
+ return this._label;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'scaleColLabels'.\r
+ * \r
+ * @return the value of field 'ScaleColLabels'.\r
+ */\r
+ public boolean getScaleColLabels()\r
+ {\r
+ return this._scaleColLabels;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'score'.\r
+ * \r
+ * @return the value of field 'Score'.\r
+ */\r
+ public double getScore()\r
+ {\r
+ return this._score;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'scoreOnly'.\r
+ * \r
+ * @return the value of field 'ScoreOnly'.\r
+ */\r
+ public boolean getScoreOnly()\r
+ {\r
+ return this._scoreOnly;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'sequenceRef'.\r
+ * \r
+ * @return the value of field 'SequenceRef'.\r
+ */\r
+ public java.lang.String getSequenceRef()\r
+ {\r
+ return this._sequenceRef;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showAllColLabels'.\r
+ * \r
+ * @return the value of field 'ShowAllColLabels'.\r
+ */\r
+ public boolean getShowAllColLabels()\r
+ {\r
+ return this._showAllColLabels;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'thresholdLine'.\r
+ * \r
+ * @return the value of field 'ThresholdLine'.\r
+ */\r
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine()\r
+ {\r
+ return this._thresholdLine;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'visible'.\r
+ * \r
+ * @return the value of field 'Visible'.\r
+ */\r
+ public boolean getVisible()\r
+ {\r
+ return this._visible;\r
+ }\r
+\r
+ /**\r
+ * Method hasAutoCalculated.\r
+ * \r
+ * @return true if at least one AutoCalculated has been added\r
+ */\r
+ public boolean hasAutoCalculated()\r
+ {\r
+ return this._has_autoCalculated;\r
+ }\r
+\r
+ /**\r
+ * Method hasCentreColLabels.\r
+ * \r
+ * @return true if at least one CentreColLabels has been added\r
+ */\r
+ public boolean hasCentreColLabels()\r
+ {\r
+ return this._has_centreColLabels;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraph.\r
+ * \r
+ * @return true if at least one Graph has been added\r
+ */\r
+ public boolean hasGraph()\r
+ {\r
+ return this._has_graph;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraphColour.\r
+ * \r
+ * @return true if at least one GraphColour has been added\r
+ */\r
+ public boolean hasGraphColour()\r
+ {\r
+ return this._has_graphColour;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraphGroup.\r
+ * \r
+ * @return true if at least one GraphGroup has been added\r
+ */\r
+ public boolean hasGraphGroup()\r
+ {\r
+ return this._has_graphGroup;\r
+ }\r
+\r
+ /**\r
+ * Method hasGraphType.\r
+ * \r
+ * @return true if at least one GraphType has been added\r
+ */\r
+ public boolean hasGraphType()\r
+ {\r
+ return this._has_graphType;\r
+ }\r
+\r
+ /**\r
+ * Method hasScaleColLabels.\r
+ * \r
+ * @return true if at least one ScaleColLabels has been added\r
+ */\r
+ public boolean hasScaleColLabels()\r
+ {\r
+ return this._has_scaleColLabels;\r
+ }\r
+\r
+ /**\r
+ * Method hasScore.\r
+ * \r
+ * @return true if at least one Score has been added\r
+ */\r
+ public boolean hasScore()\r
+ {\r
+ return this._has_score;\r
+ }\r
+\r
+ /**\r
+ * Method hasScoreOnly.\r
+ * \r
+ * @return true if at least one ScoreOnly has been added\r
+ */\r
+ public boolean hasScoreOnly()\r
+ {\r
+ return this._has_scoreOnly;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowAllColLabels.\r
+ * \r
+ * @return true if at least one ShowAllColLabels has been added\r
+ */\r
+ public boolean hasShowAllColLabels()\r
+ {\r
+ return this._has_showAllColLabels;\r
+ }\r
+\r
+ /**\r
+ * Method hasVisible.\r
+ * \r
+ * @return true if at least one Visible has been added\r
+ */\r
+ public boolean hasVisible()\r
+ {\r
+ return this._has_visible;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has\r
+ * the following description: is an autocalculated annotation row\r
+ * \r
+ * @return the value of field 'AutoCalculated'.\r
+ */\r
+ public boolean isAutoCalculated()\r
+ {\r
+ return this._autoCalculated;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'centreColLabels'.\r
+ * \r
+ * @return the value of field 'CentreColLabels'.\r
+ */\r
+ public boolean isCentreColLabels()\r
+ {\r
+ return this._centreColLabels;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graph'.\r
+ * \r
+ * @return the value of field 'Graph'.\r
+ */\r
+ public boolean isGraph()\r
+ {\r
+ return this._graph;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'scaleColLabels'.\r
+ * \r
+ * @return the value of field 'ScaleColLabels'.\r
+ */\r
+ public boolean isScaleColLabels()\r
+ {\r
+ return this._scaleColLabels;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'scoreOnly'.\r
+ * \r
+ * @return the value of field 'ScoreOnly'.\r
+ */\r
+ public boolean isScoreOnly()\r
+ {\r
+ return this._scoreOnly;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showAllColLabels'.\r
+ * \r
+ * @return the value of field 'ShowAllColLabels'.\r
+ */\r
+ public boolean isShowAllColLabels()\r
+ {\r
+ return this._showAllColLabels;\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
+ * Returns the value of field 'visible'.\r
+ * \r
+ * @return the value of field 'Visible'.\r
+ */\r
+ public boolean isVisible()\r
+ {\r
+ return this._visible;\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
+ */\r
+ public void removeAllAnnotationElement()\r
+ {\r
+ this._annotationElementList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElement.\r
+ * \r
+ * @param vAnnotationElement\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotationElement(\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ {\r
