JAL-1713 update from Jalview 2.11.3 develop

[jalview.git] / src / jalview / xml / binding / uniprot / FeatureType.java

diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java
index d1ba929..0a6f7fe 100644 (file)
--- a/src/jalview/xml/binding/uniprot/FeatureType.java
+++ b/src/jalview/xml/binding/uniprot/FeatureType.java
@@ -1,8 +1,8 @@
 //
-// 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // 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: 2023.01.31 at 04:07:10 PM GMT 
 //
 
 
@@ -21,81 +21,81 @@ import javax.xml.bind.annotation.XmlType;
  * Describes different types of sequence annotations.
  *             Equivalent to the flat file FT-line.
  * 
- * &lt;p&gt;Java class for featureType complex type.
+ * <p>Java class for featureType complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt;
- * &amp;lt;complexType name="featureType"&amp;gt;
- *   &amp;lt;complexContent&amp;gt;
- *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- *       &amp;lt;sequence&amp;gt;
- *         &amp;lt;element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
- *         &amp;lt;element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
- *         &amp;lt;element name="location" type="{http://uniprot.org/uniprot}locationType"/&amp;gt;
- *       &amp;lt;/sequence&amp;gt;
- *       &amp;lt;attribute name="type" use="required"&amp;gt;
- *         &amp;lt;simpleType&amp;gt;
- *           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
- *             &amp;lt;enumeration value="active site"/&amp;gt;
- *             &amp;lt;enumeration value="binding site"/&amp;gt;
- *             &amp;lt;enumeration value="calcium-binding region"/&amp;gt;
- *             &amp;lt;enumeration value="chain"/&amp;gt;
- *             &amp;lt;enumeration value="coiled-coil region"/&amp;gt;
- *             &amp;lt;enumeration value="compositionally biased region"/&amp;gt;
- *             &amp;lt;enumeration value="cross-link"/&amp;gt;
- *             &amp;lt;enumeration value="disulfide bond"/&amp;gt;
- *             &amp;lt;enumeration value="DNA-binding region"/&amp;gt;
- *             &amp;lt;enumeration value="domain"/&amp;gt;
- *             &amp;lt;enumeration value="glycosylation site"/&amp;gt;
- *             &amp;lt;enumeration value="helix"/&amp;gt;
- *             &amp;lt;enumeration value="initiator methionine"/&amp;gt;
- *             &amp;lt;enumeration value="lipid moiety-binding region"/&amp;gt;
- *             &amp;lt;enumeration value="metal ion-binding site"/&amp;gt;
- *             &amp;lt;enumeration value="modified residue"/&amp;gt;
- *             &amp;lt;enumeration value="mutagenesis site"/&amp;gt;
- *             &amp;lt;enumeration value="non-consecutive residues"/&amp;gt;
- *             &amp;lt;enumeration value="non-terminal residue"/&amp;gt;
- *             &amp;lt;enumeration value="nucleotide phosphate-binding region"/&amp;gt;
- *             &amp;lt;enumeration value="peptide"/&amp;gt;
- *             &amp;lt;enumeration value="propeptide"/&amp;gt;
- *             &amp;lt;enumeration value="region of interest"/&amp;gt;
- *             &amp;lt;enumeration value="repeat"/&amp;gt;
- *             &amp;lt;enumeration value="non-standard amino acid"/&amp;gt;
- *             &amp;lt;enumeration value="sequence conflict"/&amp;gt;
- *             &amp;lt;enumeration value="sequence variant"/&amp;gt;
- *             &amp;lt;enumeration value="short sequence motif"/&amp;gt;
- *             &amp;lt;enumeration value="signal peptide"/&amp;gt;
- *             &amp;lt;enumeration value="site"/&amp;gt;
- *             &amp;lt;enumeration value="splice variant"/&amp;gt;
- *             &amp;lt;enumeration value="strand"/&amp;gt;
- *             &amp;lt;enumeration value="topological domain"/&amp;gt;
- *             &amp;lt;enumeration value="transit peptide"/&amp;gt;
- *             &amp;lt;enumeration value="transmembrane region"/&amp;gt;
- *             &amp;lt;enumeration value="turn"/&amp;gt;
- *             &amp;lt;enumeration value="unsure residue"/&amp;gt;
- *             &amp;lt;enumeration value="zinc finger region"/&amp;gt;
- *             &amp;lt;enumeration value="intramembrane region"/&amp;gt;
- *           &amp;lt;/restriction&amp;gt;
- *         &amp;lt;/simpleType&amp;gt;
- *       &amp;lt;/attribute&amp;gt;
- *       &amp;lt;attribute name="status"&amp;gt;
- *         &amp;lt;simpleType&amp;gt;
- *           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
- *             &amp;lt;enumeration value="by similarity"/&amp;gt;
- *             &amp;lt;enumeration value="probable"/&amp;gt;
- *             &amp;lt;enumeration value="potential"/&amp;gt;
- *           &amp;lt;/restriction&amp;gt;
- *         &amp;lt;/simpleType&amp;gt;
- *       &amp;lt;/attribute&amp;gt;
