JAL-4366 avoid corrupting map when no complete mapping available for chain to sequence

[jalview.git] / src / jalview / xml / binding / jalview / FeatureMatcherSet.java

diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index a071af8..cf81588 100644 (file)
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -1,8 +1,8 @@
 //
-// 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> 
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
+// See https://eclipse-ee4j.github.io/jaxb-ri 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.03.17 at 05:31:44 PM GMT 
+// Generated on: 2023.11.01 at 07:03:09 PM GMT 
 //
 
 package jalview.xml.binding.jalview;
@@ -18,36 +18,27 @@ import javax.xml.bind.annotation.XmlType;
 /**
  * A feature match condition, which may be simple or compound
  * 
- * <p>
- * Java class for FeatureMatcherSet complex type.
+ * &lt;p&gt;Java class for FeatureMatcherSet complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content
+ * contained within this class.
  * 
- * <pre>
- * &lt;complexType name="FeatureMatcherSet">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;choice>
- *         &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
- *         &lt;element name="compoundMatcher">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;sequence>
- *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
- *                 &lt;/sequence>
- *                 &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/choice>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt; &amp;lt;complexType name="FeatureMatcherSet"&amp;gt;
+ * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ * &amp;lt;choice&amp;gt; &amp;lt;element name="matchCondition"
+ * type="{www.jalview.org/colours}FeatureMatcher"/&amp;gt; &amp;lt;element
+ * name="compoundMatcher"&amp;gt; &amp;lt;complexType&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="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
+ * minOccurs="2"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="and"
+ * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;/choice&amp;gt;
+ * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
  * 
  * 
  */
@@ -113,25 +104,20 @@ public class FeatureMatcherSet
   }
 
   /**
-   * <p>
-   * Java class for anonymous complex type.
+   * &lt;p&gt;Java class for anonymous complex type.
    * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
+   * &lt;p&gt;The following schema fragment specifies the expected content
+   * contained within this class.
    * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
-   *       &lt;/sequence>
-   *       &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
+   * &lt;pre&gt; &amp;lt;complexType&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="matcherSet"
+   * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
+   * minOccurs="2"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute
+   * name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
+   * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
+   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
    * 
    * 
    */
@@ -149,22 +135,16 @@ public class FeatureMatcherSet
     /**
      * Gets the value of the matcherSet 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
+     * &lt;p&gt; 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 matcherSet property.
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the matcherSet property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getMatcherSet().add(newItem); &lt;/pre&gt;
      * 
-     * <pre>
-     * getMatcherSet().add(newItem);
-     * </pre>
      * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link FeatureMatcherSet }
      * 
      *