+ boolean removed = _annotationElementList.remove(vAnnotationElement);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationElementAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._annotationElementList.remove(index);\r
+ return (jalview.schemabinding.version2.AnnotationElement) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotationElement\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setAnnotationElement(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationElementList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException(\r
+ "setAnnotationElement: Index value '" + index\r
+ + "' not in range [0.."\r
+ + (this._annotationElementList.size() - 1) + "]");\r
+ }\r
+\r
+ this._annotationElementList.set(index, vAnnotationElement);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotationElementArray\r
+ */\r
+ public void setAnnotationElement(\r
+ final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray)\r
+ {\r
+ // -- copy array\r
+ _annotationElementList.clear();\r
+\r
+ for (int i = 0; i < vAnnotationElementArray.length; i++)\r
+ {\r
+ this._annotationElementList.add(vAnnotationElementArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has\r
+ * the following description: is an autocalculated annotation row\r
+ * \r
+ * @param autoCalculated\r
+ * the value of field 'autoCalculated'.\r
+ */\r
+ public void setAutoCalculated(final boolean autoCalculated)\r
+ {\r
+ this._autoCalculated = autoCalculated;\r
+ this._has_autoCalculated = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'centreColLabels'.\r
+ * \r
+ * @param centreColLabels\r
+ * the value of field 'centreColLabels'.\r
+ */\r
+ public void setCentreColLabels(final boolean centreColLabels)\r
+ {\r
+ this._centreColLabels = centreColLabels;\r
+ this._has_centreColLabels = 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 'graph'.\r
+ * \r
+ * @param graph\r
+ * the value of field 'graph'.\r
+ */\r
+ public void setGraph(final boolean graph)\r
+ {\r
+ this._graph = graph;\r
+ this._has_graph = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphColour'.\r
+ * \r
+ * @param graphColour\r
+ * the value of field 'graphColour'.\r
+ */\r
+ public void setGraphColour(final int graphColour)\r
+ {\r
+ this._graphColour = graphColour;\r
+ this._has_graphColour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphGroup'.\r
+ * \r
+ * @param graphGroup\r
+ * the value of field 'graphGroup'.\r
+ */\r
+ public void setGraphGroup(final int graphGroup)\r
+ {\r
+ this._graphGroup = graphGroup;\r
+ this._has_graphGroup = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graphType'.\r
+ * \r
+ * @param graphType\r
+ * the value of field 'graphType'.\r
+ */\r
+ public void setGraphType(final int graphType)\r
+ {\r
+ this._graphType = graphType;\r
+ this._has_graphType = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'groupRef'.\r
+ * \r
+ * @param groupRef\r
+ * the value of field 'groupRef'.\r
+ */\r
+ public void setGroupRef(final java.lang.String groupRef)\r
+ {\r
+ this._groupRef = groupRef;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'.\r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'label'.\r
+ * \r
+ * @param label\r
+ * the value of field 'label'.\r
+ */\r
+ public void setLabel(final java.lang.String label)\r
+ {\r
+ this._label = label;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'scaleColLabels'.\r
+ * \r
+ * @param scaleColLabels\r
+ * the value of field 'scaleColLabels'.\r
+ */\r
+ public void setScaleColLabels(final boolean scaleColLabels)\r
+ {\r
+ this._scaleColLabels = scaleColLabels;\r
+ this._has_scaleColLabels = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'score'.\r
+ * \r
+ * @param score\r
+ * the value of field 'score'.\r
+ */\r
+ public void setScore(final double score)\r
+ {\r
+ this._score = score;\r
+ this._has_score = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'scoreOnly'.\r
+ * \r
+ * @param scoreOnly\r
+ * the value of field 'scoreOnly'.\r
+ */\r
+ public void setScoreOnly(final boolean scoreOnly)\r
+ {\r
+ this._scoreOnly = scoreOnly;\r
+ this._has_scoreOnly = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequenceRef'.\r
+ * \r
+ * @param sequenceRef\r
+ * the value of field 'sequenceRef'.\r
+ */\r
+ public void setSequenceRef(final java.lang.String sequenceRef)\r
+ {\r
+ this._sequenceRef = sequenceRef;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showAllColLabels'.\r
+ * \r
+ * @param showAllColLabels\r
+ * the value of field 'showAllColLabels'\r
+ */\r
+ public void setShowAllColLabels(final boolean showAllColLabels)\r
+ {\r
+ this._showAllColLabels = showAllColLabels;\r
+ this._has_showAllColLabels = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'thresholdLine'.\r
+ * \r
+ * @param thresholdLine\r
+ * the value of field 'thresholdLine'.\r
+ */\r
+ public void setThresholdLine(\r
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine)\r
+ {\r
+ this._thresholdLine = thresholdLine;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'visible'.\r
+ * \r
+ * @param visible\r
+ * the value of field 'visible'.\r
+ */\r
+ public void setVisible(final boolean visible)\r
+ {\r
+ this._visible = visible;\r
+ this._has_visible = 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.Annotation\r
+ */\r
+ public static jalview.schemabinding.version2.Annotation 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.Annotation) Unmarshaller\r
+ .unmarshal(jalview.schemabinding.version2.Annotation.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