X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotation.java;h=475aef1812692cbf29624f741b84bff05db539b9;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=884f15905c4d2d82e940c95aedda5484787e991b;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;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 884f159..475aef1 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -1,780 +1,1238 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -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 _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(); - 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 deleteGraph( - ) { - this._has_graph= false; - } - - /** - */ - public void deleteGraphColour( - ) { - this._has_graphColour= false; - } - - /** - */ - public void deleteGraphGroup( - ) { - this._has_graphGroup= false; - } - - /** - */ - public void deleteGraphType( - ) { - this._has_graphType= false; - } - - /** - */ - public void deleteScore( - ) { - this._has_score= false; - } - - /** - */ - public void deleteScoreOnly( - ) { - this._has_scoreOnly= 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 '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 'graphType'.
- *
- * @return the value of field 'GraphType'.
- */
- public int getGraphType(
- ) {
- return this._graphType;
- }
-
- /**
- * 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 '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 '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 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 hasGraphType.
- *
- * @return true if at least one GraphType has been added
- */
- public boolean hasGraphType(
- ) {
- return this._has_graphType;
- }
-
- /**
- * 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 hasVisible.
- *
- * @return true if at least one Visible has been added
- */
- public boolean hasVisible(
- ) {
- return this._has_visible;
- }
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return the value of field 'Graph'.
- */
- public boolean isGraph(
- ) {
- return this._graph;
- }
-
- /**
- * Returns the value of field 'scoreOnly'.
- *
- * @return the value of field 'ScoreOnly'.
- */
- public boolean isScoreOnly(
- ) {
- return this._scoreOnly;
- }
-
- /**
- * 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 '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 '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 '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 '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 '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);
- }
-
-}
+/*
+ * 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
+ * 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); + } + +}