Java class for JalviewModel complex type. + *
+ * Java class for JalviewModel complex type. * - *
The following schema fragment specifies the expected content contained within this class. + *
+ * The following schema fragment specifies the expected content contained within + * this class. * *
* <complexType name="JalviewModel">
@@ -165,6 +166,20 @@ import javax.xml.datatype.XMLGregorianCalendar;
* </complexContent>
* </complexType>
* </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
* </sequence>
* <attGroup ref="{www.jalview.org}swingwindow"/>
* <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
@@ -196,6 +211,8 @@ import javax.xml.datatype.XMLGregorianCalendar;
* <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
* <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
* <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
* <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
* <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
@@ -244,6 +261,8 @@ import javax.xml.datatype.XMLGregorianCalendar;
* <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
* <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
* </restriction>
@@ -294,8 +313,8 @@ import javax.xml.datatype.XMLGregorianCalendar;
* </element>
* <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
* </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
* <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
* <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
@@ -363,1595 +382,2401 @@ import javax.xml.datatype.XMLGregorianCalendar;
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@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 jSeq;
- @XmlElement(name = "JGroup")
- protected List jGroup;
- @XmlElement(name = "Viewport")
- protected List viewport;
- @XmlElement(name = "UserColours")
- protected List userColours;
- protected List tree;
- @XmlElement(name = "PcaViewer")
- protected List 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;
+@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 jSeq;
+
+ @XmlElement(name = "JGroup")
+ protected List jGroup;
+
+ @XmlElement(name = "Viewport")
+ protected List viewport;
+
+ @XmlElement(name = "UserColours")
+ protected List userColours;
+
+ protected List tree;
+
+ @XmlElement(name = "PcaViewer")
+ protected List 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.
+ *
+ *
+ * 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 set method
+ * for the jSeq property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getJSeq().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
+ *
+ *
+ */
+ public List getJSeq()
+ {
+ if (jSeq == null)
+ {
+ jSeq = new ArrayList();
}
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup property.
+ *
+ *
+ * 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 set method
+ * for the jGroup property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getJGroup().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
+ *
+ *
+ */
+ public List getJGroup()
+ {
+ if (jGroup == null)
+ {
+ jGroup = new ArrayList();
}
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport property.
+ *
+ *
+ * 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 set method
+ * for the viewport property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getViewport().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
+ *
+ *
+ */
+ public List getViewport()
+ {
+ if (viewport == null)
+ {
+ viewport = new ArrayList();
}
-
- /**
- * Gets the value of the vamsasModel property.
- *
- * @return
- * possible object is
- * {@link VAMSAS }
- *
- */
- public VAMSAS getVamsasModel() {
- return vamsasModel;
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours property.
+ *
+ *
+ * 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 set method
+ * for the userColours property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getUserColours().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
+ *
+ *
+ */
+ public List getUserColours()
+ {
+ if (userColours == null)
+ {
+ userColours = new ArrayList();
}
-
- /**
- * Sets the value of the vamsasModel property.
- *
- * @param value
- * allowed object is
- * {@link VAMSAS }
- *
- */
- public void setVamsasModel(VAMSAS value) {
- this.vamsasModel = value;
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree property.
+ *
+ *
+ * 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 set method
+ * for the tree property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getTree().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
+ *
+ *
+ */
+ public List getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList();
}
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the pcaViewer property.
+ *
+ *
+ * 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 set method
+ * for the pcaViewer property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getPcaViewer().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ *
+ *
+ */
+ public List getPcaViewer()
+ {
+ if (pcaViewer == null)
+ {
+ pcaViewer = new ArrayList();
+ }
+ 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;
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "setting", "group" })
+ public static class FeatureSettings
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List setting;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List group;
/**
- * Gets the value of the jSeq property.
+ * Gets the value of the setting property.
*
*
- * 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 set method for the jSeq property.
+ * 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
+ * set method for the setting property.
*
*
* For example, to add a new item, do as follows:
+ *
*
- * getJSeq().add(newItem);
+ * getSetting().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
+ * {@link JalviewModel.FeatureSettings.Setting }
*
*
*/
- public List getJSeq() {
- if (jSeq == null) {
- jSeq = new ArrayList();
- }
- return this.jSeq;
+ public List getSetting()
+ {
+ if (setting == null)
+ {
+ setting = new ArrayList();
+ }
+ return this.setting;
}
/**
- * Gets the value of the jGroup property.
+ * Gets the value of the group property.
*
*
- * 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 set method for the jGroup property.
+ * 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
+ * set method for the group property.
*
*
* For example, to add a new item, do as follows:
+ *
*
- * getJGroup().add(newItem);
+ * getGroup().add(newItem);
*
*
*
*
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JGroup }
+ * {@link JalviewModel.FeatureSettings.Group }
*
*
*/
- public List getJGroup() {
- if (jGroup == null) {
- jGroup = new ArrayList();
- }
- return this.jGroup;
+ public List getGroup()
+ {
+ if (group == null)
+ {
+ group = new ArrayList();
+ }
+ return this.group;
}
/**
- * Gets the value of the viewport property.
- *
*
- * 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 set method for the viewport property.
+ * Java class for anonymous complex type.
*
*
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
*
- * getViewport().add(newItem);
+ * <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>
*
*
*
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport }
- *
- *
*/
- public List getViewport() {
- if (viewport == null) {
- viewport = new ArrayList();
- }
- return this.viewport;
+ @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;
+ }
+
}
/**
- * Gets the value of the userColours property.
- *
*
- * 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 set method for the userColours property.
+ * Java class for anonymous complex type.
*
*
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
*
- * getUserColours().add(newItem);
+ * <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>
*
*
*
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.UserColours }
- *
- *
*/
- public List getUserColours() {
- if (userColours == null) {
- userColours = new ArrayList();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+ public static class Setting
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List 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.
+ *
+ *
+ * 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
+ * set method for the attributeName property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getAttributeName().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list {@link String
+ * }
+ *
+ *
+ */
+ public List getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList();
+ }
+ 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;
}
- return this.userColours;
+ 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;
+ }
+
}
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+ public static class JGroup
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List 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 tree property.
+ * Gets the value of the seq property.
*
*
- * 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 set method for the tree property.
+ * 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
+ * set method for the seq property.
*
*
* For example, to add a new item, do as follows:
+ *
*
- * getTree().add(newItem);
+ * getSeq().add(newItem);
*
*
*
*
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Tree }
+ * Objects of the following type(s) are allowed in the list {@link String }
*
*
*/
- public List getTree() {
- if (tree == null) {
- tree = new ArrayList();
- }
- return this.tree;
+ public List getSeq()
+ {
+ if (seq == null)
+ {
+ seq = new ArrayList();
+ }
+ return this.seq;
}
/**
- * Gets the value of the pcaViewer property.
