-/*\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 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 Annotation.\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
- // - 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Annotation.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Annotation implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _graphType.
+ */
+ private int _graphType;
+
+ /**
+ * keeps track of state for field: _graphType
+ */
+ private boolean _has_graphType;
+
+ /**
+ * Field _sequenceRef.
+ */
+ private java.lang.String _sequenceRef;
+
+ /**
+ * Field _groupRef.
+ */
+ private java.lang.String _groupRef;
+
+ /**
+ * Field _graphColour.
+ */
+ private int _graphColour;
+
+ /**
+ * keeps track of state for field: _graphColour
+ */
+ private boolean _has_graphColour;
+
+ /**
+ * Field _graphGroup.
+ */
+ private int _graphGroup;
+
+ /**
+ * keeps track of state for field: _graphGroup
+ */
+ private boolean _has_graphGroup;
+
+ /**
+ * height in pixels for the graph if this is a graph-type annotation.
+ */
+ private int _graphHeight;
+
+ /**
+ * keeps track of state for field: _graphHeight
+ */
+ private boolean _has_graphHeight;
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _scoreOnly.
+ */
+ private boolean _scoreOnly = false;
+
+ /**
+ * keeps track of state for field: _scoreOnly
+ */
+ private boolean _has_scoreOnly;
+
+ /**
+ * Field _score.
+ */
+ private double _score;
+
+ /**
+ * keeps track of state for field: _score
+ */
+ private boolean _has_score;
+
+ /**
+ * Field _visible.
+ */
+ private boolean _visible;
+
+ /**
+ * keeps track of state for field: _visible
+ */
+ private boolean _has_visible;
+
+ /**
+ * Field _centreColLabels.
+ */
+ private boolean _centreColLabels;
+
+ /**
+ * keeps track of state for field: _centreColLabels
+ */
+ private boolean _has_centreColLabels;
+
+ /**
+ * Field _scaleColLabels.
+ */
+ private boolean _scaleColLabels;
+
+ /**
+ * keeps track of state for field: _scaleColLabels
+ */
+ private boolean _has_scaleColLabels;
+
+ /**
+ * Field _showAllColLabels.
+ */
+ private boolean _showAllColLabels;
+
+ /**
+ * keeps track of state for field: _showAllColLabels
+ */
+ private boolean _has_showAllColLabels;
+
+ /**
+ * is an autocalculated annotation row
+ */
+ private boolean _autoCalculated = false;
+
+ /**
+ * keeps track of state for field: _autoCalculated
+ */
+ private boolean _has_autoCalculated;
+
+ /**
+ * is to be shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ */
+ private boolean _belowAlignment = true;
+
+ /**
+ * keeps track of state for field: _belowAlignment
+ */
+ private boolean _has_belowAlignment;
+
+ /**
+ * Optional string identifier used to group sets of annotation produced by a
+ * particular calculation. Values are opaque strings but have semantic meaning
+ * to Jalview's renderer, data importer and calculation system.
+ */
+ private java.lang.String _calcId;
+
+ /**
+ * Field _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _thresholdLine.
+ */
+ private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Annotation()
+ {
+ super();
+ this._annotationElementList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.addElement(vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final int index,
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteAutoCalculated()
+ {
+ this._has_autoCalculated = false;
+ }
+
+ /**
+ */
+ public void deleteBelowAlignment()
+ {
+ this._has_belowAlignment = false;
+ }
+
+ /**
+ */
+ public void deleteCentreColLabels()
+ {
+ this._has_centreColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteGraph()
+ {
+ this._has_graph = false;
+ }
+
+ /**
+ */
+ public void deleteGraphColour()
+ {
+ this._has_graphColour = false;
+ }
+
+ /**
+ */
+ public void deleteGraphGroup()
+ {
+ this._has_graphGroup = false;
+ }
+
+ /**
+ */
+ public void deleteGraphHeight()
+ {
+ this._has_graphHeight = false;
+ }
+
+ /**
+ */
+ public void deleteGraphType()
+ {
+ this._has_graphType = false;
+ }
+
+ /**
+ */
+ public void deleteScaleColLabels()
+ {
+ this._has_scaleColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteScore()
+ {
+ this._has_score = false;
+ }
+
+ /**
+ */
+ public void deleteScoreOnly()
+ {
+ this._has_scoreOnly = false;
+ }
+
+ /**
+ */
+ public void deleteShowAllColLabels()
+ {
+ this._has_showAllColLabels = false;
+ }
+
+ /**
+ */
+ public void deleteVisible()
+ {
+ this._has_visible = false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.AnnotationElement
+ * at the given index
+ */
+ public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList
+ .get(index);
+ }
+
+ /**
+ * Method getAnnotationElement.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
+ {
+ jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0];
+ return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAnnotationElementCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationElementCount()
+ {
+ return this._annotationElementList.size();
+ }
+
+ /**
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @return the value of field 'AutoCalculated'.
