X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotation.java;h=ddf63fbdbd9fc88aee5aea78a475b1c2e9ceab27;hb=78f929d85e95b6445f7fab46504abc394d8c3fe9;hp=e6c8e5a3274a861ae6300d4889be2d057d5a9d51;hpb=a2a842580f86bd847b07cd2f75b26c74ec752fd7;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index e6c8e5a..ddf63fb 100755
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,484 +1,1082 @@
/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 '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 '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 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 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 '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 { - this._graphType = graphType; - this._has_graphType = true; - } //-- void setGraphType(int) - - /** - * Sets the value of field 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel(java.lang.String label) + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { - this._label = label; - } //-- void setLabel(java.lang.String) + return false; + } + return true; + } - /** - * 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) + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean isVisible() + { + return this._visible; + } - /** - * 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 + /** + * + * + * @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 static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + 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()) { - return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + throw new IndexOutOfBoundsException( + "setAnnotationElement: Index value '" + index + + "' not in range [0.." + + (this._annotationElementList.size() - 1) + "]"); + } - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException + 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++) { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() + 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 '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 '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); + } }