+ * Gets the value of the annotationColours property.
*
- *
- * 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 set method for the pcaViewer property.
+ * @return possible object is {@link AnnotationColourScheme }
*
- *
- * For example, to add a new item, do as follows:
- *
- * getPcaViewer().add(newItem);
- *
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
*
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
*
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer }
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the start property.
*
+ * @return possible object is {@link Integer }
*
*/
- public List getPcaViewer() {
- if (pcaViewer == null) {
- pcaViewer = new ArrayList();
- }
- return this.pcaViewer;
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
}
/**
- * Gets the value of the featureSettings property.
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link JalviewModel.FeatureSettings }
- *
*/
- public JalviewModel.FeatureSettings getFeatureSettings() {
- return featureSettings;
+ public Integer getEnd()
+ {
+ return end;
}
/**
- * Sets the value of the featureSettings property.
+ * Sets the value of the end property.
*
* @param value
- * allowed object is
- * {@link JalviewModel.FeatureSettings }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setFeatureSettings(JalviewModel.FeatureSettings value) {
- this.featureSettings = value;
+ public void setEnd(Integer value)
+ {
+ this.end = value;
}
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
/**
- * Java class for anonymous complex type.
+ * Sets the value of the name property.
*
- *
The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link String }
*
- *
- * <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>
- *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
*
+ * @return possible object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "setting",
- "group"
- })
- public static class FeatureSettings {
+ public String getColour()
+ {
+ return colour;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected List setting;
- @XmlElement(namespace = "www.jalview.org")
- protected List group;
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColour(String value)
+ {
+ this.colour = value;
+ }
- /**
- * Gets the value of the setting property.
- *
- *
- * 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 set method for the setting property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getSetting().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Setting }
- *
- *
- */
- public List getSetting() {
- if (setting == null) {
- setting = new ArrayList();
- }
- return this.setting;
- }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * Gets the value of the group property.
- *
- *
- * 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 set method for the group property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getGroup().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Group }
- *
- *
- */
- public List getGroup() {
- if (group == null) {
- group = new ArrayList();
- }
- return this.group;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <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>
- *
- *
- *
- */
- @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;
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
- }
+ /**
+ * Gets the value of the outlineColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getOutlineColour()
+ {
+ return outlineColour;
+ }
+ /**
+ * Sets the value of the outlineColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setOutlineColour(Integer value)
+ {
+ this.outlineColour = value;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <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>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "attributeName",
- "matcherSet"
- })
- public static class Setting {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List 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.
- *
- *
- * 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 set method for the attributeName property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getAttributeName().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList();
- }
- 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;
- }
+ /**
+ * Gets the value of the displayBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDisplayBoxes()
+ {
+ return displayBoxes;
+ }
- }
+ /**
+ * Sets the value of the displayBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDisplayBoxes(Boolean value)
+ {
+ this.displayBoxes = value;
+ }
+ /**
+ * Gets the value of the displayText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDisplayText()
+ {
+ return displayText;
}
+ /**
+ * Sets the value of the displayText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDisplayText(Boolean value)
+ {
+ this.displayText = value;
+ }
/**
- * Java class for anonymous complex type.
+ * Gets the value of the colourText property.
*
- *
The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link Boolean }
*
- *
- * <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>
- *
+ */
+ public Boolean isColourText()
+ {
+ return colourText;
+ }
+
+ /**
+ * Sets the value of the colourText property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "seq",
- "annotationColours"
- })
- public static class JGroup {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List 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;
+ public void setColourText(Boolean value)
+ {
+ this.colourText = value;
+ }
- /**
- * Gets the value of the seq property.
- *
- *
- * 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 set method for the seq property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getSeq().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List getSeq() {
- if (seq == null) {
- seq = new ArrayList();
- }
- return this.seq;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowUnconserved()
+ {
+ return showUnconserved;
+ }
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
- /**
- * 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 ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColour() {
- return colour;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColour(String value) {
- this.colour = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the consThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the outlineColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getOutlineColour() {
- return outlineColour;
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Sets the value of the outlineColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setOutlineColour(Integer value) {
- this.outlineColour = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Gets the value of the displayBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDisplayBoxes() {
- return displayBoxes;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Sets the value of the displayBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDisplayBoxes(Boolean value) {
- this.displayBoxes = value;
- }
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "features", "pdbids", "hiddenSequences", "rnaViewer" })
+ public static class JSeq
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List features;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List pdbids;
+
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List hiddenSequences;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List rnaViewer;
+
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
+
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
+
+ /**
+ * Gets the value of the features property.
+ *
+ *
+ * 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
+ * set method for the features property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getFeatures().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list {@link Feature }
+ *
+ *
+ */
+ public List getFeatures()
+ {
+ if (features == null)
+ {
+ features = new ArrayList();
+ }
+ return this.features;
+ }
+
+ /**
+ * Gets the value of the pdbids property.
+ *
+ *
+ * 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
+ * set method for the pdbids property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getPdbids().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids }
+ *
+ *
+ */
+ public List getPdbids()
+ {
+ if (pdbids == null)
+ {
+ pdbids = new ArrayList();
+ }
+ return this.pdbids;
+ }
+
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ *
+ * 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
+ * set method for the hiddenSequences property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getHiddenSequences().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List getHiddenSequences()
+ {
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new ArrayList();
+ }
+ return this.hiddenSequences;
+ }
+
+ /**
+ * Gets the value of the rnaViewer property.
+ *
+ *
+ * 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
+ * set method for the rnaViewer property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getRnaViewer().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List getRnaViewer()
+ {
+ if (rnaViewer == null)
+ {
+ rnaViewer = new ArrayList();
+ }
+ return this.rnaViewer;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value)
+ {
+ this.end = 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 hidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isHidden()
+ {
+ return hidden;
+ }
+
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value)
+ {
+ this.hidden = value;
+ }
+
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isViewreference()
+ {
+ return viewreference;
+ }
+
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value)
+ {
+ this.viewreference = value;
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "structureState" })
+ public static class Pdbids extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ *
+ * 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
+ * set method for the structureState property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getStructureState().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List getStructureState()
+ {
+ if (structureState == null)
+ {
+ structureState = new ArrayList();
+ }
+ return this.structureState;
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class StructureState
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
/**
- * Gets the value of the displayText property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayText() {
- return displayText;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the displayText property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setDisplayText(Boolean value) {
- this.displayText = value;
+ public void setValue(String value)
+ {
+ this.value = value;
}
/**
- * Gets the value of the colourText property.
+ * Gets the value of the visible property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isColourText() {
- return colourText;
+ public Boolean isVisible()
+ {
+ return visible;
}
/**
- * Sets the value of the colourText property.
