-@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>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </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>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </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>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </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>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </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 }
- *