X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotation.java;h=b9b13cbb034a9003d50967cfdd8c9e20dc4f28fe;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=61f9413a153e7c9ab093c96c69667a36386ef573;hpb=77dd1ea813b06b331614520a8b3d561435f27880;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java old mode 100755 new mode 100644 index 61f9413..b9b13cb --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -1,616 +1,1246 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * 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 _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; - - /** - * Field _id - */ - private java.lang.String _id; - - /** - * 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(); - _annotationElementList = new Vector(); - } //-- jalview.schemabinding.version2.Annotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotationElement - * - * - * - * @param vAnnotationElement - */ - public void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) - - /** - * Method addAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void addAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) - - /** - * Method deleteGraph - * - */ - public void deleteGraph() - { - this._has_graph= false; - } //-- void deleteGraph() - - /** - * Method deleteGraphColour - * - */ - public void deleteGraphColour() - { - this._has_graphColour= false; - } //-- void deleteGraphColour() - - /** - * Method deleteGraphGroup - * - */ - public void deleteGraphGroup() - { - this._has_graphGroup= false; - } //-- void deleteGraphGroup() - - /** - * Method deleteGraphType - * - */ - public void deleteGraphType() - { - this._has_graphType= false; - } //-- void deleteGraphType() - - /** - * Method enumerateAnnotationElement - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() - - /** - * Method getAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index); - } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) - - /** - * Method getAnnotationElement - * - * - * - * @return AnnotationElement - */ - public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() - { - int size = _annotationElementList.size(); - jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() - - /** - * Method getAnnotationElementCount - * - * - * - * @return int - */ - public int getAnnotationElementCount() - { - return _annotationElementList.size(); - } //-- int getAnnotationElementCount() - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'graph'. - * - * @return boolean - * @return the value of field 'graph'. - */ - public boolean getGraph() - { - return this._graph; - } //-- boolean getGraph() - - /** - * Returns the value of field 'graphColour'. - * - * @return int - * @return the value of field 'graphColour'. - */ - public int getGraphColour() - { - return this._graphColour; - } //-- int getGraphColour() - - /** - * Returns the value of field 'graphGroup'. - * - * @return int - * @return the value of field 'graphGroup'. - */ - public int getGraphGroup() - { - return this._graphGroup; - } //-- int getGraphGroup() - - /** - * Returns the value of field 'graphType'. - * - * @return int - * @return the value of field 'graphType'. - */ - public int getGraphType() - { - return this._graphType; - } //-- int getGraphType() - - /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'label'. - * - * @return String - * @return the value of field 'label'. - */ - public java.lang.String getLabel() - { - return this._label; - } //-- java.lang.String getLabel() - - /** - * Returns the value of field 'sequenceRef'. - * - * @return String - * @return the value of field 'sequenceRef'. - */ - public java.lang.String getSequenceRef() - { - return this._sequenceRef; - } //-- java.lang.String getSequenceRef() - - /** - * Returns the value of field 'thresholdLine'. - * - * @return ThresholdLine - * @return the value of field 'thresholdLine'. - */ - public jalview.schemabinding.version2.ThresholdLine getThresholdLine() - { - return this._thresholdLine; - } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() - - /** - * Method hasGraph - * - * - * - * @return boolean - */ - public boolean hasGraph() - { - return this._has_graph; - } //-- boolean hasGraph() - - /** - * Method hasGraphColour - * - * - * - * @return boolean - */ - public boolean hasGraphColour() - { - return this._has_graphColour; - } //-- boolean hasGraphColour() - - /** - * Method hasGraphGroup - * - * - * - * @return boolean - */ - public boolean hasGraphGroup() - { - return this._has_graphGroup; - } //-- boolean hasGraphGroup() - - /** - * Method hasGraphType - * - * - * - * @return boolean - */ - public boolean hasGraphType() - { - return this._has_graphType; - } //-- boolean hasGraphType() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllAnnotationElement - * - */ - public void removeAllAnnotationElement() - { - _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() - - /** - * Method removeAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index) - { - java.lang.Object obj = _annotationElementList.elementAt(index); - _annotationElementList.removeElementAt(index); - return (jalview.schemabinding.version2.AnnotationElement) obj; - } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) - - /** - * Method setAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException(); - } - _annotationElementList.setElementAt(vAnnotationElement, index); - } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) - - /** - * Method setAnnotationElement - * - * - * - * @param annotationElementArray - */ - public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray) - { - //-- copy array - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { - _annotationElementList.addElement(annotationElementArray[i]); - } - } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'graph'. - * - * @param graph the value of field 'graph'. - */ - public void setGraph(boolean graph) - { - this._graph = graph; - this._has_graph = true; - } //-- void setGraph(boolean) - - /** - * Sets the value of field 'graphColour'. - * - * @param graphColour the value of field 'graphColour'. - */ - public void setGraphColour(int graphColour) - { - this._graphColour = graphColour; - this._has_graphColour = true; - } //-- void setGraphColour(int) - - /** - * Sets the value of field 'graphGroup'. - * - * @param graphGroup the value of field 'graphGroup'. - */ - public void setGraphGroup(int graphGroup) - { - this._graphGroup = graphGroup; - this._has_graphGroup = true; - } //-- void setGraphGroup(int) - - /** - * Sets the value of field 'graphType'. - * - * @param graphType the value of field 'graphType'. - */ - public void setGraphType(int graphType) - { - this._graphType = graphType; - this._has_graphType = true; - } //-- void setGraphType(int) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel(java.lang.String label) - { - this._label = label; - } //-- void setLabel(java.lang.String) - - /** - * Sets the value of field 'sequenceRef'. - * - * @param sequenceRef the value of field 'sequenceRef'. - */ - public void setSequenceRef(java.lang.String sequenceRef) - { - this._sequenceRef = sequenceRef; - } //-- void setSequenceRef(java.lang.String) - - /** - * Sets the value of field 'thresholdLine'. - * - * @param thresholdLine the value of field 'thresholdLine'. - */ - public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine thresholdLine) - { - this._thresholdLine = thresholdLine; - } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(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); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/******************************************************************************* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + ******************************************************************************/ +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +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. + *

+ * 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 + * know 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); + } + +}