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

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

diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java
index 23aa9ac..65e65f6 100644 (file)
--- a/src/jalview/xml/binding/jalview/MatrixType.java
+++ b/src/jalview/xml/binding/jalview/MatrixType.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;
@@ -17,33 +17,37 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
 /**
- * <p>
- * Java class for MatrixType complex type.
+ * Represents matrix data imported to Jalview, and the results of any derived
+ * calculations (independent of a particular view on the matrix).
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
  * 
- * <pre>
- * &lt;complexType name="MatrixType">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="elements" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         &lt;element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- *         &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
- *       &lt;/sequence>
- *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- *       &lt;attribute name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- *       &lt;attribute name="treeMethod" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" />
- *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;p&gt;Java class for MatrixType complex type.
+ * 
+ * &lt;p&gt;The following schema fragment specifies the expected content
+ * contained within this class.
+ * 
+ * &lt;pre&gt; &amp;lt;complexType name="MatrixType"&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="elements"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt; &amp;lt;element
+ * name="groups" type="{http://www.w3.org/2001/XMLSchema}string"
+ * maxOccurs="unbounded" minOccurs="0"/&amp;gt; &amp;lt;element name="newick"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"
+ * minOccurs="0"/&amp;gt; &amp;lt;element name="property"
+ * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded"
+ * minOccurs="0"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute
+ * name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&amp;gt; &amp;lt;attribute name="rows" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt; &amp;lt;attribute
+ * name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer"
+ * /&amp;gt; &amp;lt;attribute name="treeMethod"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
+ * name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" /&amp;gt;
+ * &amp;lt;attribute name="id" use="required"
+ * 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;
  * 
  * 
  */
@@ -79,7 +83,7 @@ public class MatrixType
   @XmlAttribute(name = "cutHeight")
   protected Double cutHeight;
 
-  @XmlAttribute(name = "id")
+  @XmlAttribute(name = "id", required = true)
   protected String id;
 
   /**
@@ -108,22 +112,17 @@ public class MatrixType
   /**
    * Gets the value of the groups 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 groups property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &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
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the groups property.
    * 
-   * <pre>
-   * getGroups().add(newItem);
-   * </pre>
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getGroups().add(newItem); &lt;/pre&gt;
    * 
    * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
+   * {@link String }
    * 
    * 
    */
@@ -139,22 +138,17 @@ public class MatrixType
   /**
    * Gets the value of the newick 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 newick property.
+   * &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
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the newick 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;
+   * getNewick().add(newItem); &lt;/pre&gt;
    * 
-   * <pre>
-   * getNewick().add(newItem);
-   * </pre>
    * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
+   * {@link String }
    * 
    * 
    */
@@ -170,22 +164,17 @@ public class MatrixType
   /**
    * Gets the value of the property 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 property property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &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
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the property property.
    * 
-   * <pre>
-   * getProperty().add(newItem);
-   * </pre>
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getProperty().add(newItem); &lt;/pre&gt;
    * 
    * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Property }
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
+   * {@link Property }
    * 
    * 
    */