X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModel.java;h=2de1ebad2823e16c949c0162e8d74146d579e269;hb=9d9ad2a9237a50e305349a63eb01bb5548d028d0;hp=0f538f2f4a68d436f60529c3f5217b82cba22906;hpb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 0f538f2..2de1eba 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -2,7 +2,7 @@ // 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: 2018.09.28 at 12:18:54 PM BST +// Generated on: 2023.01.31 at 04:07:08 PM GMT // @@ -165,6 +165,20 @@ import javax.xml.datatype.XMLGregorianCalendar; * </complexContent> * </complexType> * </element> + * <element name="overview" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> * </sequence> * <attGroup ref="{www.jalview.org}swingwindow"/> * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> @@ -208,6 +222,8 @@ import javax.xml.datatype.XMLGregorianCalendar; * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * </restriction> * </complexContent> * </complexType> @@ -243,6 +259,66 @@ import javax.xml.datatype.XMLGregorianCalendar; * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="sequencePoint" maxOccurs="unbounded"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="axis" maxOccurs="3" minOccurs="3"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMin"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMax"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="pcaData" type="{www.jalview.org}PcaDataType"/> + * </sequence> + * <attGroup ref="{www.jalview.org}SimilarityParams"/> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * </restriction> * </complexContent> * </complexType> @@ -310,6 +386,7 @@ import javax.xml.datatype.XMLGregorianCalendar; "viewport", "userColours", "tree", + "pcaViewer", "featureSettings" }) public class JalviewModel { @@ -330,6 +407,8 @@ public class JalviewModel { @XmlElement(name = "UserColours") protected List userColours; protected List tree; + @XmlElement(name = "PcaViewer") + protected List pcaViewer; @XmlElement(name = "FeatureSettings") protected JalviewModel.FeatureSettings featureSettings; @@ -551,6 +630,35 @@ public class JalviewModel { } /** + * Gets the value of the pcaViewer property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the pcaViewer property. + * + *

+ * For example, to add a new item, do as follows: + *

+     *    getPcaViewer().add(newItem);
+     * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.PcaViewer } + * + * + */ + public List getPcaViewer() { + if (pcaViewer == null) { + pcaViewer = new ArrayList(); + } + return this.pcaViewer; + } + + /** * Gets the value of the featureSettings property. * * @return @@ -2974,21 +3082,57 @@ public class JalviewModel { * <complexType> * <complexContent> * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence minOccurs="0"> - * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/> - * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/> + * <sequence> + * <element name="sequencePoint" maxOccurs="unbounded"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="axis" maxOccurs="3" minOccurs="3"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMin"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMax"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="pcaData" type="{www.jalview.org}PcaDataType"/> * </sequence> + * <attGroup ref="{www.jalview.org}SimilarityParams"/> * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> - * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * </restriction> * </complexContent> * </complexType> @@ -2998,38 +3142,50 @@ public class JalviewModel { */ @XmlAccessorType(XmlAccessType.FIELD) @XmlType(name = "", propOrder = { - "title", - "newick" + "sequencePoint", + "axis", + "seqPointMin", + "seqPointMax", + "pcaData" }) - public static class Tree { + public static class PcaViewer { - @XmlElement(namespace = "www.jalview.org") + @XmlElement(namespace = "www.jalview.org", required = true) + protected List sequencePoint; + @XmlElement(namespace = "www.jalview.org", required = true) + protected List axis; + @XmlElement(namespace = "www.jalview.org", required = true) + protected JalviewModel.PcaViewer.SeqPointMin seqPointMin; + @XmlElement(namespace = "www.jalview.org", required = true) + protected JalviewModel.PcaViewer.SeqPointMax seqPointMax; + @XmlElement(namespace = "www.jalview.org", required = true) + protected PcaDataType pcaData; + @XmlAttribute(name = "title") protected String title; - @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 = "scoreModelName") + protected String scoreModelName; + @XmlAttribute(name = "xDim") + protected Integer xDim; + @XmlAttribute(name = "yDim") + protected Integer yDim; + @XmlAttribute(name = "zDim") + protected Integer zDim; + @XmlAttribute(name = "bgColour") + protected Integer bgColour; + @XmlAttribute(name = "scaleFactor") + protected Float scaleFactor; + @XmlAttribute(name = "showLabels") + protected Boolean showLabels; + @XmlAttribute(name = "linkToAllViews") + protected Boolean linkToAllViews; + @XmlAttribute(name = "includeGaps") + protected Boolean includeGaps; + @XmlAttribute(name = "matchGaps") + protected Boolean matchGaps; + @XmlAttribute(name = "includeGappedColumns") + protected Boolean includeGappedColumns; + @XmlAttribute(name = "denominateByShortestLength") + protected Boolean denominateByShortestLength; @XmlAttribute(name = "width") protected Integer width; @XmlAttribute(name = "height") @@ -3040,179 +3196,1236 @@ public class JalviewModel { protected Integer ypos; /** - * Gets the value of the title property. + * Gets the value of the sequencePoint property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the sequencePoint property. + * + *

