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=0000000000000000000000000000000000000000;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=f084bc3f05021c6c5567ca476a553b63130affbd;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java deleted file mode 100644 index f084bc3..0000000 --- a/src/jalview/xml/binding/jalview/JalviewModelType.java +++ /dev/null @@ -1,5090 +0,0 @@ -// -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb -// Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2018.09.18 at 01:33:02 PM BST -// - - -package jalview.xml.binding.jalview; - -import java.util.ArrayList; -import java.util.List; -import javax.xml.bind.annotation.XmlAccessType; -import javax.xml.bind.annotation.XmlAccessorType; -import javax.xml.bind.annotation.XmlAttribute; -import javax.xml.bind.annotation.XmlElement; -import javax.xml.bind.annotation.XmlID; -import javax.xml.bind.annotation.XmlSchemaType; -import javax.xml.bind.annotation.XmlType; -import javax.xml.bind.annotation.XmlValue; -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. - * - *
The following schema fragment specifies the expected content contained within this class. - * - *
- * <complexType name="JalviewModelType"> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/> - * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/> - * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/> - * <sequence> - * <element name="JSeq" maxOccurs="unbounded" minOccurs="0"> - * <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> - * </element> - * <element name="JGroup" maxOccurs="unbounded" minOccurs="0"> - * <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> - * </element> - * <element name="Viewport" maxOccurs="unbounded" minOccurs="0"> - * <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> - * </element> - * <element name="UserColours" maxOccurs="unbounded" minOccurs="0"> - * <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> - * </element> - * <element name="tree" maxOccurs="unbounded" minOccurs="0"> - * <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> - * </element> - * <element name="FeatureSettings" minOccurs="0"> - * <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> - * </element> - * </sequence> - * </sequence> - * </restriction> - * </complexContent> - * </complexType> - *- * - * - */ -@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 List
- * 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
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JGroup }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.UserColours }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Tree }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- *
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.FeatureSettings.Setting }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.FeatureSettings.Group }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- * Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- *
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- *
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- *
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link Feature }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.Pdbids }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.RnaViewer }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- *
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- * Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- *
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- * Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- * Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- * Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- *
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport.HiddenColumns }
- *
- *
- */
- public List
- * 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
- * For example, to add a new item, do as follows:
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport.CalcIdParam }
- *
- *
- */
- public List Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- * Java class for anonymous complex type.
- *
- * The following schema fragment specifies the expected content contained within this class.
- *
- * set
method for the jGroup property.
- *
- *
- * getJGroup().add(newItem);
- *
- *
- *
- * set
method for the viewport property.
- *
- *
- * getViewport().add(newItem);
- *
- *
- *
- * set
method for the userColours property.
- *
- *
- * getUserColours().add(newItem);
- *
- *
- *
- * set
method for the tree property.
- *
- *
- * getTree().add(newItem);
- *
- *
- *
- *
- * <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 Listset
method for the setting property.
- *
- *
- * getSetting().add(newItem);
- *
- *
- *
- * set
method for the group property.
- *
- *
- * getGroup().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>
- *
- *
- *
- */
- @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;
- }
-
- }
-
-
- /**
- *
- * <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 Listset
method for the attributeName property.
- *
- *
- * getAttributeName().add(newItem);
- *
- *
- *
- *
- * <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 Listset
method for the seq property.
- *
- *
- * getSeq().add(newItem);
- *
- *
- *
- *
- * <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 Listset
method for the features property.
- *
- *
- * getFeatures().add(newItem);
- *
- *
- *
- * set
method for the pdbids property.
- *
- *
- * getPdbids().add(newItem);
- *
- *
- *
- * set
method for the hiddenSequences property.
- *
- *
- * getHiddenSequences().add(newItem);
- *
- *
- *
- * set
method for the rnaViewer property.
- *
- *
- * getRnaViewer().add(newItem);
- *
- *
- *
- *
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "structureState"
- })
- public static class Pdbids
- extends Pdbentry
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected Listset
method for the structureState property.
- *
- *
- * getStructureState().add(newItem);
- *
- *
- *
- *
- * <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;
- }
-
- }
-
- }
-
-
- /**
- *
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- *
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "secondaryStructure"
- })
- public static class RnaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected Listset
method for the secondaryStructure property.
- *
- *
- * getSecondaryStructure().add(newItem);
- *
- *
- *
- *
- * <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;
- }
-
- }
-
- }
-
- }
-
-
- /**
- *
- * <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 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 newick property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNewick() {
- return newick;
- }
-
- /**
- * 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 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 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;
- }
-
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isFitToWindow() {
- return fitToWindow;
- }
-
- /**
- * 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 currentTree property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCurrentTree() {
- return currentTree;
- }
-
- /**
- * 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 id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the 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;
- }
-
- }
-
-
- /**
- *
- * <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;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- }
-
-
- /**
- *
- * <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 Listset
method for the hiddenColumns property.
- *
- *
- * getHiddenColumns().add(newItem);
- *
- *
- *
- * set
method for the calcIdParam property.
- *
- *
- * getCalcIdParam().add(newItem);
- *
- *
- *
- *
- * <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;
- }
-
- }
-
-
- /**
- *
- * <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;
- }
-
- }
-
- }
-
-}