+ * Sets the value of the visible property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setColourText(Boolean value) {
- this.colourText = value;
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
}
/**
- * Gets the value of the textCol1 property.
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol1() {
- return textCol1;
+ public String getViewId()
+ {
+ return viewId;
}
/**
- * Sets the value of the textCol1 property.
+ * Sets the value of the viewId property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
+ public void setViewId(String value)
+ {
+ this.viewId = value;
}
/**
- * Gets the value of the textCol2 property.
+ * Gets the value of the alignwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol2() {
- return textCol2;
+ public boolean isAlignwithAlignPanel()
+ {
+ if (alignwithAlignPanel == null)
+ {
+ return true;
+ }
+ else
+ {
+ return alignwithAlignPanel;
+ }
}
/**
- * Sets the value of the textCol2 property.
+ * Sets the value of the alignwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
+ public void setAlignwithAlignPanel(Boolean value)
+ {
+ this.alignwithAlignPanel = value;
}
/**
- * Gets the value of the textColThreshold property.
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextColThreshold() {
- return textColThreshold;
+ public boolean isColourwithAlignPanel()
+ {
+ if (colourwithAlignPanel == null)
+ {
+ return false;
+ }
+ else
+ {
+ return colourwithAlignPanel;
+ }
}
/**
- * Sets the value of the textColThreshold property.
+ * Sets the value of the colourwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
+ public void setColourwithAlignPanel(Boolean value)
+ {
+ this.colourwithAlignPanel = value;
}
/**
- * Gets the value of the showUnconserved property.
+ * Gets the value of the colourByJmol property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowUnconserved() {
- return showUnconserved;
+ public boolean isColourByJmol()
+ {
+ if (colourByJmol == null)
+ {
+ return true;
+ }
+ else
+ {
+ return colourByJmol;
+ }
}
/**
- * Sets the value of the showUnconserved property.
+ * Sets the value of the colourByJmol property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
+ public void setColourByJmol(Boolean value)
+ {
+ this.colourByJmol = value;
}
/**
- * Gets the value of the ignoreGapsinConsensus property.
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
+ public String getType()
+ {
+ return type;
}
/**
- * Sets the value of the ignoreGapsinConsensus property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the showConsensusHistogram property.
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
+ public Integer getWidth()
+ {
+ return width;
}
/**
- * Sets the value of the showConsensusHistogram property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
+ public void setWidth(Integer value)
+ {
+ this.width = value;
}
/**
- * Gets the value of the showSequenceLogo property.
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
+ public Integer getHeight()
+ {
+ return height;
}
/**
- * Sets the value of the showSequenceLogo property.
+ * Sets the value of the height property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
+ public void setHeight(Integer value)
+ {
+ this.height = value;
}
/**
- * Gets the value of the normaliseSequenceLogo property.
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
+ public Integer getXpos()
+ {
+ return xpos;
}
/**
- * Sets the value of the normaliseSequenceLogo property.
+ * Sets the value of the xpos property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
}
/**
- * Gets the value of the id property.
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public Integer getYpos()
+ {
+ return ypos;
}
/**
- * Sets the value of the id property.
+ * Sets the value of the ypos property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setId(String value) {
- this.id = value;
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
}
- }
+ }
+ }
/**
- * Java class for anonymous complex type.
+ *
+ * Java class for anonymous complex type.
*
- *
The following schema fragment specifies the expected content contained within this class.
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <element name="secondaryStructure" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
* <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
* </restriction>
* </complexContent>
* </complexType>
@@ -1960,1165 +2785,1072 @@ public class JalviewModel {
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "features",
- "pdbids",
- "hiddenSequences",
- "rnaViewer"
- })
- public static class JSeq {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List features;
- @XmlElement(namespace = "www.jalview.org")
- protected List pdbids;
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List hiddenSequences;
- @XmlElement(namespace = "www.jalview.org")
- protected List rnaViewer;
- @XmlAttribute(name = "colour")
- protected Integer colour;
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
+ @XmlType(name = "", propOrder = { "secondaryStructure" })
+ public static class RnaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List secondaryStructure;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ *
+ * 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
+ * set method for the secondaryStructure property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getSecondaryStructure().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List getSecondaryStructure()
+ {
+ if (secondaryStructure == null)
+ {
+ secondaryStructure = new ArrayList();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewId()
+ {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewId(String value)
+ {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getDividerLocation()
+ {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value)
+ {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getSelectedRna()
+ {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value)
+ {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure
+ {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
/**
- * Gets the value of the features property.
- *
- *
- * 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 set method for the features property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getFeatures().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link Feature }
+ * Gets the value of the title property.
*
+ * @return possible object is {@link String }
*
*/
- public List getFeatures() {
- if (features == null) {
- features = new ArrayList();
- }
- return this.features;
+ public String getTitle()
+ {
+ return title;
}
/**
- * Gets the value of the pdbids property.
- *
- *
- * 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 set method for the pdbids property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getPdbids().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids }
+ * Sets the value of the title property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List getPdbids() {
- if (pdbids == null) {
- pdbids = new ArrayList();
- }
- return this.pdbids;
+ public void setTitle(String value)
+ {
+ this.title = value;
}
/**
- * Gets the value of the hiddenSequences property.
- *
- *
- * 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 set method for the hiddenSequences property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getHiddenSequences().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
+ * Gets the value of the annotationId property.
*
+ * @return possible object is {@link String }
*
*/
- public List getHiddenSequences() {
- if (hiddenSequences == null) {
- hiddenSequences = new ArrayList();
- }
- return this.hiddenSequences;
+ public String getAnnotationId()
+ {
+ return annotationId;
}
/**
- * Gets the value of the rnaViewer property.
- *
- *
- * 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 set method for the rnaViewer property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getRnaViewer().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer }
+ * Sets the value of the annotationId property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List getRnaViewer() {
- if (rnaViewer == null) {
- rnaViewer = new ArrayList();
- }
- return this.rnaViewer;
+ public void setAnnotationId(String value)
+ {
+ this.annotationId = value;
}
/**
- * Gets the value of the colour property.
+ * Gets the value of the gapped property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getColour() {
- return colour;
+ public Boolean isGapped()
+ {
+ return gapped;
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the gapped property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
-
- /**
- * Gets the value of the start property.
+ * allowed object is {@link Boolean }
*
*/
- public int getStart() {
- return start;
+ public void setGapped(Boolean value)
+ {
+ this.gapped = value;
}
/**
- * Sets the value of the start property.
+ * Gets the value of the viewerState property.
*
- */
- public void setStart(int value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
+ * @return possible object is {@link String }
*
*/
- public int getEnd() {
- return end;
+ public String getViewerState()
+ {
+ return viewerState;
}
/**
- * Sets the value of the end property.
+ * Sets the value of the viewerState property.