+ * For example, to add a new item, do as follows: + *

+         *    getSequencePoint().add(newItem);
+         * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.PcaViewer.SequencePoint } + * * - * @return - * possible object is - * {@link String } - * */ - public String getTitle() { - return title; + public List getSequencePoint() { + if (sequencePoint == null) { + sequencePoint = new ArrayList(); + } + return this.sequencePoint; } /** - * Sets the value of the title property. + * Gets the value of the axis property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the axis property. + * + *

+ * For example, to add a new item, do as follows: + *

+         *    getAxis().add(newItem);
+         * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.PcaViewer.Axis } + * * - * @param value - * allowed object is - * {@link String } - * */ - public void setTitle(String value) { - this.title = value; + public List getAxis() { + if (axis == null) { + axis = new ArrayList(); + } + return this.axis; } /** - * Gets the value of the newick property. + * Gets the value of the seqPointMin property. * * @return * possible object is - * {@link String } + * {@link JalviewModel.PcaViewer.SeqPointMin } * */ - public String getNewick() { - return newick; + public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() { + return seqPointMin; } /** - * Sets the value of the newick property. + * Sets the value of the seqPointMin property. * * @param value * allowed object is - * {@link String } + * {@link JalviewModel.PcaViewer.SeqPointMin } * */ - public void setNewick(String value) { - this.newick = value; + public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) { + this.seqPointMin = value; } /** - * Gets the value of the fontName property. + * Gets the value of the seqPointMax property. * * @return * possible object is - * {@link String } + * {@link JalviewModel.PcaViewer.SeqPointMax } * */ - public String getFontName() { - return fontName; + public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() { + return seqPointMax; } /** - * Sets the value of the fontName property. + * Sets the value of the seqPointMax property. * * @param value * allowed object is - * {@link String } + * {@link JalviewModel.PcaViewer.SeqPointMax } * */ - public void setFontName(String value) { - this.fontName = value; + public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) { + this.seqPointMax = value; } /** - * Gets the value of the fontSize property. + * Gets the value of the pcaData property. * * @return * possible object is - * {@link Integer } + * {@link PcaDataType } * */ - public Integer getFontSize() { - return fontSize; + public PcaDataType getPcaData() { + return pcaData; } /** - * Sets the value of the fontSize property. + * Sets the value of the pcaData property. * * @param value * allowed object is - * {@link Integer } + * {@link PcaDataType } * */ - public void setFontSize(Integer value) { - this.fontSize = value; + public void setPcaData(PcaDataType value) { + this.pcaData = value; } /** - * Gets the value of the fontStyle property. + * Gets the value of the title property. * * @return * possible object is - * {@link Integer } + * {@link String } * */ - public Integer getFontStyle() { - return fontStyle; + public String getTitle() { + return title; } /** - * Sets the value of the fontStyle property. + * Sets the value of the title property. * * @param value * allowed object is - * {@link Integer } + * {@link String } * */ - public void setFontStyle(Integer value) { - this.fontStyle = value; + public void setTitle(String value) { + this.title = value; } /** - * Gets the value of the threshold property. + * Gets the value of the scoreModelName property. * * @return * possible object is - * {@link Float } + * {@link String } * */ - public Float getThreshold() { - return threshold; + public String getScoreModelName() { + return scoreModelName; } /** - * Sets the value of the threshold property. + * Sets the value of the scoreModelName property. * * @param value * allowed object is - * {@link Float } + * {@link String } * */ - public void setThreshold(Float value) { - this.threshold = value; + public void setScoreModelName(String value) { + this.scoreModelName = value; } /** - * Gets the value of the showBootstrap property. + * Gets the value of the xDim property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isShowBootstrap() { - return showBootstrap; + public Integer getXDim() { + return xDim; } /** - * Sets the value of the showBootstrap property. + * Sets the value of the xDim property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setShowBootstrap(Boolean value) { - this.showBootstrap = value; + public void setXDim(Integer value) { + this.xDim = value; } /** - * Gets the value of the showDistances property. + * Gets the value of the yDim property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } + * + */ + public Integer getYDim() { + return yDim; + } + + /** + * Sets the value of the yDim property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYDim(Integer value) { + this.yDim = value; + } + + /** + * Gets the value of the zDim property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getZDim() { + return zDim; + } + + /** + * Sets the value of the zDim property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setZDim(Integer value) { + this.zDim = value; + } + + /** + * Gets the value of the bgColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getBgColour() { + return bgColour; + } + + /** + * Sets the value of the bgColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setBgColour(Integer value) { + this.bgColour = value; + } + + /** + * Gets the value of the scaleFactor property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getScaleFactor() { + return scaleFactor; + } + + /** + * Sets the value of the scaleFactor property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setScaleFactor(Float value) { + this.scaleFactor = value; + } + + /** + * Gets the value of the showLabels property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowLabels() { + return showLabels; + } + + /** + * Sets the value of the showLabels property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowLabels(Boolean value) { + this.showLabels = value; + } + + /** + * Gets the value of the linkToAllViews property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isLinkToAllViews() { + return linkToAllViews; + } + + /** + * Sets the value of the linkToAllViews property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setLinkToAllViews(Boolean value) { + this.linkToAllViews = value; + } + + /** + * Gets the value of the includeGaps property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isIncludeGaps() { + return includeGaps; + } + + /** + * Sets the value of the includeGaps property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIncludeGaps(Boolean value) { + this.includeGaps = value; + } + + /** + * Gets the value of the matchGaps property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isMatchGaps() { + return matchGaps; + } + + /** + * Sets the value of the matchGaps property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setMatchGaps(Boolean value) { + this.matchGaps = value; + } + + /** + * Gets the value of the includeGappedColumns property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isIncludeGappedColumns() { + return includeGappedColumns; + } + + /** + * Sets the value of the includeGappedColumns property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIncludeGappedColumns(Boolean value) { + this.includeGappedColumns = value; + } + + /** + * Gets the value of the denominateByShortestLength property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isDenominateByShortestLength() { + return denominateByShortestLength; + } + + /** + * Sets the value of the denominateByShortestLength property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setDenominateByShortestLength(Boolean value) { + this.denominateByShortestLength = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + *

