X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModelType.java;fp=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModelType.java;h=0541d7a4624d35f10f5168635d619fe837f3e32a;hb=afbff636fa2dfa01daa1f4ec4e8a936e61e3cf16;hp=f084bc3f05021c6c5567ca476a553b63130affbd;hpb=c6df3928336440918d23b4e7cb579f134e2f48dd;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java index f084bc3..0541d7a 100644 --- a/src/jalview/xml/binding/jalview/JalviewModelType.java +++ b/src/jalview/xml/binding/jalview/JalviewModelType.java @@ -5,7 +5,6 @@ // Generated on: 2018.09.18 at 01:33:02 PM BST // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -22,11 +21,13 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; import javax.xml.datatype.XMLGregorianCalendar; - /** - *
Java class for JalviewModelType complex type. + *
+ * Java class for JalviewModelType 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="JalviewModelType"> @@ -301,1564 +302,1947 @@ import javax.xml.datatype.XMLGregorianCalendar; * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "JalviewModelType", namespace = "www.jalview.org", propOrder = { - "creationDate", - "version", - "vamsasModel", - "jSeq", - "jGroup", - "viewport", - "userColours", - "tree", - "featureSettings" -}) -public class JalviewModelType { - - @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 ListjSeq; - @XmlElement(name = "JGroup") - protected List jGroup; - @XmlElement(name = "Viewport") - protected List viewport; - @XmlElement(name = "UserColours") - protected List userColours; - protected List tree; - @XmlElement(name = "FeatureSettings") - protected JalviewModelType.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 = "JalviewModelType", + namespace = "www.jalview.org", + propOrder = + { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport", + "userColours", "tree", "featureSettings" }) +public class JalviewModelType +{ + + @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 = "FeatureSettings") + protected JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.Tree } + * + * + */ + public List
getTree() + { + if (tree == null) + { + tree = new ArrayList (); } + return this.tree; + } + + /** + * Gets the value of the featureSettings property. + * + * @return possible object is {@link JalviewModelType.FeatureSettings } + * + */ + public JalviewModelType.FeatureSettings getFeatureSettings() + { + return featureSettings; + } + + /** + * Sets the value of the featureSettings property. + * + * @param value + * allowed object is {@link JalviewModelType.FeatureSettings } + * + */ + public void setFeatureSettings(JalviewModelType.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 Listsetting; + + @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 JalviewModelType.JSeq } + * {@link JalviewModelType.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 JalviewModelType.JGroup } + * {@link JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 Listseq; + + @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 JalviewModelType.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 featureSettings property. + * Gets the value of the annotationColours property. + * + * @return possible object is {@link AnnotationColourScheme } * - * @return - * possible object is - * {@link JalviewModelType.FeatureSettings } - * */ - public JalviewModelType.FeatureSettings getFeatureSettings() { - return featureSettings; + public AnnotationColourScheme getAnnotationColours() + { + return annotationColours; } /** - * Sets the value of the featureSettings property. + * Sets the value of the annotationColours property. * * @param value - * allowed object is - * {@link JalviewModelType.FeatureSettings } - * + * allowed object is {@link AnnotationColourScheme } + * */ - public void setFeatureSettings(JalviewModelType.FeatureSettings value) { - this.featureSettings = value; + public void setAnnotationColours(AnnotationColourScheme value) + { + this.annotationColours = value; } - /** - * Java class for anonymous complex type. + * Gets the value of the start property. * - *
The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link Integer } * - *
- * <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 Integer getStart() + { + return start; + } + + /** + * Sets the value of the start property. * + * @param value + * allowed object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "setting", - "group" - }) - public static class FeatureSettings { + public void setStart(Integer value) + { + this.start = value; + } - @XmlElement(namespace = "www.jalview.org") - protected Listsetting; - @XmlElement(namespace = "www.jalview.org") - protected List group; + /** + * Gets the value of the end property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getEnd() + { + return end; + } - /** - * 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 JalviewModelType.FeatureSettings.Setting } - * - * - */ - public List
getSetting() { - if (setting == null) { - setting = new ArrayList (); - } - return this.setting; - } + /** + * 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 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 JalviewModelType.FeatureSettings.Group } - * - * - */ - public List
getGroup() { - if (group == null) { - group = new ArrayList (); - } - return this.group; - } + /** + * 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; + } - /** - * 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; - } + /** + * Gets the value of the colour property. + * + * @return possible object is {@link String } + * + */ + public String getColour() + { + return colour; + } - } + /** + * 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 consThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getConsThreshold() + { + return consThreshold; + } - /** - *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 ListattributeName; - @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; - } + /** + * 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; + } + /** + * 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; + } /** - * Java class for anonymous complex type. + * Sets the value of the outlineColour property. * - *
The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link Integer } * - *
