+@XmlType(
+ name = "JalviewModel",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+ "userColours", "tree", "pcaViewer", "featureSettings" })
+public class JalviewModel
+{
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+
+ @XmlElement(required = true)
+ protected String version;
+
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModel.JSeq> jSeq;
+
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModel.JGroup> jGroup;
+
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModel.Viewport> viewport;
+
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModel.UserColours> userColours;
+
+ protected List<JalviewModel.Tree> tree;
+
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
+
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModel.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate()
+ {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreationDate(XMLGregorianCalendar value)
+ {
+ this.creationDate = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the vamsasModel property.
+ *
+ * @return possible object is {@link VAMSAS }
+ *
+ */
+ public VAMSAS getVamsasModel()
+ {
+ return vamsasModel;
+ }
+
+ /**
+ * Sets the value of the vamsasModel property.
+ *
+ * @param value
+ * allowed object is {@link VAMSAS }
+ *
+ */
+ public void setVamsasModel(VAMSAS value)
+ {
+ this.vamsasModel = value;
+ }
+
+ /**
+ * Gets the value of the jSeq 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 jSeq property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getJSeq().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq> getJSeq()
+ {
+ if (jSeq == null)
+ {
+ jSeq = new ArrayList<JalviewModel.JSeq>();
+ }
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup 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 jGroup property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getJGroup().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
+ *
+ *
+ */
+ public List<JalviewModel.JGroup> getJGroup()
+ {
+ if (jGroup == null)
+ {
+ jGroup = new ArrayList<JalviewModel.JGroup>();
+ }
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport 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 viewport property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getViewport().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport> getViewport()
+ {
+ if (viewport == null)
+ {
+ viewport = new ArrayList<JalviewModel.Viewport>();
+ }
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours 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 userColours property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getUserColours().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
+ *
+ *
+ */
+ public List<JalviewModel.UserColours> getUserColours()
+ {
+ if (userColours == null)
+ {
+ userColours = new ArrayList<JalviewModel.UserColours>();
+ }
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree 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 tree property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getTree().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
+ *
+ *
+ */
+ public List<JalviewModel.Tree> getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList<JalviewModel.Tree>();
+ }
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the pcaViewer 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 pcaViewer property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getPcaViewer().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer> getPcaViewer()
+ {
+ if (pcaViewer == null)
+ {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+ }
+ return this.pcaViewer;
+ }
+
+ /**
+ * Gets the value of the featureSettings property.
+ *
+ * @return possible object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings getFeatureSettings()
+ {
+ return featureSettings;
+ }
+
+ /**
+ * Sets the value of the featureSettings property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModel.FeatureSettings value)
+ {
+ this.featureSettings = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="setting"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour"
+ * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "setting", "group" })
+ public static class FeatureSettings
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Setting> setting;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Group> group;
+
+ /**
+ * Gets the value of the setting 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 setting property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSetting().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Setting }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Setting> getSetting()
+ {
+ if (setting == null)
+ {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
+ }
+
+ /**
+ * Gets the value of the group 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 group property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getGroup().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Group }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Group> getGroup()
+ {
+ if (group == null)
+ {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
+ * default="Min" /&gt; &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+ public static class Setting
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ @XmlAttribute(name = "order")
+ protected Float order;
+
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+
+ @XmlAttribute(name = "max")
+ protected Float max;
+
+ @XmlAttribute(name = "min")
+ protected Float min;
+
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName 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 attributeName property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAttributeName().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return possible object is {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value)
+ {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getOrder()
+ {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setOrder(Float value)
+ {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMincolour()
+ {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value)
+ {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
+ }
+ else
+ {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getThreshstate()
+ {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value)
+ {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMax(Float value)
+ {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMin()
+ {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMin(Float value)
+ {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel()
+ {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value)
+ {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale()
+ {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value)
+ {
+ this.autoScale = value;
+ }
+
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="seq"
+ * type="{http://www.w3.org/2001/XMLSchema}string"
+ * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="start"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="displayText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="ignoreGapsinConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+ public static class JGroup
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "colour")
+ protected String colour;
+
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the seq 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 seq property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSeq().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getSeq()
+ {
+ if (seq == null)
+ {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
+ }
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.