X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fxml%2Fbinding%2FjalviewBH%2FJalviewModel.java;fp=src%2Fjalview%2Fxml%2Fbinding%2FjalviewBH%2FJalviewModel.java;h=0000000000000000000000000000000000000000;hb=962217a2b1ded38f78ff36d1875253caa04b0060;hp=413c3dd6dfa0932f531ac0b7a2db602b6fe2de50;hpb=72c5b516b20097c63eee46b63e3074d279252664;p=jalview.git diff --git a/src/jalview/xml/binding/jalviewBH/JalviewModel.java b/src/jalview/xml/binding/jalviewBH/JalviewModel.java deleted file mode 100644 index 413c3dd..0000000 --- a/src/jalview/xml/binding/jalviewBH/JalviewModel.java +++ /dev/null @@ -1,5241 +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 04:36:20 PM BST -// - -package jalview.xml.binding.jalviewBH; - -import jalview.schemabinding.version2.AnnotationColourScheme; -import jalview.schemabinding.version2.WebServiceParameterSet; - -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 JalviewModel complex type. - * - *
- * The following schema fragment specifies the expected content contained within - * this class. - * - *
- * <complexType name="JalviewModel"> - * <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 = "JalviewModel", - namespace = "www.jalview.org", - propOrder = - { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport", - "userColours", "tree", "featureSettings" }) -public class JalviewModel -{ - - @XmlElement(required = true) - @XmlSchemaType(name = "dateTime") - protected XMLGregorianCalendar creationDate; - - @XmlElement(required = true) - protected String version; - - @XmlElement(required = true) - protected VAMSAS vamsasModel; - - @XmlElement(name = "JSeq") - protected List
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a set
method
- * for the jSeq property.
- *
- *
- * For example, to add a new item, do as follows: - * - *
- * getJSeq().add(newItem); - *- * - * - *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
- *
- *
- */
- public List
- * 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 JalviewModel.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 JalviewModel.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 JalviewModel.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 JalviewModel.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 JalviewModel.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 JalviewModel.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 getFeatures()
- {
- if (features == null)
- {
- features = new ArrayList();
- }
- return this.features;
- }
-
- /**
- * Gets the value of the pdbids property.
- *
- *
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- *
- * For example, to add a new item, do as follows:
- *
- *
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.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 JalviewModel.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 JalviewModel.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 JalviewModel.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 JalviewModel.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 JalviewModel.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 List features;
-
- @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 Object/*JalviewUserColours*/ userColourScheme;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return possible object is {@link JalviewUserColours }
- *
- */
- public Object/*JalviewUserColours*/ getUserColourScheme()
- {
- return userColourScheme;
- }
-
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(Object/*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;
- }
-
- }
-
- }
-
-}