- * <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 void setOutlineColour(Integer value) + { + this.outlineColour = value; + } + + /** + * Gets the value of the displayBoxes property. * + * @return possible object is {@link Boolean } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "seq", - "annotationColours" - }) - public static class JGroup { - - @XmlElement(namespace = "www.jalview.org", required = true) - protected Listseq; - @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 Boolean isDisplayBoxes() + { + return displayBoxes; + } - /** - * 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; - } + /** + * 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 annotationColours property. - * - * @return - * possible object is - * {@link AnnotationColourScheme } - * - */ - public AnnotationColourScheme getAnnotationColours() { - return annotationColours; - } + /** + * Gets the value of the displayText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isDisplayText() + { + return displayText; + } - /** - * 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 displayText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setDisplayText(Boolean value) + { + this.displayText = value; + } - /** - * Gets the value of the start property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getStart() { - return start; - } + /** + * Gets the value of the colourText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isColourText() + { + return colourText; + } - /** - * 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; - } - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } + /** + * Sets the value of the colourText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColourText(Boolean value) + { + this.colourText = 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 textCol1 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol1() + { + return textCol1; + } - /** - * Gets the value of the colour property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getColour() { - return colour; - } + /** + * 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 colour property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setColour(String value) { - this.colour = value; - } + /** + * Gets the value of the textCol2 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol2() + { + return textCol2; + } - /** - * Gets the value of the consThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getConsThreshold() { - return consThreshold; - } + /** + * 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 consThreshold property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setConsThreshold(Integer value) { - this.consThreshold = value; - } + /** + * Gets the value of the textColThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextColThreshold() + { + return textColThreshold; + } - /** - * Gets the value of the pidThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getPidThreshold() { - return pidThreshold; - } + /** + * 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 pidThreshold property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setPidThreshold(Integer value) { - this.pidThreshold = value; - } + /** + * Gets the value of the showUnconserved property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowUnconserved() + { + return showUnconserved; + } - /** - * Gets the value of the outlineColour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getOutlineColour() { - return outlineColour; - } + /** + * 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 outlineColour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setOutlineColour(Integer value) { - this.outlineColour = 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 displayBoxes property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isDisplayBoxes() { - return displayBoxes; - } + /** + * 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 displayBoxes property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setDisplayBoxes(Boolean value) { - this.displayBoxes = 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 displayText property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isDisplayText() { - return displayText; - } + /** + * 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 displayText property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setDisplayText(Boolean value) { - this.displayText = 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 colourText property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isColourText() { - return colourText; - } + /** + * 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 colourText property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setColourText(Boolean value) { - this.colourText = 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 textCol1 property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextCol1() { - return textCol1; - } + /** + * 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 textCol1 property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setTextCol1(Integer value) { - this.textCol1 = value; - } + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } - /** - * Gets the value of the textCol2 property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextCol2() { - return textCol2; - } + /** + * 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 textCol2 property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setTextCol2(Integer value) { - this.textCol2 = 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 Listfeatures; + + @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 textColThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextColThreshold() { - return textColThreshold; - } + /** + * 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; + } - /** - * 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 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 JalviewModelType.JSeq.Pdbids } + * + * + */ + public List
getPdbids() + { + if (pdbids == null) + { + pdbids = new ArrayList (); + } + return this.pdbids; + } - /** - * Gets the value of the showUnconserved property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowUnconserved() { - return showUnconserved; - } + /** + * 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; + } - /** - * 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 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 JalviewModelType.JSeq.RnaViewer } + * + * + */ + public List
getRnaViewer() + { + if (rnaViewer == null) + { + rnaViewer = new ArrayList (); + } + return this.rnaViewer; + } - /** - * 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 Integer } + * + */ + public Integer 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 Integer } + * + */ + public void setColour(Integer 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 start property. + * + */ + public int getStart() + { + return start; + } - /** - * 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 start property. + * + */ + public void setStart(int value) + { + this.start = 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 end property. + * + */ + public int getEnd() + { + return end; + } - /** - * 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 end property. + * + */ + public void setEnd(int value) + { + this.end = 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 id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } - /** - * 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 id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * Gets the value of the hidden property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isHidden() + { + return hidden; + } - /** - * 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 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. + *