*
- */
- public void setEnd(int value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the id property.
+ * @param value
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public void setViewerState(String value)
+ {
+ this.viewerState = value;
}
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ }
+
+ }
+
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
+ public static class PcaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List sequencePoint;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List axis;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected PcaDataType pcaData;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "scoreModelName")
+ protected String scoreModelName;
+
+ @XmlAttribute(name = "xDim")
+ protected Integer xDim;
+
+ @XmlAttribute(name = "yDim")
+ protected Integer yDim;
+
+ @XmlAttribute(name = "zDim")
+ protected Integer zDim;
+
+ @XmlAttribute(name = "bgColour")
+ protected Integer bgColour;
+
+ @XmlAttribute(name = "scaleFactor")
+ protected Float scaleFactor;
+
+ @XmlAttribute(name = "showLabels")
+ protected Boolean showLabels;
+
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
+
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
+
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the sequencePoint property.
+ *
+ *
+ * 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
+ * set method for the sequencePoint property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getSequencePoint().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ *
+ */
+ public List getSequencePoint()
+ {
+ if (sequencePoint == null)
+ {
+ sequencePoint = new ArrayList();
+ }
+ return this.sequencePoint;
+ }
+
+ /**
+ * Gets the value of the axis property.
+ *
+ *
+ * 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
+ * set method for the axis property.
+ *
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * getAxis().add(newItem);
+ *
+ *
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ *
+ *
+ */
+ public List getAxis()
+ {
+ if (axis == null)
+ {
+ axis = new ArrayList();
+ }
+ return this.axis;
+ }
+
+ /**
+ * Gets the value of the seqPointMin property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
+ {
+ return seqPointMin;
+ }
+
+ /**
+ * Sets the value of the seqPointMin property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
+ {
+ this.seqPointMin = value;
+ }
+
+ /**
+ * Gets the value of the seqPointMax property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
+ {
+ return seqPointMax;
+ }
+
+ /**
+ * Sets the value of the seqPointMax property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
+ {
+ this.seqPointMax = value;
+ }
+
+ /**
+ * Gets the value of the pcaData property.
+ *
+ * @return possible object is {@link PcaDataType }
+ *
+ */
+ public PcaDataType getPcaData()
+ {
+ return pcaData;
+ }
+
+ /**
+ * Sets the value of the pcaData property.
+ *
+ * @param value
+ * allowed object is {@link PcaDataType }
+ *
+ */
+ public void setPcaData(PcaDataType value)
+ {
+ this.pcaData = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the scoreModelName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScoreModelName()
+ {
+ return scoreModelName;
+ }
+
+ /**
+ * Sets the value of the scoreModelName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScoreModelName(String value)
+ {
+ this.scoreModelName = value;
+ }
+
+ /**
+ * Gets the value of the xDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXDim()
+ {
+ return xDim;
+ }
+
+ /**
+ * Sets the value of the xDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXDim(Integer value)
+ {
+ this.xDim = value;
+ }
+
+ /**
+ * Gets the value of the yDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYDim()
+ {
+ return yDim;
+ }
+
+ /**
+ * Sets the value of the yDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYDim(Integer value)
+ {
+ this.yDim = value;
+ }
+
+ /**
+ * Gets the value of the zDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getZDim()
+ {
+ return zDim;
+ }
+
+ /**
+ * Sets the value of the zDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setZDim(Integer value)
+ {
+ this.zDim = value;
+ }
+
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getBgColour()
+ {
+ return bgColour;
+ }
+
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value)
+ {
+ this.bgColour = value;
+ }
+
+ /**
+ * Gets the value of the scaleFactor property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getScaleFactor()
+ {
+ return scaleFactor;
+ }
+
+ /**
+ * Sets the value of the scaleFactor property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setScaleFactor(Float value)
+ {
+ this.scaleFactor = value;
+ }
+
+ /**
+ * Gets the value of the showLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowLabels()
+ {
+ return showLabels;
+ }
+
+ /**
+ * Sets the value of the showLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowLabels(Boolean value)
+ {
+ this.showLabels = value;
+ }
+
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews()
+ {
+ return linkToAllViews;
+ }
+
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
+
+ /**
+ * Gets the value of the includeGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGaps()
+ {
+ return includeGaps;
+ }
+
+ /**
+ * Sets the value of the includeGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIncludeGaps(Boolean value)
+ {
+ this.includeGaps = value;
+ }
+
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps()
+ {
+ return matchGaps;
+ }
- /**
- * Gets the value of the hidden property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isHidden() {
- return hidden;
- }
+ /**
+ * Sets the value of the matchGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMatchGaps(Boolean value)
+ {
+ this.matchGaps = value;
+ }
- /**
- * Sets the value of the hidden property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setHidden(Boolean value) {
- this.hidden = value;
- }
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns()
+ {
+ return includeGappedColumns;
+ }
- /**
- * Gets the value of the viewreference property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isViewreference() {
- return viewreference;
- }
+ /**
+ * Sets the value of the includeGappedColumns property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIncludeGappedColumns(Boolean value)
+ {
+ this.includeGappedColumns = value;
+ }
- /**
- * Sets the value of the viewreference property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setViewreference(Boolean value) {
- this.viewreference = value;
- }
+ /**
+ * Gets the value of the denominateByShortestLength property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDenominateByShortestLength()
+ {
+ return denominateByShortestLength;
+ }
+ /**
+ * Sets the value of the denominateByShortestLength property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDenominateByShortestLength(Boolean value)
+ {
+ this.denominateByShortestLength = value;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "structureState"
- })
- public static class Pdbids
- extends Pdbentry
- {
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected List structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- *
- * 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 set method for the structureState property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getStructureState().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List getStructureState() {
- if (structureState == null) {
- structureState = new ArrayList();
- }
- return this.structureState;
- }
-
-
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class StructureState {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = 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 viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the alignwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isAlignwithAlignPanel() {
- if (alignwithAlignPanel == null) {
- return true;
- } else {
- return alignwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the alignwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAlignwithAlignPanel(Boolean value) {
- this.alignwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourwithAlignPanel() {
- if (colourwithAlignPanel == null) {
- return false;
- } else {
- return colourwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the colourwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourwithAlignPanel(Boolean value) {
- this.colourwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourByJmol property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourByJmol() {
- if (colourByJmol == null) {
- return true;
- } else {
- return colourByJmol;
- }
- }
-
- /**
- * Sets the value of the colourByJmol property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByJmol(Boolean value) {
- this.colourByJmol = 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 width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "secondaryStructure"
- })
- public static class RnaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List secondaryStructure;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- *
- * 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 set method for the secondaryStructure property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getSecondaryStructure().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List getSecondaryStructure() {
- if (secondaryStructure == null) {
- secondaryStructure = new ArrayList();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the dividerLocation property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getDividerLocation() {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setDividerLocation(Integer value) {
- this.dividerLocation = value;
- }
-
- /**
- * Gets the value of the selectedRna property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getSelectedRna() {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setSelectedRna(Integer value) {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
-
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure {
-
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the annotationId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotationId() {
- return annotationId;
- }
-
- /**
- * Sets the value of the annotationId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAnnotationId(String value) {
- this.annotationId = value;
- }
-
- /**
- * Gets the value of the gapped property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGapped() {
- return gapped;
- }
-
- /**
- * Sets the value of the gapped property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGapped(Boolean value) {
- this.gapped = value;
- }
-
- /**
- * Gets the value of the viewerState property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewerState() {
- return viewerState;
- }
-
- /**
- * Sets the value of the viewerState property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewerState(String value) {
- this.viewerState = value;
- }
-
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
}
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
/**
- * Java class for anonymous complex type.