- *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- *       &amp;lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- *       &amp;lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&amp;gt;
- *       &amp;lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- *     &amp;lt;/restriction&amp;gt;
- *   &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt;
- * &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="featureType">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element name="location" type="{http://uniprot.org/uniprot}locationType"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="type" use="required">
+ *         &lt;simpleType>
+ *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *             &lt;enumeration value="active site"/>
+ *             &lt;enumeration value="binding site"/>
+ *             &lt;enumeration value="calcium-binding region"/>
+ *             &lt;enumeration value="chain"/>
+ *             &lt;enumeration value="coiled-coil region"/>
+ *             &lt;enumeration value="compositionally biased region"/>
+ *             &lt;enumeration value="cross-link"/>
+ *             &lt;enumeration value="disulfide bond"/>
+ *             &lt;enumeration value="DNA-binding region"/>
+ *             &lt;enumeration value="domain"/>
+ *             &lt;enumeration value="glycosylation site"/>
+ *             &lt;enumeration value="helix"/>
+ *             &lt;enumeration value="initiator methionine"/>
+ *             &lt;enumeration value="lipid moiety-binding region"/>
+ *             &lt;enumeration value="metal ion-binding site"/>
+ *             &lt;enumeration value="modified residue"/>
+ *             &lt;enumeration value="mutagenesis site"/>
+ *             &lt;enumeration value="non-consecutive residues"/>
+ *             &lt;enumeration value="non-terminal residue"/>
+ *             &lt;enumeration value="nucleotide phosphate-binding region"/>
+ *             &lt;enumeration value="peptide"/>
+ *             &lt;enumeration value="propeptide"/>
+ *             &lt;enumeration value="region of interest"/>
+ *             &lt;enumeration value="repeat"/>
+ *             &lt;enumeration value="non-standard amino acid"/>
+ *             &lt;enumeration value="sequence conflict"/>
+ *             &lt;enumeration value="sequence variant"/>
+ *             &lt;enumeration value="short sequence motif"/>
+ *             &lt;enumeration value="signal peptide"/>
+ *             &lt;enumeration value="site"/>
+ *             &lt;enumeration value="splice variant"/>
+ *             &lt;enumeration value="strand"/>
+ *             &lt;enumeration value="topological domain"/>
+ *             &lt;enumeration value="transit peptide"/>
+ *             &lt;enumeration value="transmembrane region"/>
+ *             &lt;enumeration value="turn"/>
+ *             &lt;enumeration value="unsure residue"/>
+ *             &lt;enumeration value="zinc finger region"/>
+ *             &lt;enumeration value="intramembrane region"/>
+ *           &lt;/restriction>
+ *         &lt;/simpleType>
+ *       &lt;/attribute>
+ *       &lt;attribute name="status">
+ *         &lt;simpleType>
+ *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *             &lt;enumeration value="by similarity"/>
+ *             &lt;enumeration value="probable"/>
+ *             &lt;enumeration value="potential"/>
+ *           &lt;/restriction>
+ *         &lt;/simpleType>
+ *       &lt;/attribute>
+ *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
@@ -151,20 +151,20 @@ public class FeatureType {
     /**
      * Gets the value of the variation property.
      * 
-     * &lt;p&gt;
+     * <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 &lt;CODE&gt;set&lt;/CODE&gt; method for the variation property.
+     * This is why there is not a <CODE>set</CODE> method for the variation property.
      * 
-     * &lt;p&gt;
+     * <p>
      * For example, to add a new item, do as follows:
-     * &lt;pre&gt;
+     * <pre>
      *    getVariation().add(newItem);
-     * &lt;/pre&gt;
+     * </pre>
      * 
      * 
-     * &lt;p&gt;
+     * <p>
      * Objects of the following type(s) are allowed in the list
      * {@link String }
      * 
@@ -300,20 +300,20 @@ public class FeatureType {
     /**
      * Gets the value of the evidence property.
      * 
-     * &lt;p&gt;
+     * <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 &lt;CODE&gt;set&lt;/CODE&gt; method for the evidence property.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
      * 
-     * &lt;p&gt;
+     * <p>
      * For example, to add a new item, do as follows:
-     * &lt;pre&gt;
+     * <pre>
      *    getEvidence().add(newItem);
-     * &lt;/pre&gt;
+     * </pre>
      * 
      * 
-     * &lt;p&gt;
+     * <p>
      * Objects of the following type(s) are allowed in the list
      * {@link Integer }
      *