+ * 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"> + * <extension base="{www.jalview.org}pdbentry"> * <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="structureState" 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> + * <simpleContent> + * <extension base="<http://www.w3.org/2001/XMLSchema>string"> * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * <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> + * <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> - * <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> + * </extension> * </complexContent> * </complexType> *@@ -1866,1129 +2250,418 @@ public class JalviewModelType { * */ @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "features", - "pdbids", - "hiddenSequences", - "rnaViewer" - }) - public static class JSeq { - - @XmlElement(namespace = "www.jalview.org") - protected Listfeatures; - @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 = { "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 JalviewModelType.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 features property. + * Gets the value of the value 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. + * @return possible object is {@link String } * - *- * For example, to add a new item, do as follows: - *
- * getFeatures().add(newItem); - *+ */ + public String getValue() + { + return value; + } + + /** + * Sets the value of the value property. * + * @param value + * allowed object is {@link String } * - *- * Objects of the following type(s) are allowed in the list - * {@link Feature } + */ + public void setValue(String value) + { + this.value = value; + } + + /** + * Gets the value of the visible property. * + * @return possible object is {@link Boolean } * */ - public List
getFeatures() { - if (features == null) { - features = new ArrayList (); - } - return this.features; + public Boolean isVisible() + { + return visible; } /** - * Gets the value of the pdbids property. + * Sets the value of the visible 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. + * @param value + * allowed object is {@link Boolean } * - *- * For example, to add a new item, do as follows: - *
- * getPdbids().add(newItem); - *+ */ + public void setVisible(Boolean value) + { + this.visible = value; + } + + /** + * Gets the value of the viewId property. * + * @return possible object is {@link String } * - *- * Objects of the following type(s) are allowed in the list - * {@link JalviewModelType.JSeq.Pdbids } + */ + public String getViewId() + { + return viewId; + } + + /** + * Sets the value of the viewId property. * + * @param value + * allowed object is {@link String } * */ - public List
getPdbids() { - if (pdbids == null) { - pdbids = new ArrayList (); - } - return this.pdbids; + public void setViewId(String value) + { + this.viewId = 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 alignwithAlignPanel property. * + * @return possible object is {@link Boolean } * */ - public List
getHiddenSequences() { - if (hiddenSequences == null) { - hiddenSequences = new ArrayList (); - } - return this.hiddenSequences; + public boolean isAlignwithAlignPanel() + { + if (alignwithAlignPanel == null) + { + return true; + } + else + { + return alignwithAlignPanel; + } } /** - * 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 JalviewModelType.JSeq.RnaViewer } + * Sets the value of the alignwithAlignPanel property. * + * @param value + * allowed object is {@link Boolean } * */ - public List
getRnaViewer() { - if (rnaViewer == null) { - rnaViewer = new ArrayList (); - } - return this.rnaViewer; + public void setAlignwithAlignPanel(Boolean value) + { + this.alignwithAlignPanel = value; } /** - * Gets the value of the colour property. + * Gets the value of the colourwithAlignPanel property. + * + * @return possible object is {@link Boolean } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getColour() { - return colour; + public boolean isColourwithAlignPanel() + { + if (colourwithAlignPanel == null) + { + return false; + } + else + { + return colourwithAlignPanel; + } } /** - * Sets the value of the colour property. + * Sets the value of the colourwithAlignPanel property. * * @param value - * allowed object is - * {@link Integer } - * + * allowed object is {@link Boolean } + * */ - public void setColour(Integer value) { - this.colour = value; + public void setColourwithAlignPanel(Boolean value) + { + this.colourwithAlignPanel = value; } /** - * Gets the value of the start property. + * Gets the value of the colourByJmol property. + * + * @return possible object is {@link Boolean } * */ - public int getStart() { - return start; + public boolean isColourByJmol() + { + if (colourByJmol == null) + { + return true; + } + else + { + return colourByJmol; + } } /** - * Sets the value of the start property. + * Sets the value of the colourByJmol property. + * + * @param value + * allowed object is {@link Boolean } * */ - public void setStart(int value) { - this.start = value; + public void setColourByJmol(Boolean value) + { + this.colourByJmol = value; } /** - * Gets the value of the end property. + * Gets the value of the type property. + * + * @return possible object is {@link String } * */ - public int getEnd() { - return end; + public String getType() + { + return type; } /** - * Sets the value of the end property. + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } * */ - public void setEnd(int value) { - this.end = value; + public void setType(String value) + { + this.type = value; } /** - * Gets the value of the id property. + * Gets the value of the width property. + * + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link String } - * */ - public String getId() { - return id; + public Integer getWidth() + { + return width; } /** - * Sets the value of the id property. + * Sets the value of the width property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link Integer } + * */ - public void setId(String value) { - this.id = value; + public void setWidth(Integer value) + { + this.width = value; } /** - * Gets the value of the hidden property. + * Gets the value of the height property. + * + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isHidden() { - return hidden; + public Integer getHeight() + { + return height; } /** - * Sets the value of the hidden property. + * Sets the value of the height property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link Integer } + * */ - public void setHidden(Boolean value) { - this.hidden = value; + public void setHeight(Integer value) + { + this.height = value; } /** - * Gets the value of the viewreference property. + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isViewreference() { - return viewreference; + public Integer getXpos() + { + return xpos; } /** - * Sets the value of the viewreference property. + * Sets the value of the xpos property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link Integer } + * */ - public void setViewreference(Boolean value) { - this.viewreference = value; + public void setXpos(Integer value) + { + this.xpos = 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> - *+ * Gets the value of the ypos property. * + * @return possible object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "structureState" - }) - public static class Pdbids - extends Pdbentry + public Integer getYpos() { - - @XmlElement(namespace = "www.jalview.org") - protected ListstructureState; - - /** - * 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 JalviewModelType.