+ *
+ * Java class for anonymous complex type.
*
- *
The following schema fragment specifies the expected content contained within this class.
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
*
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequencePoint" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="axis" maxOccurs="3" minOccurs="3">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMin">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMax">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attGroup ref="{www.jalview.org}SimilarityParams"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attGroup ref="{www.jalview.org}position"/>
* </restriction>
* </complexContent>
* </complexType>
@@ -3127,3253 +3859,3130 @@ public class JalviewModel {
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "sequencePoint",
- "axis",
- "seqPointMin",
- "seqPointMax",
- "pcaData"
- })
- public static class PcaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List sequencePoint;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List axis;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected PcaDataType pcaData;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "scoreModelName")
- protected String scoreModelName;
- @XmlAttribute(name = "xDim")
- protected Integer xDim;
- @XmlAttribute(name = "yDim")
- protected Integer yDim;
- @XmlAttribute(name = "zDim")
- protected Integer zDim;
- @XmlAttribute(name = "bgColour")
- protected Integer bgColour;
- @XmlAttribute(name = "scaleFactor")
- protected Float scaleFactor;
- @XmlAttribute(name = "showLabels")
- protected Boolean showLabels;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
- @XmlAttribute(name = "includeGaps")
- protected Boolean includeGaps;
- @XmlAttribute(name = "matchGaps")
- protected Boolean matchGaps;
- @XmlAttribute(name = "includeGappedColumns")
- protected Boolean includeGappedColumns;
- @XmlAttribute(name = "denominateByShortestLength")
- protected Boolean denominateByShortestLength;
-
- /**
- * Gets the value of the sequencePoint property.
- *
- *
- * 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 set method for the sequencePoint property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getSequencePoint().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.SequencePoint }
- *
- *
- */
- public List getSequencePoint() {
- if (sequencePoint == null) {
- sequencePoint = new ArrayList();
- }
- return this.sequencePoint;
- }
-
- /**
- * Gets the value of the axis property.
- *
- *
- * 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 set method for the axis property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getAxis().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.Axis }
- *
- *
- */
- public List getAxis() {
- if (axis == null) {
- axis = new ArrayList();
- }
- return this.axis;
- }
-
- /**
- * Gets the value of the seqPointMin property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
- return seqPointMin;
- }
-
- /**
- * Sets the value of the seqPointMin property.
- *
- * @param value
- * allowed object is
- * {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
- this.seqPointMin = value;
- }
-
- /**
- * Gets the value of the seqPointMax property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
- return seqPointMax;
- }
-
- /**
- * Sets the value of the seqPointMax property.
- *
- * @param value
- * allowed object is
- * {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
- this.seqPointMax = value;
- }
+ @XmlType(name = "")
+ public static class Axis
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the pcaData property.
- *
- * @return
- * possible object is
- * {@link PcaDataType }
- *
- */
- public PcaDataType getPcaData() {
- return pcaData;
- }
-
- /**
- * Sets the value of the pcaData property.
- *
- * @param value
- * allowed object is
- * {@link PcaDataType }
- *
- */
- public void setPcaData(PcaDataType value) {
- this.pcaData = value;
- }
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ }
- /**
- * Gets the value of the scoreModelName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScoreModelName() {
- return scoreModelName;
- }
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMin
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the scoreModelName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScoreModelName(String value) {
- this.scoreModelName = value;
- }
+ }
- /**
- * Gets the value of the xDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXDim() {
- return xDim;
- }
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint
+ {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * 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 xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the xDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXDim(Integer value) {
- this.xDim = value;
- }
+ }
- /**
- * Gets the value of the yDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYDim() {
- return yDim;
- }
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "title", "newick" })
+ public static class Tree
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+
+ @XmlAttribute(name = "columnWise")
+ protected Boolean columnWise;
+
+ @XmlAttribute(name = "columnReference")
+ protected String columnReference;
+
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Sets the value of the yDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYDim(Integer value) {
- this.yDim = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Gets the value of the zDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getZDim() {
- return zDim;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Sets the value of the zDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setZDim(Integer value) {
- this.zDim = value;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNewick()
+ {
+ return newick;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getBgColour() {
- return bgColour;
- }
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNewick(String value)
+ {
+ this.newick = value;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setBgColour(Integer value) {
- this.bgColour = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the scaleFactor property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getScaleFactor() {
- return scaleFactor;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Sets the value of the scaleFactor property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setScaleFactor(Float value) {
- this.scaleFactor = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Gets the value of the showLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowLabels() {
- return showLabels;
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * Sets the value of the showLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowLabels(Boolean value) {
- this.showLabels = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isLinkToAllViews() {
- return linkToAllViews;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap()
+ {
+ return showBootstrap;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value)
+ {
+ this.showBootstrap = value;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances()
+ {
+ return showDistances;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value)
+ {
+ this.showDistances = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked()
+ {
+ return markUnlinked;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value)
+ {
+ this.markUnlinked = value;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow()
+ {
+ return fitToWindow;
+ }
- /**
- * Gets the value of the includeGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGaps() {
- return includeGaps;
- }
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value)
+ {
+ this.fitToWindow = value;
+ }
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
- }
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree()
+ {
+ return currentTree;
+ }
- /**
- * Gets the value of the matchGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMatchGaps() {
- return matchGaps;
- }
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value)
+ {
+ this.currentTree = value;
+ }
- /**
- * Sets the value of the matchGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
- }
+ /**
+ * Gets the value of the columnWise property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isColumnWise()
+ {
+ if (columnWise == null)
+ {
+ return false;
+ }
+ else
+ {
+ return columnWise;
+ }
+ }
- /**
- * Gets the value of the includeGappedColumns property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
- }
+ /**
+ * Sets the value of the columnWise property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColumnWise(Boolean value)
+ {
+ this.columnWise = value;
+ }
- /**
- * Sets the value of the includeGappedColumns property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
- }
+ /**
+ * Gets the value of the columnReference property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColumnReference()
+ {
+ return columnReference;
+ }
- /**
- * Gets the value of the denominateByShortestLength property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
- }
+ /**
+ * Sets the value of the columnReference property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColumnReference(String value)
+ {
+ this.columnReference = value;
+ }
- /**
- * Sets the value of the denominateByShortestLength property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = 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;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Axis {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews()
+ {
+ if (linkToAllViews == null)
+ {
+ return false;
+ }
+ else
+ {
+ return linkToAllViews;
+ }
+ }
- }
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMax {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMin {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequencePoint {
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * 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 xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- }
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "userColourScheme" })
+ public static class UserColours
+ {
+
+ @XmlElement(
+ name = "UserColourScheme",
+ namespace = "www.jalview.org",
+ required = true)
+ protected JalviewUserColours userColourScheme;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return possible object is {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme()
+ {
+ return userColourScheme;
}
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value)
+ {
+ this.userColourScheme = value;
+ }
/**
- * Java class for anonymous complex type.