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Axis { + + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + *

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SeqPointMax { + + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + *

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SeqPointMin { + + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + *

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SequencePoint { + + @XmlAttribute(name = "sequenceRef") + protected String sequenceRef; + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the sequenceRef property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSequenceRef() { + return sequenceRef; + } + + /** + * Sets the value of the sequenceRef property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSequenceRef(String value) { + this.sequenceRef = value; + } + + /** + * Gets the value of the xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } + + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + *

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence minOccurs="0">
+     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "title", + "newick" + }) + public static class Tree { + + @XmlElement(namespace = "www.jalview.org") + protected String title; + @XmlElement(namespace = "www.jalview.org") + protected String newick; + @XmlAttribute(name = "fontName") + protected String fontName; + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + @XmlAttribute(name = "threshold") + protected Float threshold; + @XmlAttribute(name = "showBootstrap") + protected Boolean showBootstrap; + @XmlAttribute(name = "showDistances") + protected Boolean showDistances; + @XmlAttribute(name = "markUnlinked") + protected Boolean markUnlinked; + @XmlAttribute(name = "fitToWindow") + protected Boolean fitToWindow; + @XmlAttribute(name = "currentTree") + protected Boolean currentTree; + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + @XmlAttribute(name = "linkToAllViews") + protected Boolean linkToAllViews; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * 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() { @@ -3328,6 +4541,34 @@ public class JalviewModel { } /** + * Gets the value of the linkToAllViews property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isLinkToAllViews() { + if (linkToAllViews == null) { + return false; + } else { + return linkToAllViews; + } + } + + /** + * Sets the value of the linkToAllViews property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setLinkToAllViews(Boolean value) { + this.linkToAllViews = value; + } + + /** * Gets the value of the width property. * * @return @@ -3540,6 +4781,20 @@ public class JalviewModel { * </complexContent> * </complexType> * </element> + * <element name="overview" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> * </sequence> * <attGroup ref="{www.jalview.org}swingwindow"/> * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> @@ -3583,6 +4838,8 @@ public class JalviewModel { * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * </restriction> * </complexContent> * </complexType> @@ -3594,7 +4851,8 @@ public class JalviewModel { @XmlType(name = "", propOrder = { "annotationColours", "hiddenColumns", - "calcIdParam" + "calcIdParam", + "overview" }) public static class Viewport { @@ -3604,6 +4862,8 @@ public class JalviewModel { protected List hiddenColumns; @XmlElement(namespace = "www.jalview.org") protected List calcIdParam; + @XmlElement(namespace = "www.jalview.org") + protected JalviewModel.Viewport.Overview overview; @XmlAttribute(name = "conservationSelected") protected Boolean conservationSelected; @XmlAttribute(name = "pidSelected") @@ -3689,6 +4949,10 @@ public class JalviewModel { protected String id; @XmlAttribute(name = "complementId") protected String complementId; + @XmlAttribute(name = "showComplementFeatures") + protected Boolean showComplementFeatures; + @XmlAttribute(name = "showComplementFeaturesOnTop") + protected Boolean showComplementFeaturesOnTop; @XmlAttribute(name = "width") protected Integer width; @XmlAttribute(name = "height") @@ -3781,6 +5045,30 @@ public class JalviewModel { } /** + * Gets the value of the overview property. + * + * @return + * possible object is + * {@link