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; - } - - } - + 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"> - * <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> - *+ * Sets the value of the ypos property. * + * @param value + * allowed object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "secondaryStructure" - }) - public static class RnaViewer { - - @XmlElement(namespace = "www.jalview.org", required = true) - protected ListsecondaryStructure; - @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 JalviewModelType.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; - } - - } - + 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 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> + * <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="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="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> @@ -2997,2094 +2670,2564 @@ public class JalviewModelType { * */ @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "title", - "newick" - }) - public static class Tree { + @XmlType(name = "", propOrder = { "secondaryStructure" }) + public static class RnaViewer + { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected ListsecondaryStructure; + + @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 JalviewModelType.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 + { - @XmlElement(namespace = "www.jalview.org") + @XmlAttribute(name = "title") 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 = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; + + @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 } - * + * @return possible object is {@link String } + * */ - public String getTitle() { - return title; + 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 newick property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getNewick() { - return newick; + public void setTitle(String value) + { + this.title = value; } /** - * Sets the value of the newick property. + * Gets the value of the annotationId property. * - * @param value - * allowed object is - * {@link String } - * - */ - public void setNewick(String value) { - this.newick = value; - } - - /** - * Gets the value of the fontName property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getFontName() { - return fontName; + public String getAnnotationId() + { + return annotationId; } /** - * Sets the value of the fontName property. + * Sets the value of the annotationId property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setFontName(String value) { - this.fontName = value; - } - - /** - * Gets the value of the fontSize property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getFontSize() { - return fontSize; + public void setAnnotationId(String value) + { + this.annotationId = value; } /** - * Sets the value of the fontSize property. + * Gets the value of the gapped 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 Boolean } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getFontStyle() { - return fontStyle; + public Boolean isGapped() + { + return gapped; } /** - * Sets the value of the fontStyle property. + * Sets the value of the gapped property. * * @param value - * allowed object is - * {@link Integer } - * - */ - public void setFontStyle(Integer value) { - this.fontStyle = value; - } - - /** - * Gets the value of the threshold property. + * allowed object is {@link Boolean } * - * @return - * possible object is - * {@link Float } - * */ - public Float getThreshold() { - return threshold; + public void setGapped(Boolean value) + { + this.gapped = value; } /** - * Sets the value of the threshold property. + * Gets the value of the viewerState property. * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setThreshold(Float value) { - this.threshold = value; - } - - /** - * Gets the value of the showBootstrap property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isShowBootstrap() { - return showBootstrap; + public String getViewerState() + { + return viewerState; } /** - * Sets the value of the showBootstrap property. + * Sets the value of the viewerState property. * * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowBootstrap(Boolean value) { - this.showBootstrap = value; - } - - /** - * Gets the value of the showDistances property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isShowDistances() { - return showDistances; + public void setViewerState(String value) + { + this.viewerState = value; } - /** - * Sets the value of the showDistances property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowDistances(Boolean value) { - this.showDistances = value; - } + } - /** - * Gets the value of the markUnlinked property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isMarkUnlinked() { - return markUnlinked; - } + } - /** - * Sets the value of the markUnlinked property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setMarkUnlinked(Boolean value) { - this.markUnlinked = 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 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" /> + * </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 = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + + @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 fitToWindow property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isFitToWindow() { - return fitToWindow; - } + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } - /** - * 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 title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } - /** - * Gets the value of the currentTree property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isCurrentTree() { - return currentTree; - } + /** + * Gets the value of the newick property. + * + * @return possible object is {@link String } + * + */ + public String getNewick() + { + return newick; + } - /** - * 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 newick property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setNewick(String value) + { + this.newick = value; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * 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; + } + + /** + * 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; + } + + /** + * 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; + } + + /** + * 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 showBootstrap property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowBootstrap() + { + return showBootstrap; + } + + /** + * Sets the value of the showBootstrap property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowBootstrap(Boolean value) + { + this.showBootstrap = value; + } + + /** + * Gets the value of the showDistances property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowDistances() + { + return showDistances; + } - /** - * 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 showDistances property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowDistances(Boolean value) + { + this.showDistances = value; + } - /** - * Gets the value of the width property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getWidth() { - return width; - } + /** + * Gets the value of the markUnlinked property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isMarkUnlinked() + { + return markUnlinked; + } - /** - * 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 markUnlinked property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setMarkUnlinked(Boolean value) + { + this.markUnlinked = value; + } - /** - * Gets the value of the height property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHeight() { - return height; - } + /** + * Gets the value of the fitToWindow property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isFitToWindow() + { + return fitToWindow; + } - /** - * 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 fitToWindow property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFitToWindow(Boolean value) + { + this.fitToWindow = value; + } - /** - * Gets the value of the xpos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXpos() { - return xpos; - } + /** + * Gets the value of the currentTree property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isCurrentTree() + { + return currentTree; + } - /** - * 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 currentTree property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setCurrentTree(Boolean value) + { + this.currentTree = value; + } - /** - * Gets the value of the ypos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYpos() { - return ypos; - } + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } - /** - * 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 id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = 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; + } /** - *Java class for anonymous complex type. + * Gets the value of the height property. * - *
The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link Integer } * - *
- * <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> - *+ */ + public Integer getHeight() + { + return height; + } + + /** + * Sets the value of the height property. * + * @param value + * allowed object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "userColourScheme" - }) - public static class UserColours { + public void setHeight(Integer value) + { + this.height = value; + } - @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true) - protected JalviewUserColours userColourScheme; - @XmlAttribute(name = "id") - protected String id; + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } - /** - * Gets the value of the userColourScheme property. - * - * @return - * possible object is - * {@link JalviewUserColours } - * - */ - public JalviewUserColours getUserColourScheme() { - return userColourScheme; - } + /** + * 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 userColourScheme property. - * - * @param value - * allowed object is - * {@link JalviewUserColours } - * - */ - public void setUserColourScheme(JalviewUserColours value) { - this.userColourScheme = value; - } + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * 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 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="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> - * <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" /> - * </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 = { - "annotationColours", - "hiddenColumns", - "calcIdParam" - }) - public static class Viewport { - - @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org") - protected AnnotationColourScheme annotationColours; - @XmlElement(namespace = "www.jalview.org") - protected ListhiddenColumns; - @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 = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; + public void setId(String value) + { + this.id = value; + } - /** - * Gets the value of the annotationColours property. - * - * @return - * possible object is - * {@link AnnotationColourScheme } - * - */ - public AnnotationColourScheme getAnnotationColours() { - return annotationColours; - } + } + + /** + * + * 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> + * </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" /> + * </restriction> + * </complexContent> + * </complexType> + *+ * + * + */ + @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 ListhiddenColumns; + + @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; - /** - * Sets the value of the annotationColours property. - * - * @param value - * allowed object is - * {@link AnnotationColourScheme } - * - */ - public void setAnnotationColours(AnnotationColourScheme value) { - this.annotationColours = value; - } + @XmlAttribute(name = "showSequenceFeatures") + protected Boolean showSequenceFeatures; - /** - * 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 JalviewModelType.Viewport.HiddenColumns } - * - * - */ - public List
getHiddenColumns() { - if (hiddenColumns == null) { - hiddenColumns = new ArrayList (); - } - return this.hiddenColumns; - } + @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; - /** - * 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 JalviewModelType.Viewport.CalcIdParam } - * - * - */ - public List