+ * Gets the value of the id property.
*
- *
The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "newick"
- })
- public static class Tree {
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ }
+
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" 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="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <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="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" 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="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
+ public static class Viewport
+ {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List hiddenColumns;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List calcIdParam;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected JalviewModel.Viewport.Overview overview;
+
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
- /**
- * Gets the value of the newick property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNewick() {
- return newick;
- }
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
- /**
- * Sets the value of the newick property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNewick(String value) {
- this.newick = value;
- }
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBootstrap() {
- return showBootstrap;
- }
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
- /**
- * Sets the value of the showBootstrap property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
- }
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
- /**
- * Gets the value of the showDistances property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDistances() {
- return showDistances;
- }
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value) {
- this.showDistances = value;
- }
+ @XmlAttribute(name = "charWidth")
+ protected Integer charWidth;
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked() {
- return markUnlinked;
- }
+ @XmlAttribute(name = "charHeight")
+ protected Integer charHeight;
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value) {
- this.markUnlinked = value;
- }
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isFitToWindow() {
- return fitToWindow;
- }
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value) {
- this.fitToWindow = value;
- }
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
- /**
- * Gets the value of the currentTree property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCurrentTree() {
- return currentTree;
- }
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value) {
- this.currentTree = value;
- }
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isLinkToAllViews() {
- if (linkToAllViews == null) {
- return false;
- } else {
- return linkToAllViews;
- }
- }
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ @XmlAttribute(name = "width")
+ protected Integer width;
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ @XmlAttribute(name = "height")
+ protected Integer height;
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * 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.
+ *
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
+ }
/**
- * Java class for anonymous complex type.
+ * Gets the value of the hiddenColumns property.
+ *
+ *
+ * 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
+ * set method for the hiddenColumns property.
*
- *
The following schema fragment specifies the expected content contained within this class.
+ *
+ * For example, to add a new item, do as follows:
*
*
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getHiddenColumns().add(newItem);
*
*
*
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "userColourScheme"
- })
- public static class UserColours {
-
- @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
- protected JalviewUserColours userColourScheme;
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return
- * possible object is
- * {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme() {
- return userColourScheme;
- }
-
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is
- * {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value) {
- this.userColourScheme = 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;
- }
-
+ public List getHiddenColumns()
+ {
+ if (hiddenColumns == null)
+ {
+ hiddenColumns = new ArrayList();
+ }
+ return this.hiddenColumns;
}
-
/**
- * Java class for anonymous complex type.
+ * Gets the value of the calcIdParam property.
+ *
+ *
+ * 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
+ * set method for the calcIdParam property.
*
- *
The following schema fragment specifies the expected content contained within this class.
+ *
+ * For example, to add a new item, do as follows:
*
*
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" 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="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <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="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" 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="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getCalcIdParam().add(newItem);
*
*
*
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "annotationColours",
- "hiddenColumns",
- "calcIdParam"
- })
- public static class Viewport {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlElement(namespace = "www.jalview.org")
- protected List hiddenColumns;
- @XmlElement(namespace = "www.jalview.org")
- protected List calcIdParam;
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
- @XmlAttribute(name = "bgColour")
- protected String bgColour;
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "showFullId")
- protected Boolean showFullId;
- @XmlAttribute(name = "rightAlignIds")
- protected Boolean rightAlignIds;
- @XmlAttribute(name = "showText")
- protected Boolean showText;
- @XmlAttribute(name = "showColourText")
- protected Boolean showColourText;
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
- @XmlAttribute(name = "showBoxes")
- protected Boolean showBoxes;
- @XmlAttribute(name = "wrapAlignment")
- protected Boolean wrapAlignment;
- @XmlAttribute(name = "renderGaps")
- protected Boolean renderGaps;
- @XmlAttribute(name = "showSequenceFeatures")
- protected Boolean showSequenceFeatures;
- @XmlAttribute(name = "showNPfeatureTooltip")
- protected Boolean showNPfeatureTooltip;
- @XmlAttribute(name = "showDbRefTooltip")
- protected Boolean showDbRefTooltip;
- @XmlAttribute(name = "followHighlight")
- protected Boolean followHighlight;
- @XmlAttribute(name = "followSelection")
- protected Boolean followSelection;
- @XmlAttribute(name = "showAnnotation")
- protected Boolean showAnnotation;
- @XmlAttribute(name = "centreColumnLabels")
- protected Boolean centreColumnLabels;
- @XmlAttribute(name = "showGroupConservation")
- protected Boolean showGroupConservation;
- @XmlAttribute(name = "showGroupConsensus")
- protected Boolean showGroupConsensus;
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
- @XmlAttribute(name = "startRes")
- protected Integer startRes;
- @XmlAttribute(name = "startSeq")
- protected Integer startSeq;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "scaleProteinAsCdna")
- protected Boolean scaleProteinAsCdna;
- @XmlAttribute(name = "viewName")
- protected String viewName;
- @XmlAttribute(name = "sequenceSetId")
- protected String sequenceSetId;
- @XmlAttribute(name = "gatheredViews")
- protected Boolean gatheredViews;
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "complementId")
- protected String complementId;
- @XmlAttribute(name = "showComplementFeatures")
- protected Boolean showComplementFeatures;
- @XmlAttribute(name = "showComplementFeaturesOnTop")
- protected Boolean showComplementFeaturesOnTop;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ public List getCalcIdParam()
+ {
+ if (calcIdParam == null)
+ {
+ calcIdParam = new ArrayList();
+ }
+ return this.calcIdParam;
+ }
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ /**
+ * Gets the value of the overview property.
