X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fxml%2Fbinding%2Funiprot%2FFeatureType.java;h=791aa0ecd0ecf01024d7f5a8e7cac6e32e978b7f;hb=7b5d11bce39b76612773aa4d606ffbe55bb86a02;hp=d1ba929b8abc33781862a40a4a98fd15994b318e;hpb=7b32d373b60d0af55481cfd6d377b2cc1ec035c0;p=jalview.git diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java index d1ba929..791aa0e 100644 --- a/src/jalview/xml/binding/uniprot/FeatureType.java +++ b/src/jalview/xml/binding/uniprot/FeatureType.java @@ -1,11 +1,10 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 -// See https://eclipse-ee4j.github.io/jaxb-ri +// 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: 2022.02.07 at 04:44:21 PM GMT +// Generated on: 2023.05.13 at 06:58:42 PM BST // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,338 +15,345 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - * Describes different types of sequence annotations. - * Equivalent to the flat file FT-line. + * Describes different types of sequence annotations. Equivalent to the flat + * file FT-line. * - * <p>Java class for featureType complex type. + *

+ * Java class for featureType complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * - * <pre> - * &lt;complexType name="featureType"&gt; - * &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; - * &lt;element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; - * &lt;element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; - * &lt;element name="location" type="{http://uniprot.org/uniprot}locationType"/&gt; - * &lt;/sequence&gt; - * &lt;attribute name="type" use="required"&gt; - * &lt;simpleType&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; - * &lt;enumeration value="active site"/&gt; - * &lt;enumeration value="binding site"/&gt; - * &lt;enumeration value="calcium-binding region"/&gt; - * &lt;enumeration value="chain"/&gt; - * &lt;enumeration value="coiled-coil region"/&gt; - * &lt;enumeration value="compositionally biased region"/&gt; - * &lt;enumeration value="cross-link"/&gt; - * &lt;enumeration value="disulfide bond"/&gt; - * &lt;enumeration value="DNA-binding region"/&gt; - * &lt;enumeration value="domain"/&gt; - * &lt;enumeration value="glycosylation site"/&gt; - * &lt;enumeration value="helix"/&gt; - * &lt;enumeration value="initiator methionine"/&gt; - * &lt;enumeration value="lipid moiety-binding region"/&gt; - * &lt;enumeration value="metal ion-binding site"/&gt; - * &lt;enumeration value="modified residue"/&gt; - * &lt;enumeration value="mutagenesis site"/&gt; - * &lt;enumeration value="non-consecutive residues"/&gt; - * &lt;enumeration value="non-terminal residue"/&gt; - * &lt;enumeration value="nucleotide phosphate-binding region"/&gt; - * &lt;enumeration value="peptide"/&gt; - * &lt;enumeration value="propeptide"/&gt; - * &lt;enumeration value="region of interest"/&gt; - * &lt;enumeration value="repeat"/&gt; - * &lt;enumeration value="non-standard amino acid"/&gt; - * &lt;enumeration value="sequence conflict"/&gt; - * &lt;enumeration value="sequence variant"/&gt; - * &lt;enumeration value="short sequence motif"/&gt; - * &lt;enumeration value="signal peptide"/&gt; - * &lt;enumeration value="site"/&gt; - * &lt;enumeration value="splice variant"/&gt; - * &lt;enumeration value="strand"/&gt; - * &lt;enumeration value="topological domain"/&gt; - * &lt;enumeration value="transit peptide"/&gt; - * &lt;enumeration value="transmembrane region"/&gt; - * &lt;enumeration value="turn"/&gt; - * &lt;enumeration value="unsure residue"/&gt; - * &lt;enumeration value="zinc finger region"/&gt; - * &lt;enumeration value="intramembrane region"/&gt; - * &lt;/restriction&gt; - * &lt;/simpleType&gt; - * &lt;/attribute&gt; - * &lt;attribute name="status"&gt; - * &lt;simpleType&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; - * &lt;enumeration value="by similarity"/&gt; - * &lt;enumeration value="probable"/&gt; - * &lt;enumeration value="potential"/&gt; - * &lt;/restriction&gt; - * &lt;/simpleType&gt; - * &lt;/attribute&gt; - * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; - * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; - * &lt;/complexContent&gt; - * &lt;/complexType&gt; - * </pre> + * 