+ */
+ public boolean getAutoCalculated()
+ {
+ return this._autoCalculated;
+ }
+
+ /**
+ * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean getBelowAlignment()
+ {
+ return this._belowAlignment;
+ }
+
+ /**
+ * Returns the value of field 'calcId'. The field 'calcId' has the following
+ * description: Optional string identifier used to group sets of annotation
+ * produced by a particular calculation. Values are opaque strings but have
+ * semantic meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @return the value of field 'CalcId'.
+ */
+ public java.lang.String getCalcId()
+ {
+ return this._calcId;
+ }
+
+ /**
+ * Returns the value of field 'centreColLabels'.
+ *
+ * @return the value of field 'CentreColLabels'.
+ */
+ public boolean getCentreColLabels()
+ {
+ return this._centreColLabels;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'graphColour'.
+ *
+ * @return the value of field 'GraphColour'.
+ */
+ public int getGraphColour()
+ {
+ return this._graphColour;
+ }
+
+ /**
+ * Returns the value of field 'graphGroup'.
+ *
+ * @return the value of field 'GraphGroup'.
+ */
+ public int getGraphGroup()
+ {
+ return this._graphGroup;
+ }
+
+ /**
+ * Returns the value of field 'graphHeight'. The field 'graphHeight' has the
+ * following description: height in pixels for the graph if this is a
+ * graph-type annotation.
+ *
+ * @return the value of field 'GraphHeight'.
+ */
+ public int getGraphHeight()
+ {
+ return this._graphHeight;
+ }
+
+ /**
+ * Returns the value of field 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType()
+ {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'groupRef'.
+ *
+ * @return the value of field 'GroupRef'.
+ */
+ public java.lang.String getGroupRef()
+ {
+ return this._groupRef;
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel()
+ {
+ return this._label;
+ }
+
+ /**
+ * Returns the value of field 'scaleColLabels'.
+ *
+ * @return the value of field 'ScaleColLabels'.
+ */
+ public boolean getScaleColLabels()
+ {
+ return this._scaleColLabels;
+ }
+
+ /**
+ * Returns the value of field 'score'.
+ *
+ * @return the value of field 'Score'.
+ */
+ public double getScore()
+ {
+ return this._score;
+ }
+
+ /**
+ * Returns the value of field 'scoreOnly'.
+ *
+ * @return the value of field 'ScoreOnly'.
+ */
+ public boolean getScoreOnly()
+ {
+ return this._scoreOnly;
+ }
+
+ /**
+ * Returns the value of field 'sequenceRef'.
+ *
+ * @return the value of field 'SequenceRef'.
+ */
+ public java.lang.String getSequenceRef()
+ {
+ return this._sequenceRef;
+ }
+
+ /**
+ * Returns the value of field 'showAllColLabels'.
+ *
+ * @return the value of field 'ShowAllColLabels'.
+ */
+ public boolean getShowAllColLabels()
+ {
+ return this._showAllColLabels;
+ }
+
+ /**
+ * Returns the value of field 'thresholdLine'.
+ *
+ * @return the value of field 'ThresholdLine'.
+ */
+ public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+ {
+ return this._thresholdLine;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean getVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ * Method hasAutoCalculated.
+ *
+ * @return true if at least one AutoCalculated has been added
+ */
+ public boolean hasAutoCalculated()
+ {
+ return this._has_autoCalculated;
+ }
+
+ /**
+ * Method hasBelowAlignment.
+ *
+ * @return true if at least one BelowAlignment has been added
+ */
+ public boolean hasBelowAlignment()
+ {
+ return this._has_belowAlignment;
+ }
+
+ /**
+ * Method hasCentreColLabels.
+ *
+ * @return true if at least one CentreColLabels has been added
+ */
+ public boolean hasCentreColLabels()
+ {
+ return this._has_centreColLabels;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph()
+ {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphColour.
