- public void setTextCol1(Integer value)
- {
- this.textCol1 = value;
- }
-
- /**
- * Gets the value of the textCol2 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol2()
- {
- return textCol2;
- }
-
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol2(Integer value)
- {
- this.textCol2 = value;
- }
-
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextColThreshold()
- {
- return textColThreshold;
- }
-
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value)
- {
- this.textColThreshold = value;
- }
-
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowUnconserved()
- {
- return showUnconserved;
- }
-
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value)
- {
- this.showUnconserved = value;
- }
-
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus()
- {
- if (ignoreGapsinConsensus == null)
- {
- return true;
- }
- else
- {
- return ignoreGapsinConsensus;
- }
- }
-
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value)
- {
- this.ignoreGapsinConsensus = value;
- }
-
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram()
- {
- if (showConsensusHistogram == null)
- {
- return true;
- }
- else
- {
- return showConsensusHistogram;
- }
- }
-
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value)
- {
- this.showConsensusHistogram = value;
- }
-
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo()
- {
- if (showSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return showSequenceLogo;
- }
- }
-
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value)
- {
- this.showSequenceLogo = value;
- }
-
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo()
- {
- if (normaliseSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return normaliseSequenceLogo;
- }
- }
-
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value)
- {
- this.normaliseSequenceLogo = value;
- }
-
- /**
- * Gets the value of the 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;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <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>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "features", "pdbids", "hiddenSequences", "rnaViewer" })
- public static class JSeq
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<Feature> features;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids> pdbids;
-
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List<Integer> hiddenSequences;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
-
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
-
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
-
- /**
- * Gets the value of the features property.
- *
- * <p>
- * 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
- * <CODE>set</CODE> method for the features property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getFeatures().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Feature }
- *
- *
- */
- public List<Feature> getFeatures()
- {
- if (features == null)
- {
- features = new ArrayList<Feature>();
- }
- return this.features;
- }
-
- /**
- * Gets the value of the pdbids property.
- *
- * <p>
- * 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
- * <CODE>set</CODE> method for the pdbids property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getPdbids().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids> getPdbids()
- {
- if (pdbids == null)
- {
- pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
- }
- return this.pdbids;
- }
-
- /**
- * Gets the value of the hiddenSequences property.
- *
- * <p>
- * 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
- * <CODE>set</CODE> method for the hiddenSequences property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getHiddenSequences().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getHiddenSequences()
- {
- if (hiddenSequences == null)
- {
- hiddenSequences = new ArrayList<Integer>();
- }
- return this.hiddenSequences;
- }
-
- /**
- * Gets the value of the rnaViewer property.
- *
- * <p>
- * 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
- * <CODE>set</CODE> method for the rnaViewer property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getRnaViewer().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
- {
- if (rnaViewer == null)
- {
- rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
- }
- return this.rnaViewer;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColour(Integer value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the hidden property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isHidden()
- {
- return hidden;
- }
-
- /**
- * Sets the value of the hidden property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setHidden(Boolean value)
- {
- this.hidden = value;
- }
-
- /**
- * Gets the value of the viewreference property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isViewreference()
- {
- return viewreference;
- }
-
- /**
- * Sets the value of the viewreference property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setViewreference(Boolean value)
- {
- this.viewreference = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <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>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "structureState" })
- public static class Pdbids extends Pdbentry
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p>
- * 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
- * <CODE>set</CODE> method for the structureState property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getStructureState().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
- {
- if (structureState == null)
- {
- structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <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>
- * </pre>
- *
- *
- */
- @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;