+ *
+ * @return possible object is {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview getOverview()
+ {
+ return overview;
+ }
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ /**
+ * Sets the value of the overview property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public void setOverview(JalviewModel.Viewport.Overview value)
+ {
+ this.overview = value;
+ }
- /**
- * Gets the value of the hiddenColumns property.
- *
- *
- * 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 set method for the hiddenColumns property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getHiddenColumns().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.HiddenColumns }
- *
- *
- */
- public List getHiddenColumns() {
- if (hiddenColumns == null) {
- hiddenColumns = new ArrayList();
- }
- return this.hiddenColumns;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected()
+ {
+ return conservationSelected;
+ }
- /**
- * Gets the value of the calcIdParam property.
- *
- *
- * 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 set method for the calcIdParam property.
- *
- *
- * For example, to add a new item, do as follows:
- *
- * getCalcIdParam().add(newItem);
- *
- *
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.CalcIdParam }
- *
- *
- */
- public List getCalcIdParam() {
- if (calcIdParam == null) {
- calcIdParam = new ArrayList();
- }
- return this.calcIdParam;
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value)
+ {
+ this.conservationSelected = value;
+ }
+
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected()
+ {
+ return pidSelected;
+ }
+
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value)
+ {
+ this.pidSelected = value;
+ }
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isConservationSelected() {
- return conservationSelected;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBgColour()
+ {
+ return bgColour;
+ }
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value) {
- this.conservationSelected = value;
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setBgColour(String value)
+ {
+ this.bgColour = value;
+ }
- /**
- * Gets the value of the pidSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPidSelected() {
- return pidSelected;
- }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value) {
- this.pidSelected = value;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBgColour() {
- return bgColour;
- }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setBgColour(String value) {
- this.bgColour = value;
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
- /**
- * Gets the value of the consThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId()
+ {
+ return showFullId;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value)
+ {
+ this.showFullId = value;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value)
+ {
+ this.rightAlignIds = value;
+ }
- /**
- * Gets the value of the showFullId property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowFullId() {
- return showFullId;
- }
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowText()
+ {
+ return showText;
+ }
- /**
- * Sets the value of the showFullId property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value) {
- this.showFullId = value;
- }
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value)
+ {
+ this.showText = value;
+ }
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRightAlignIds() {
- return rightAlignIds;
- }
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText()
+ {
+ return showColourText;
+ }
- /**
- * Sets the value of the rightAlignIds property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value) {
- this.rightAlignIds = value;
- }
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value)
+ {
+ this.showColourText = value;
+ }
- /**
- * Gets the value of the showText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowText() {
- return showText;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved()
+ {
+ if (showUnconserved == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showUnconserved;
+ }
+ }
- /**
- * Sets the value of the showText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowText(Boolean value) {
- this.showText = value;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
- /**
- * Gets the value of the showColourText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowColourText() {
- return showColourText;
- }
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes()
+ {
+ return showBoxes;
+ }
- /**
- * Sets the value of the showColourText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value) {
- this.showColourText = value;
- }
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value)
+ {
+ this.showBoxes = value;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowUnconserved() {
- if (showUnconserved == null) {
- return false;
- } else {
- return showUnconserved;
- }
- }
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment()
+ {
+ return wrapAlignment;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
- }
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value)
+ {
+ this.wrapAlignment = value;
+ }
- /**
- * Gets the value of the showBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBoxes() {
- return showBoxes;
- }
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps()
+ {
+ return renderGaps;
+ }
- /**
- * Sets the value of the showBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value) {
- this.showBoxes = value;
- }
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value)
+ {
+ this.renderGaps = value;
+ }
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isWrapAlignment() {
- return wrapAlignment;
- }
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value)
+ {
+ this.showSequenceFeatures = value;
+ }
- /**
- * Sets the value of the wrapAlignment property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value) {
- this.wrapAlignment = value;
- }
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip()
+ {
+ return showNPfeatureTooltip;
+ }
- /**
- * Gets the value of the renderGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRenderGaps() {
- return renderGaps;
- }
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value)
+ {
+ this.showNPfeatureTooltip = value;
+ }
- /**
- * Sets the value of the renderGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value) {
- this.renderGaps = value;
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip()
+ {
+ return showDbRefTooltip;
+ }
- /**
- * Gets the value of the showSequenceFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures() {
- return showSequenceFeatures;
- }
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value)
+ {
+ this.showDbRefTooltip = value;
+ }
- /**
- * Sets the value of the showSequenceFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value) {
- this.showSequenceFeatures = value;
- }
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight()
+ {
+ if (followHighlight == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followHighlight;
+ }
+ }
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip() {
- return showNPfeatureTooltip;
- }
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value)
+ {
+ this.followHighlight = value;
+ }
- /**
- * Sets the value of the showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value) {
- this.showNPfeatureTooltip = value;
- }
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection()
+ {
+ if (followSelection == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followSelection;
+ }
+ }
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip() {
- return showDbRefTooltip;
- }
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value)
+ {
+ this.followSelection = value;
+ }
- /**
- * Sets the value of the showDbRefTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value) {
- this.showDbRefTooltip = value;
- }
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
- /**
- * Gets the value of the followHighlight property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowHighlight() {
- if (followHighlight == null) {
- return true;
- } else {
- return followHighlight;
- }
- }
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value)
+ {
+ this.showAnnotation = value;
+ }
- /**
- * Sets the value of the followHighlight property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowHighlight(Boolean value) {
- this.followHighlight = value;
- }
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels()
+ {
+ if (centreColumnLabels == null)
+ {
+ return false;
+ }
+ else
+ {
+ return centreColumnLabels;
+ }
+ }
- /**
- * Gets the value of the followSelection property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowSelection() {
- if (followSelection == null) {
- return true;
- } else {
- return followSelection;
- }
- }
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value)
+ {
+ this.centreColumnLabels = value;
+ }
- /**
- * Sets the value of the followSelection property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowSelection(Boolean value) {
- this.followSelection = value;
- }
+ /**
+ * Gets the value of the showGroupConservation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation()
+ {
+ if (showGroupConservation == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConservation;
+ }
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowAnnotation() {
- return showAnnotation;
- }
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value)
+ {
+ this.showGroupConservation = value;
+ }
- /**
- * Sets the value of the showAnnotation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value) {
- this.showAnnotation = value;
- }
+ /**
+ * Gets the value of the showGroupConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus()
+ {
+ if (showGroupConsensus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConsensus;
+ }
+ }
- /**
- * Gets the value of the centreColumnLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isCentreColumnLabels() {
- if (centreColumnLabels == null) {
- return false;
- } else {
- return centreColumnLabels;
- }
- }