+ *
+ * @return true if at least one GraphColour has been added
+ */
+ public boolean hasGraphColour()
+ {
+ return this._has_graphColour;
+ }
+
+ /**
+ * Method hasGraphGroup.
+ *
+ * @return true if at least one GraphGroup has been added
+ */
+ public boolean hasGraphGroup()
+ {
+ return this._has_graphGroup;
+ }
+
+ /**
+ * Method hasGraphHeight.
+ *
+ * @return true if at least one GraphHeight has been added
+ */
+ public boolean hasGraphHeight()
+ {
+ return this._has_graphHeight;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType()
+ {
+ return this._has_graphType;
+ }
+
+ /**
+ * Method hasScaleColLabels.
+ *
+ * @return true if at least one ScaleColLabels has been added
+ */
+ public boolean hasScaleColLabels()
+ {
+ return this._has_scaleColLabels;
+ }
+
+ /**
+ * Method hasScore.
+ *
+ * @return true if at least one Score has been added
+ */
+ public boolean hasScore()
+ {
+ return this._has_score;
+ }
+
+ /**
+ * Method hasScoreOnly.
+ *
+ * @return true if at least one ScoreOnly has been added
+ */
+ public boolean hasScoreOnly()
+ {
+ return this._has_scoreOnly;
+ }
+
+ /**
+ * Method hasShowAllColLabels.
+ *
+ * @return true if at least one ShowAllColLabels has been added
+ */
+ public boolean hasShowAllColLabels()
+ {
+ return this._has_showAllColLabels;
+ }
+
+ /**
+ * Method hasVisible.
+ *
+ * @return true if at least one Visible has been added
+ */
+ public boolean hasVisible()
+ {
+ return this._has_visible;
+ }
+
+ /**
+ * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @return the value of field 'AutoCalculated'.
+ */
+ public boolean isAutoCalculated()
+ {
+ return this._autoCalculated;
+ }
+
+ /**
+ * Returns the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean isBelowAlignment()
+ {
+ return this._belowAlignment;
+ }
+
+ /**
+ * Returns the value of field 'centreColLabels'.
+ *
+ * @return the value of field 'CentreColLabels'.
+ */
+ public boolean isCentreColLabels()
+ {
+ return this._centreColLabels;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph()
+ {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'scaleColLabels'.
+ *
+ * @return the value of field 'ScaleColLabels'.
+ */
+ public boolean isScaleColLabels()
+ {
+ return this._scaleColLabels;
+ }
+
+ /**
+ * Returns the value of field 'scoreOnly'.
+ *
+ * @return the value of field 'ScoreOnly'.
+ */
+ public boolean isScoreOnly()
+ {
+ return this._scoreOnly;
+ }
+
+ /**
+ * Returns the value of field 'showAllColLabels'.
+ *
+ * @return the value of field 'ShowAllColLabels'.
+ */
+ public boolean isShowAllColLabels()
+ {
+ return this._showAllColLabels;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean isVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ */
+ public void removeAllAnnotationElement()
+ {
+ this._annotationElementList.clear();
+ }
+
+ /**
+ * Method removeAnnotationElement.
+ *
+ * @param vAnnotationElement
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(
+ final int index)
+ {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.schemabinding.version2.AnnotationElement) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAnnotationElement(
+ final int index,
+ final jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setAnnotationElement: Index value '" + index
+ + "' not in range [0.."
+ + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ this._annotationElementList.set(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationElementArray
+ */
+ public void setAnnotationElement(
+ final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray)
+ {
+ // -- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++)
+ {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has
+ * the following description: is an autocalculated annotation row
+ *
+ * @param autoCalculated
+ * the value of field 'autoCalculated'.
+ */
+ public void setAutoCalculated(final boolean autoCalculated)
+ {
+ this._autoCalculated = autoCalculated;
+ this._has_autoCalculated = true;
+ }
+
+ /**
+ * Sets the value of field 'belowAlignment'. The field 'belowAlignment' has
+ * the following description: is to be shown below the alignment - introduced
+ * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ *
+ * @param belowAlignment
+ * the value of field 'belowAlignment'.
+ */
+ public void setBelowAlignment(final boolean belowAlignment)
+ {
+ this._belowAlignment = belowAlignment;
+ this._has_belowAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'calcId'. The field 'calcId' has the following
+ * description: Optional string identifier used to group sets of annotation
+ * produced by a particular calculation. Values are opaque strings but have
+ * semantic meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @param calcId
+ * the value of field 'calcId'.