JalviewModel.Viewport.Overview } + * + */ + public JalviewModel.Viewport.Overview getOverview() { + return overview; + } + + /** + * Sets the value of the overview property. + * + * @param value + * allowed object is + * {@link JalviewModel.Viewport.Overview } + * + */ + public void setOverview(JalviewModel.Viewport.Overview value) { + this.overview = value; + } + + /** * Gets the value of the conservationSelected property. * * @return @@ -4756,56 +6044,112 @@ public class JalviewModel { * {@link Integer } * */ - public void setTextColThreshold(Integer value) { - this.textColThreshold = value; + public void setTextColThreshold(Integer value) { + this.textColThreshold = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the complementId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getComplementId() { + return complementId; + } + + /** + * Sets the value of the complementId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setComplementId(String value) { + this.complementId = value; } /** - * Gets the value of the id property. + * Gets the value of the showComplementFeatures property. * * @return * possible object is - * {@link String } + * {@link Boolean } * */ - public String getId() { - return id; + public boolean isShowComplementFeatures() { + if (showComplementFeatures == null) { + return false; + } else { + return showComplementFeatures; + } } /** - * Sets the value of the id property. + * Sets the value of the showComplementFeatures property. * * @param value * allowed object is - * {@link String } + * {@link Boolean } * */ - public void setId(String value) { - this.id = value; + public void setShowComplementFeatures(Boolean value) { + this.showComplementFeatures = value; } /** - * Gets the value of the complementId property. + * Gets the value of the showComplementFeaturesOnTop property. * * @return * possible object is - * {@link String } + * {@link Boolean } * */ - public String getComplementId() { - return complementId; + public boolean isShowComplementFeaturesOnTop() { + if (showComplementFeaturesOnTop == null) { + return false; + } else { + return showComplementFeaturesOnTop; + } } /** - * Sets the value of the complementId property. + * Sets the value of the showComplementFeaturesOnTop property. * * @param value * allowed object is - * {@link String } + * {@link Boolean } * */ - public void setComplementId(String value) { - this.complementId = value; + public void setShowComplementFeaturesOnTop(Boolean value) { + this.showComplementFeaturesOnTop = value; } /** @@ -5085,6 +6429,270 @@ public class JalviewModel { } + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + *

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Overview { + + @XmlAttribute(name = "showHidden") + protected Boolean showHidden; + @XmlAttribute(name = "residueColour") + protected Integer residueColour; + @XmlAttribute(name = "gapColour") + protected Integer gapColour; + @XmlAttribute(name = "hiddenColour") + protected Integer hiddenColour; + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the showHidden property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowHidden() { + return showHidden; + } + + /** + * Sets the value of the showHidden property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowHidden(Boolean value) { + this.showHidden = value; + } + + /** + * Gets the value of the residueColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getResidueColour() { + return residueColour; + } + + /** + * Sets the value of the residueColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setResidueColour(Integer value) { + this.residueColour = value; + } + + /** + * Gets the value of the gapColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getGapColour() { + return gapColour; + } + + /** + * Sets the value of the gapColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGapColour(Integer value) { + this.gapColour = value; + } + + /** + * Gets the value of the hiddenColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHiddenColour() { + return hiddenColour; + } + + /** + * Sets the value of the hiddenColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHiddenColour(Integer value) { + this.hiddenColour = value; + } + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + } + } }