- * 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; - } - - /** - * Method getProperty. - * - * @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.Property at the - * given index - */ - public jalview.schemabinding.version2.Property getProperty(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException("getProperty: Index value '" - + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Property) _propertyList - .get(index); - } - - /** - * Method getProperty.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.Property[] getProperty() - { - jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; - return (jalview.schemabinding.version2.Property[]) this._propertyList - .toArray(array); - } - - /** - * Method getPropertyCount. - * - * @return the size of this collection - */ - public int getPropertyCount() - { - return this._propertyList.size(); - } - - /** - * 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(); - } - - /** - */ - public void removeAllProperty() - { - this._propertyList.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; - } - - /** - * Method removeProperty. - * - * @param vProperty - * @return true if the object was removed from the collection. - */ - public boolean removeProperty( - final jalview.schemabinding.version2.Property vProperty) - { - boolean removed = _propertyList.remove(vProperty); - return removed; - } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Property removePropertyAt( - final int index) - { - java.lang.Object obj = this._propertyList.remove(index); - return (jalview.schemabinding.version2.Property) 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; - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setProperty(final int index, - final jalview.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException("setProperty: Index value '" - + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - this._propertyList.set(index, vProperty); - } - - /** - * - * - * @param vPropertyArray - */ - public void setProperty( - final jalview.schemabinding.version2.Property[] vPropertyArray) - { - // -- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) - { - this._propertyList.add(vPropertyArray[i]); - } - } - - /** - * 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); - } - -}