+ */
+ public void setCalcId(final java.lang.String calcId)
+ {
+ this._calcId = calcId;
+ }
+
+ /**
+ * Sets the value of field 'centreColLabels'.
+ *
+ * @param centreColLabels
+ * the value of field 'centreColLabels'.
+ */
+ public void setCentreColLabels(final boolean centreColLabels)
+ {
+ this._centreColLabels = centreColLabels;
+ this._has_centreColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description)
+ {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph
+ * the value of field 'graph'.
+ */
+ public void setGraph(final boolean graph)
+ {
+ this._graph = graph;
+ this._has_graph = true;
+ }
+
+ /**
+ * Sets the value of field 'graphColour'.
+ *
+ * @param graphColour
+ * the value of field 'graphColour'.
+ */
+ public void setGraphColour(final int graphColour)
+ {
+ this._graphColour = graphColour;
+ this._has_graphColour = true;
+ }
+
+ /**
+ * Sets the value of field 'graphGroup'.
+ *
+ * @param graphGroup
+ * the value of field 'graphGroup'.
+ */
+ public void setGraphGroup(final int graphGroup)
+ {
+ this._graphGroup = graphGroup;
+ this._has_graphGroup = true;
+ }
+
+ /**
+ * Sets the value of field 'graphHeight'. The field 'graphHeight' has the
+ * following description: height in pixels for the graph if this is a
+ * graph-type annotation.
+ *
+ * @param graphHeight
+ * the value of field 'graphHeight'.
+ */
+ public void setGraphHeight(final int graphHeight)
+ {
+ this._graphHeight = graphHeight;
+ this._has_graphHeight = true;
+ }
+
+ /**
+ * Sets the value of field 'graphType'.
+ *
+ * @param graphType
+ * the value of field 'graphType'.
+ */
+ public void setGraphType(final int graphType)
+ {
+ this._graphType = graphType;
+ this._has_graphType = true;
+ }
+
+ /**
+ * Sets the value of field 'groupRef'.
+ *
+ * @param groupRef
+ * the value of field 'groupRef'.
+ */
+ public void setGroupRef(final java.lang.String groupRef)
+ {
+ this._groupRef = groupRef;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label
+ * the value of field 'label'.
+ */
+ public void setLabel(final java.lang.String label)
+ {
+ this._label = label;
+ }
+
+ /**
+ * Sets the value of field 'scaleColLabels'.
+ *
+ * @param scaleColLabels
+ * the value of field 'scaleColLabels'.
+ */
+ public void setScaleColLabels(final boolean scaleColLabels)
+ {
+ this._scaleColLabels = scaleColLabels;
+ this._has_scaleColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'score'.
+ *
+ * @param score
+ * the value of field 'score'.
+ */
+ public void setScore(final double score)
+ {
+ this._score = score;
+ this._has_score = true;
+ }
+
+ /**
+ * Sets the value of field 'scoreOnly'.
+ *
+ * @param scoreOnly
+ * the value of field 'scoreOnly'.
+ */
+ public void setScoreOnly(final boolean scoreOnly)
+ {
+ this._scoreOnly = scoreOnly;
+ this._has_scoreOnly = true;
+ }
+
+ /**
+ * Sets the value of field 'sequenceRef'.
+ *
+ * @param sequenceRef
+ * the value of field 'sequenceRef'.
+ */
+ public void setSequenceRef(final java.lang.String sequenceRef)
+ {
+ this._sequenceRef = sequenceRef;
+ }
+
+ /**
+ * Sets the value of field 'showAllColLabels'.
+ *
+ * @param showAllColLabels
+ * the value of field 'showAllColLabels'
+ */
+ public void setShowAllColLabels(final boolean showAllColLabels)
+ {
+ this._showAllColLabels = showAllColLabels;
+ this._has_showAllColLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'thresholdLine'.
+ *
+ * @param thresholdLine
+ * the value of field 'thresholdLine'.
+ */
+ public void setThresholdLine(
+ final jalview.schemabinding.version2.ThresholdLine thresholdLine)
+ {
+ this._thresholdLine = thresholdLine;
+ }
+
+ /**
+ * Sets the value of field 'visible'.
+ *
+ * @param visible
+ * the value of field 'visible'.
+ */
+ public void setVisible(final boolean visible)
+ {
+ this._visible = visible;
+ this._has_visible = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Annotation
+ */
+ public static jalview.schemabinding.version2.Annotation unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Annotation) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Annotation.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