+ * <complexType name="featureType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="location" type="{http://uniprot.org/uniprot}locationType"/>
+ *       </sequence>
+ *       <attribute name="type" use="required">
+ *         <simpleType>
+ *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *             <enumeration value="active site"/>
+ *             <enumeration value="binding site"/>
+ *             <enumeration value="calcium-binding region"/>
+ *             <enumeration value="chain"/>
+ *             <enumeration value="coiled-coil region"/>
+ *             <enumeration value="compositionally biased region"/>
+ *             <enumeration value="cross-link"/>
+ *             <enumeration value="disulfide bond"/>
+ *             <enumeration value="DNA-binding region"/>
+ *             <enumeration value="domain"/>
+ *             <enumeration value="glycosylation site"/>
+ *             <enumeration value="helix"/>
+ *             <enumeration value="initiator methionine"/>
+ *             <enumeration value="lipid moiety-binding region"/>
+ *             <enumeration value="metal ion-binding site"/>
+ *             <enumeration value="modified residue"/>
+ *             <enumeration value="mutagenesis site"/>
+ *             <enumeration value="non-consecutive residues"/>
+ *             <enumeration value="non-terminal residue"/>
+ *             <enumeration value="nucleotide phosphate-binding region"/>
+ *             <enumeration value="peptide"/>
+ *             <enumeration value="propeptide"/>
+ *             <enumeration value="region of interest"/>
+ *             <enumeration value="repeat"/>
+ *             <enumeration value="non-standard amino acid"/>
+ *             <enumeration value="sequence conflict"/>
+ *             <enumeration value="sequence variant"/>
+ *             <enumeration value="short sequence motif"/>
+ *             <enumeration value="signal peptide"/>
+ *             <enumeration value="site"/>
+ *             <enumeration value="splice variant"/>
+ *             <enumeration value="strand"/>
+ *             <enumeration value="topological domain"/>
+ *             <enumeration value="transit peptide"/>
+ *             <enumeration value="transmembrane region"/>
+ *             <enumeration value="turn"/>
+ *             <enumeration value="unsure residue"/>
+ *             <enumeration value="zinc finger region"/>
+ *             <enumeration value="intramembrane region"/>
+ *           </restriction>
+ *         </simpleType>
+ *       </attribute>
+ *       <attribute name="status">
+ *         <simpleType>
+ *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *             <enumeration value="by similarity"/>
+ *             <enumeration value="probable"/>
+ *             <enumeration value="potential"/>
+ *           </restriction>
+ *         </simpleType>
+ *       </attribute>
+ *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "featureType", propOrder = { - "original", - "variation", - "location" -}) -public class FeatureType { +@XmlType( + name = "featureType", + propOrder = + { "original", "variation", "location" }) +public class FeatureType +{ - protected String original; - protected List variation; - @XmlElement(required = true) - protected LocationType location; - @XmlAttribute(name = "type", required = true) - protected String type; - @XmlAttribute(name = "status") - protected String status; - @XmlAttribute(name = "id") - protected String id; - @XmlAttribute(name = "description") - protected String description; - @XmlAttribute(name = "evidence") - protected List evidence; - @XmlAttribute(name = "ref") - protected String ref; + protected String original; - /** - * Gets the value of the original property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getOriginal() { - return original; - } + protected List variation; - /** - * Sets the value of the original property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setOriginal(String value) { - this.original = value; - } + @XmlElement(required = true) + protected LocationType location; - /** - * Gets the value of the variation 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 variation property. - * - * <p> - * For example, to add a new item, do as follows: - * <pre> - * getVariation().add(newItem); - * </pre> - * - * - * <p> - * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getVariation() { - if (variation == null) { - variation = new ArrayList(); - } - return this.variation; - } + @XmlAttribute(name = "type", required = true) + protected String type; - /** - * Gets the value of the location property. - * - * @return - * possible object is - * {@link LocationType } - * - */ - public LocationType getLocation() { - return location; - } + @XmlAttribute(name = "status") + protected String status; - /** - * Sets the value of the location property. - * - * @param value - * allowed object is - * {@link LocationType } - * - */ - public void setLocation(LocationType value) { - this.location = value; - } + @XmlAttribute(name = "id") + protected String id; - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } + @XmlAttribute(name = "description") + protected String description; - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } + @XmlAttribute(name = "evidence") + protected List evidence; - /** - * Gets the value of the status property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getStatus() { - return status; - } + @XmlAttribute(name = "ref") + protected String ref; - /** - * Sets the value of the status property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setStatus(String value) { - this.status = value; - } + /** + * Gets the value of the original property. + * + * @return possible object is {@link String } + * + */ + public String getOriginal() + { + return original; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * Sets the value of the original property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setOriginal(String value) + { + this.original = value; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; + /** + * Gets the value of the variation 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 variation property. + * + *

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

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getVariation() + { + if (variation == null) + { + variation = new ArrayList(); } + return this.variation; + } - /** - * Gets the value of the description property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDescription() { - return description; - } + /** + * Gets the value of the location property. + * + * @return possible object is {@link LocationType } + * + */ + public LocationType getLocation() + { + return location; + } - /** - * Sets the value of the description property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDescription(String value) { - this.description = value; - } + /** + * Sets the value of the location property. + * + * @param value + * allowed object is {@link LocationType } + * + */ + public void setLocation(LocationType value) + { + this.location = value; + } - /** - * Gets the value of the evidence 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 evidence property. - * - * <p> - * For example, to add a new item, do as follows: - * <pre> - * getEvidence().add(newItem); - * </pre> - * - * - * <p> - * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } - /** - * Gets the value of the ref property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getRef() { - return ref; - } + /** + * 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 status property. + * + * @return possible object is {@link String } + * + */ + public String getStatus() + { + return status; + } + + /** + * Sets the value of the status property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setStatus(String value) + { + this.status = value; + } - /** - * Sets the value of the ref property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setRef(String value) { - this.ref = 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 description property. + * + * @return possible object is {@link String } + * + */ + public String getDescription() + { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDescription(String value) + { + this.description = value; + } + + /** + * Gets the value of the evidence 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 evidence property. + * + *

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

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } + + /** + * Gets the value of the ref property. + * + * @return possible object is {@link String } + * + */ + public String getRef() + { + return ref; + } + + /** + * Sets the value of the ref property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setRef(String value) + { + this.ref = value; + } }