+ protected Annotation.ThresholdLine thresholdLine;
+
+ protected List<MatrixType> contactmatrix;
+
+ protected List<Property> property;
+
+ @XmlAttribute(name = "graph", required = true)
+ protected boolean graph;
+
+ @XmlAttribute(name = "graphType")
+ protected Integer graphType;
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "groupRef")
+ protected String groupRef;
+
+ @XmlAttribute(name = "graphColour")
+ protected Integer graphColour;
+
+ @XmlAttribute(name = "graphGroup")
+ protected Integer graphGroup;
+
+ @XmlAttribute(name = "graphHeight")
+ protected Integer graphHeight;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "scoreOnly")
+ protected Boolean scoreOnly;
+
+ @XmlAttribute(name = "score")
+ protected Double score;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "centreColLabels")
+ protected Boolean centreColLabels;
+
+ @XmlAttribute(name = "scaleColLabels")
+ protected Boolean scaleColLabels;
+
+ @XmlAttribute(name = "showAllColLabels")
+ protected Boolean showAllColLabels;
+
+ @XmlAttribute(name = "autoCalculated")
+ protected Boolean autoCalculated;
+
+ @XmlAttribute(name = "belowAlignment")
+ protected Boolean belowAlignment;
+
+ @XmlAttribute(name = "calcId")
+ protected String calcId;
+
+ /**
+ * Gets the value of the annotationElement property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the annotationElement property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAnnotationElement().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AnnotationElement }
+ *
+ *
+ */
+ public List<AnnotationElement> getAnnotationElement()
+ {
+ if (annotationElement == null)
+ {
+ annotationElement = new ArrayList<AnnotationElement>();
+ }
+ return this.annotationElement;
+ }
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLabel(String value)
+ {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the thresholdLine property.
+ *
+ * @return possible object is {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine getThresholdLine()
+ {
+ return thresholdLine;
+ }
+
+ /**
+ * Sets the value of the thresholdLine property.
+ *
+ * @param value
+ * allowed object is {@link Annotation.ThresholdLine }
+ *
+ */
+ public void setThresholdLine(Annotation.ThresholdLine value)
+ {
+ this.thresholdLine = value;
+ }
+
+ /**
+ * Gets the value of the contactmatrix property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the contactmatrix property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getContactmatrix().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link MatrixType
+ * }
+ *
+ *
+ */
+ public List<MatrixType> getContactmatrix()
+ {
+ if (contactmatrix == null)
+ {
+ contactmatrix = new ArrayList<MatrixType>();
+ }
+ return this.contactmatrix;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Property }
+ *
+ *
+ */
+ public List<Property> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the graph property.
+ *
+ */
+ public boolean isGraph()
+ {
+ return graph;
+ }
+
+ /**
+ * Sets the value of the graph property.
+ *
+ */
+ public void setGraph(boolean value)
+ {
+ this.graph = value;
+ }
+
+ /**
+ * Gets the value of the graphType property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphType()
+ {
+ return graphType;
+ }
+
+ /**
+ * Sets the value of the graphType property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphType(Integer value)
+ {
+ this.graphType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceRef(String value)
+ {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the groupRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getGroupRef()
+ {
+ return groupRef;
+ }
+
+ /**
+ * Sets the value of the groupRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setGroupRef(String value)
+ {
+ this.groupRef = value;
+ }
+
+ /**
+ * Gets the value of the graphColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphColour()
+ {
+ return graphColour;
+ }
+
+ /**
+ * Sets the value of the graphColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphColour(Integer value)
+ {
+ this.graphColour = value;
+ }
+
+ /**
+ * Gets the value of the graphGroup property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphGroup()
+ {
+ return graphGroup;
+ }
+
+ /**
+ * Sets the value of the graphGroup property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphGroup(Integer value)
+ {
+ this.graphGroup = value;
+ }
+
+ /**
+ * Gets the value of the graphHeight property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphHeight()
+ {
+ return graphHeight;
+ }
+
+ /**
+ * Sets the value of the graphHeight property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphHeight(Integer value)
+ {
+ this.graphHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the scoreOnly property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isScoreOnly()
+ {
+ if (scoreOnly == null)
+ {
+ return false;
+ }
+ else
+ {
+ return scoreOnly;
+ }
+ }
+
+ /**
+ * Sets the value of the scoreOnly property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScoreOnly(Boolean value)
+ {
+ this.scoreOnly = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return possible object is {@link Double }
+ *
+ */
+ public Double getScore()
+ {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is {@link Double }
+ *
+ */
+ public void setScore(Double value)
+ {
+ this.score = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isVisible()
+ {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the centreColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCentreColLabels()
+ {
+ return centreColLabels;
+ }
+
+ /**
+ * Sets the value of the centreColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColLabels(Boolean value)
+ {
+ this.centreColLabels = value;
+ }
+
+ /**
+ * Gets the value of the scaleColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isScaleColLabels()
+ {
+ return scaleColLabels;
+ }
+
+ /**
+ * Sets the value of the scaleColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScaleColLabels(Boolean value)
+ {
+ this.scaleColLabels = value;
+ }
+
+ /**
+ * Gets the value of the showAllColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAllColLabels()
+ {
+ return showAllColLabels;
+ }
+
+ /**
+ * Sets the value of the showAllColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAllColLabels(Boolean value)
+ {
+ this.showAllColLabels = value;
+ }
+
+ /**
+ * Gets the value of the autoCalculated property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isAutoCalculated()
+ {
+ if (autoCalculated == null)
+ {
+ return false;
+ }
+ else
+ {
+ return autoCalculated;
+ }
+ }
+
+ /**
+ * Sets the value of the autoCalculated property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoCalculated(Boolean value)
+ {
+ this.autoCalculated = value;
+ }
+
+ /**
+ * Gets the value of the belowAlignment property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isBelowAlignment()
+ {
+ if (belowAlignment == null)
+ {
+ return true;
+ }
+ else
+ {
+ return belowAlignment;
+ }
+ }
+
+ /**
+ * Sets the value of the belowAlignment property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setBelowAlignment(Boolean value)
+ {
+ this.belowAlignment = value;
+ }
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCalcId(String value)
+ {
+ this.calcId = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class ThresholdLine
+ {
+
+ @XmlAttribute(name = "label")
+ protected String label;