X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotation.java;h=2af8828ae0c504562b48a21fdb72fc69ba84f7b7;hb=682b4b598105a0024231bcf5f53206530425fd64;hp=0084c75f6c49abf18e5f2f50a16813d9191ee2a0;hpb=84c20bdc7d5c6bd3aea2c8dae5263ebd9c5e5458;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 0084c75..2af8828
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,775 +1,1237 @@
-/*
- * 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 _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 _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 deleteScore
- *
- */
- public void deleteScore()
- {
- this._has_score= false;
- } //-- void deleteScore()
-
- /**
- * Method deleteScoreOnly
- *
- */
- public void deleteScoreOnly()
- {
- this._has_scoreOnly= false;
- } //-- void deleteScoreOnly()
-
- /**
- * Method deleteVisible
- *
- */
- public void deleteVisible()
- {
- this._has_visible= false;
- } //-- void deleteVisible()
-
- /**
- * 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 'score'.
- *
- * @return double
- * @return the value of field 'score'.
- */
- public double getScore()
- {
- return this._score;
- } //-- double getScore()
-
- /**
- * Returns the value of field 'scoreOnly'.
- *
- * @return boolean
- * @return the value of field 'scoreOnly'.
- */
- public boolean getScoreOnly()
- {
- return this._scoreOnly;
- } //-- boolean getScoreOnly()
-
- /**
- * 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()
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return boolean
- * @return the value of field 'visible'.
- */
- public boolean getVisible()
- {
- return this._visible;
- } //-- boolean getVisible()
-
- /**
- * 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 hasScore
- *
- *
- *
- * @return boolean
- */
- public boolean hasScore()
- {
- return this._has_score;
- } //-- boolean hasScore()
-
- /**
- * Method hasScoreOnly
- *
- *
- *
- * @return boolean
- */
- public boolean hasScoreOnly()
- {
- return this._has_scoreOnly;
- } //-- boolean hasScoreOnly()
-
- /**
- * Method hasVisible
- *
- *
- *
- * @return boolean
- */
- public boolean hasVisible()
- {
- return this._has_visible;
- } //-- boolean hasVisible()
-
- /**
- * 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 'score'.
- *
- * @param score the value of field 'score'.
- */
- public void setScore(double score)
- {
- this._score = score;
- this._has_score = true;
- } //-- void setScore(double)
-
- /**
- * Sets the value of field 'scoreOnly'.
- *
- * @param scoreOnly the value of field 'scoreOnly'.
- */
- public void setScoreOnly(boolean scoreOnly)
- {
- this._scoreOnly = scoreOnly;
- this._has_scoreOnly = true;
- } //-- void setScoreOnly(boolean)
-
- /**
- * 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)
-
- /**
- * Sets the value of field 'visible'.
- *
- * @param visible the value of field 'visible'.
- */
- public void setVisible(boolean visible)
- {
- this._visible = visible;
- this._has_visible = true;
- } //-- void setVisible(boolean)
-
- /**
- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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
+ * 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); + } + +}