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value)
+ {
+ this.showGroupConsensus = value;
+ }
- /**
- * Sets the value of the centreColumnLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCentreColumnLabels(Boolean value) {
- this.centreColumnLabels = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the showGroupConservation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConservation() {
- if (showGroupConservation == null) {
- return false;
- } else {
- return showGroupConservation;
- }
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Sets the value of the showGroupConservation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowGroupConservation(Boolean value) {
- this.showGroupConservation = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the showGroupConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConsensus() {
- if (showGroupConsensus == null) {
- return false;
- } else {
- return showGroupConsensus;
- }
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
- /**
- * Sets the value of the showGroupConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowGroupConsensus(Boolean value) {
- this.showGroupConsensus = value;
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
- }
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartRes()
+ {
+ return startRes;
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value)
+ {
+ this.startRes = value;
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartSeq()
+ {
+ return startSeq;
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
- }
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value)
+ {
+ this.startSeq = value;
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * Gets the value of the charWidth property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getCharWidth()
+ {
+ return charWidth;
+ }
- /**
- * Gets the value of the startRes property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartRes() {
- return startRes;
- }
+ /**
+ * Sets the value of the charWidth property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setCharWidth(Integer value)
+ {
+ this.charWidth = value;
+ }
- /**
- * Sets the value of the startRes property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartRes(Integer value) {
- this.startRes = value;
- }
+ /**
+ * Gets the value of the charHeight property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getCharHeight()
+ {
+ return charHeight;
+ }
- /**
- * Gets the value of the startSeq property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartSeq() {
- return startSeq;
- }
+ /**
+ * Sets the value of the charHeight property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setCharHeight(Integer value)
+ {
+ this.charHeight = value;
+ }
- /**
- * Sets the value of the startSeq property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartSeq(Integer value) {
- this.startSeq = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna()
+ {
+ if (scaleProteinAsCdna == null)
+ {
+ return true;
+ }
+ else
+ {
+ return scaleProteinAsCdna;
+ }
+ }
- /**
- * Gets the value of the scaleProteinAsCdna property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna() {
- if (scaleProteinAsCdna == null) {
- return true;
- } else {
- return scaleProteinAsCdna;
- }
- }
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value)
+ {
+ this.scaleProteinAsCdna = value;
+ }
- /**
- * Sets the value of the scaleProteinAsCdna property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScaleProteinAsCdna(Boolean value) {
- this.scaleProteinAsCdna = value;
- }
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewName()
+ {
+ return viewName;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewName() {
- return viewName;
- }
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewName(String value)
+ {
+ this.viewName = value;
+ }
- /**
- * Sets the value of the viewName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewName(String value) {
- this.viewName = value;
- }
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceSetId()
+ {
+ return sequenceSetId;
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceSetId() {
- return sequenceSetId;
- }
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceSetId(String value)
+ {
+ this.sequenceSetId = value;
+ }
- /**
- * Sets the value of the sequenceSetId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceSetId(String value) {
- this.sequenceSetId = value;
- }
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews()
+ {
+ return gatheredViews;
+ }
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGatheredViews() {
- return gatheredViews;
- }
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value)
+ {
+ this.gatheredViews = value;
+ }
- /**
- * Sets the value of the gatheredViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value) {
- this.gatheredViews = value;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol1() {
- return textCol1;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol2() {
- return textCol2;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextColThreshold() {
- return textColThreshold;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * 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;
+ }
- /**
- * 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 complementId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComplementId()
+ {
+ return complementId;
+ }
- /**
- * Gets the value of the complementId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComplementId() {
- return complementId;
- }
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComplementId(String value)
+ {
+ this.complementId = value;
+ }
- /**
- * Sets the value of the complementId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setComplementId(String value) {
- this.complementId = value;
- }
+ /**
+ * Gets the value of the showComplementFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeatures()
+ {
+ if (showComplementFeatures == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showComplementFeatures;
+ }
+ }
- /**
- * Gets the value of the showComplementFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowComplementFeatures() {
- if (showComplementFeatures == null) {
- return false;
- } else {
- return showComplementFeatures;
- }
- }
+ /**
+ * Sets the value of the showComplementFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowComplementFeatures(Boolean value)
+ {
+ this.showComplementFeatures = value;
+ }
- /**
- * Sets the value of the showComplementFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowComplementFeatures(Boolean value) {
- this.showComplementFeatures = value;
- }
+ /**
+ * Gets the value of the showComplementFeaturesOnTop property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeaturesOnTop()
+ {
+ if (showComplementFeaturesOnTop == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showComplementFeaturesOnTop;
+ }
+ }
- /**
- * Gets the value of the showComplementFeaturesOnTop property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowComplementFeaturesOnTop() {
- if (showComplementFeaturesOnTop == null) {
- return false;
- } else {
- return showComplementFeaturesOnTop;
- }
- }
+ /**
+ * Sets the value of the showComplementFeaturesOnTop property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowComplementFeaturesOnTop(Boolean value)
+ {
+ this.showComplementFeaturesOnTop = value;
+ }
- /**
- * Sets the value of the showComplementFeaturesOnTop property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowComplementFeaturesOnTop(Boolean value) {
- this.showComplementFeaturesOnTop = value;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam extends WebServiceParameterSet
+ {
+
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate()
+ {
+ if (needsUpdate == null)
+ {
+ return false;
}
-
-
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam
- extends WebServiceParameterSet
+ else
{
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value)
+ {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate()
+ {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value)
+ {
+ this.autoUpdate = value;
+ }
- @XmlAttribute(name = "calcId", required = true)
- protected String calcId;
- @XmlAttribute(name = "needsUpdate")
- protected Boolean needsUpdate;
- @XmlAttribute(name = "autoUpdate", required = true)
- protected boolean autoUpdate;
-
- /**
- * 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;
- }
-
- /**
- * Gets the value of the needsUpdate property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNeedsUpdate() {
- if (needsUpdate == null) {
- return false;
- } else {
- return needsUpdate;
- }
- }
-
- /**
- * Sets the value of the needsUpdate property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNeedsUpdate(Boolean value) {
- this.needsUpdate = value;
- }
-
- /**
- * Gets the value of the autoUpdate property.
- *
- */
- public boolean isAutoUpdate() {
- return autoUpdate;
- }
-
- /**
- * Sets the value of the autoUpdate property.
- *
- */
- public void setAutoUpdate(boolean value) {
- this.autoUpdate = value;
- }
-
- }
+ }
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns
+ {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
- /**
- * Java class for anonymous complex type.
- *
- *
The following schema fragment specifies the expected content contained within this class.
- *
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns {
-
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
+ }
- }
+ /**
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview
+ {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden()
+ {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value)
+ {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getResidueColour()
+ {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value)
+ {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGapColour()
+ {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value)
+ {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHiddenColour()
+ {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value)
+ {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
}
+ }
+
}