getCalcIdParam() { - if (calcIdParam == null) { - calcIdParam = new ArrayList (); - } - return this.calcIdParam; - } + @XmlAttribute(name = "textCol1") + protected Integer textCol1; - /** - * Gets the value of the conservationSelected property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isConservationSelected() { - return conservationSelected; - } + @XmlAttribute(name = "textCol2") + protected Integer textCol2; - /** - * Sets the value of the conservationSelected property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setConservationSelected(Boolean value) { - this.conservationSelected = value; - } + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; - /** - * Gets the value of the pidSelected property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isPidSelected() { - return pidSelected; - } + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; - /** - * Sets the value of the pidSelected property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setPidSelected(Boolean value) { - this.pidSelected = value; - } + @XmlAttribute(name = "complementId") + protected String complementId; - /** - * Gets the value of the bgColour property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getBgColour() { - return bgColour; - } + @XmlAttribute(name = "width") + protected Integer width; - /** - * Sets the value of the bgColour property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setBgColour(String value) { - this.bgColour = value; - } + @XmlAttribute(name = "height") + protected Integer height; - /** - * Gets the value of the consThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getConsThreshold() { - return consThreshold; - } + @XmlAttribute(name = "xpos") + protected Integer xpos; - /** - * Sets the value of the consThreshold property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setConsThreshold(Integer value) { - this.consThreshold = value; - } + @XmlAttribute(name = "ypos") + protected Integer ypos; - /** - * Gets the value of the pidThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getPidThreshold() { - return pidThreshold; - } + /** + * Gets the value of the annotationColours property. + * + * @return possible object is {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() + { + return annotationColours; + } - /** - * 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 annotationColours property. + * + * @param value + * allowed object is {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) + { + this.annotationColours = value; + } - /** - * Gets the value of the title property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTitle() { - return title; - } + /** + * 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 JalviewModelType.Viewport.HiddenColumns } + * + * + */ + public List
getHiddenColumns() + { + if (hiddenColumns == null) + { + hiddenColumns = new ArrayList (); + } + return this.hiddenColumns; + } - /** - * 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 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 JalviewModelType.Viewport.CalcIdParam } + * + * + */ + public List
getCalcIdParam() + { + if (calcIdParam == null) + { + calcIdParam = new ArrayList (); + } + return this.calcIdParam; + } - /** - * Gets the value of the showFullId property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowFullId() { - return showFullId; - } + /** + * Gets the value of the conservationSelected property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isConservationSelected() + { + return conservationSelected; + } - /** - * 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 conservationSelected property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setConservationSelected(Boolean value) + { + this.conservationSelected = value; + } - /** - * Gets the value of the rightAlignIds property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isRightAlignIds() { - return rightAlignIds; - } + /** + * Gets the value of the pidSelected property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isPidSelected() + { + return pidSelected; + } - /** - * 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 pidSelected property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setPidSelected(Boolean value) + { + this.pidSelected = value; + } - /** - * Gets the value of the showText property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowText() { - return showText; - } + /** + * Gets the value of the bgColour property. + * + * @return possible object is {@link String } + * + */ + public String getBgColour() + { + return bgColour; + } - /** - * 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 bgColour property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setBgColour(String value) + { + this.bgColour = value; + } - /** - * Gets the value of the showColourText property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowColourText() { - return showColourText; - } + /** + * Gets the value of the consThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getConsThreshold() + { + return consThreshold; + } - /** - * 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 consThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setConsThreshold(Integer value) + { + this.consThreshold = 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 pidThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getPidThreshold() + { + return pidThreshold; + } - /** - * 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 pidThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setPidThreshold(Integer value) + { + this.pidThreshold = value; + } - /** - * Gets the value of the showBoxes property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowBoxes() { - return showBoxes; - } + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } - /** - * 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 title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the showFullId property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowFullId() + { + return showFullId; + } + + /** + * 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 rightAlignIds property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isRightAlignIds() + { + return rightAlignIds; + } + + /** + * 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 wrapAlignment property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isWrapAlignment() { - return wrapAlignment; - } + /** + * Gets the value of the showText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowText() + { + return showText; + } - /** - * Sets the value of the wrapAlignment property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setWrapAlignment(Boolean value) { - this.wrapAlignment = 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 renderGaps property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isRenderGaps() { - return renderGaps; - } + /** + * Gets the value of the showColourText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowColourText() + { + return showColourText; + } - /** - * Sets the value of the renderGaps property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setRenderGaps(Boolean value) { - this.renderGaps = 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 showSequenceFeatures property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowSequenceFeatures() { - return showSequenceFeatures; - } + /** + * 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 showSequenceFeatures property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowSequenceFeatures(Boolean value) { - this.showSequenceFeatures = 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 showNPfeatureTooltip property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowNPfeatureTooltip() { - return showNPfeatureTooltip; - } + /** + * Gets the value of the showBoxes property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowBoxes() + { + return showBoxes; + } - /** - * 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 showBoxes property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowBoxes(Boolean value) + { + this.showBoxes = value; + } - /** - * Gets the value of the showDbRefTooltip property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowDbRefTooltip() { - return showDbRefTooltip; - } + /** + * Gets the value of the wrapAlignment property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isWrapAlignment() + { + return wrapAlignment; + } - /** - * 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 wrapAlignment property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setWrapAlignment(Boolean value) + { + this.wrapAlignment = 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 renderGaps property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isRenderGaps() + { + return renderGaps; + } - /** - * 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 renderGaps property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setRenderGaps(Boolean value) + { + this.renderGaps = 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 showSequenceFeatures property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowSequenceFeatures() + { + return showSequenceFeatures; + } - /** - * 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 showSequenceFeatures property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowSequenceFeatures(Boolean value) + { + this.showSequenceFeatures = value; + } - /** - * Gets the value of the showAnnotation property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowAnnotation() { - return showAnnotation; - } + /** + * Gets the value of the showNPfeatureTooltip property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowNPfeatureTooltip() + { + return showNPfeatureTooltip; + } - /** - * 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 showNPfeatureTooltip property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowNPfeatureTooltip(Boolean value) + { + this.showNPfeatureTooltip = 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 showDbRefTooltip property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowDbRefTooltip() + { + return showDbRefTooltip; + } - /** - * 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 showDbRefTooltip property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowDbRefTooltip(Boolean value) + { + this.showDbRefTooltip = 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 followHighlight property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isFollowHighlight() + { + if (followHighlight == null) + { + return true; + } + else + { + return followHighlight; + } + } - /** - * 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 followHighlight property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFollowHighlight(Boolean value) + { + this.followHighlight = 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 followSelection property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isFollowSelection() + { + if (followSelection == null) + { + return true; + } + else + { + return followSelection; + } + } - /** - * 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 followSelection property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFollowSelection(Boolean value) + { + this.followSelection = 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 showAnnotation property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowAnnotation() + { + return showAnnotation; + } - /** - * 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 showAnnotation property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowAnnotation(Boolean value) + { + this.showAnnotation = 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 centreColumnLabels property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isCentreColumnLabels() + { + if (centreColumnLabels == null) + { + return false; + } + else + { + return centreColumnLabels; + } + } + + /** + * 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 showSequenceLogo property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowSequenceLogo(Boolean value) { - this.showSequenceLogo = 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 normaliseSequenceLogo property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isNormaliseSequenceLogo() { - if (normaliseSequenceLogo == null) { - return false; - } else { - return normaliseSequenceLogo; - } - } + /** + * 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 normaliseSequenceLogo property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setNormaliseSequenceLogo(Boolean value) { - this.normaliseSequenceLogo = 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 ignoreGapsinConsensus property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isIgnoreGapsinConsensus() { - if (ignoreGapsinConsensus == null) { - return true; - } else { - return ignoreGapsinConsensus; - } - } + /** + * 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 ignoreGapsinConsensus property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setIgnoreGapsinConsensus(Boolean value) { - this.ignoreGapsinConsensus = 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 startRes property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getStartRes() { - return startRes; - } + /** + * 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 startRes property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setStartRes(Integer value) { - this.startRes = 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 startSeq property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getStartSeq() { - return startSeq; - } + /** + * 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 startSeq property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setStartSeq(Integer value) { - this.startSeq = 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 fontName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getFontName() { - return fontName; - } + /** + * 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 fontName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setFontName(String value) { - this.fontName = 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 fontSize property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getFontSize() { - return fontSize; - } + /** + * 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 fontSize property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setFontSize(Integer value) { - this.fontSize = value; - } + /** + * Gets the value of the startRes property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStartRes() + { + return startRes; + } - /** - * Gets the value of the fontStyle property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getFontStyle() { - return fontStyle; - } + /** + * 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 fontStyle property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setFontStyle(Integer value) { - this.fontStyle = value; - } + /** + * Gets the value of the startSeq property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStartSeq() + { + return startSeq; + } - /** - * 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 startSeq property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStartSeq(Integer value) + { + this.startSeq = 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 fontName property. + * + * @return possible object is {@link String } + * + */ + public String getFontName() + { + return fontName; + } - /** - * Gets the value of the viewName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getViewName() { - return viewName; - } + /** + * 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 viewName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setViewName(String value) { - this.viewName = value; - } + /** + * Gets the value of the fontSize property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontSize() + { + return fontSize; + } - /** - * Gets the value of the sequenceSetId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getSequenceSetId() { - return sequenceSetId; - } + /** + * 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 sequenceSetId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setSequenceSetId(String value) { - this.sequenceSetId = value; - } + /** + * Gets the value of the fontStyle property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontStyle() + { + return fontStyle; + } - /** - * Gets the value of the gatheredViews property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isGatheredViews() { - return gatheredViews; - } + /** + * 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 gatheredViews property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setGatheredViews(Boolean value) { - this.gatheredViews = 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 textCol1 property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextCol1() { - return textCol1; - } + /** + * 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 textCol1 property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setTextCol1(Integer value) { - this.textCol1 = value; - } + /** + * 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; + } - /** - * Gets the value of the textCol2 property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextCol2() { - return textCol2; - } + /** + * Gets the value of the sequenceSetId property. + * + * @return possible object is {@link String } + * + */ + public String getSequenceSetId() + { + return sequenceSetId; + } - /** - * 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 sequenceSetId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setSequenceSetId(String value) + { + this.sequenceSetId = value; + } - /** - * Gets the value of the textColThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextColThreshold() { - return textColThreshold; - } + /** + * Gets the value of the gatheredViews property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isGatheredViews() + { + return gatheredViews; + } - /** - * 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 gatheredViews property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setGatheredViews(Boolean value) + { + this.gatheredViews = value; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * Gets the value of the textCol1 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol1() + { + return textCol1; + } - /** - * 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 textCol1 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol1(Integer value) + { + this.textCol1 = value; + } - /** - * Gets the value of the complementId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getComplementId() { - return complementId; - } + /** + * Gets the value of the textCol2 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol2() + { + return textCol2; + } - /** - * 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 textCol2 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol2(Integer value) + { + this.textCol2 = value; + } - /** - * Gets the value of the width property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getWidth() { - return width; - } + /** + * Gets the value of the textColThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextColThreshold() + { + return textColThreshold; + } - /** - * 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 textColThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextColThreshold(Integer value) + { + this.textColThreshold = value; + } - /** - * Gets the value of the height property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHeight() { - return height; - } + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } - /** - * 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 id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } - /** - * Gets the value of the xpos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXpos() { - return xpos; - } + /** + * Gets the value of the complementId property. + * + * @return possible object is {@link String } + * + */ + public String getComplementId() + { + return complementId; + } - /** - * 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 complementId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setComplementId(String value) + { + this.complementId = value; + } - /** - * Gets the value of the ypos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYpos() { - return ypos; - } + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } - /** - * 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; + } - /** - * 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 - { + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = 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; - } + /** + * 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"> - * <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; - } + /** + * 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; } + 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; + } } + } + }