Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index ed57edc..e1a7b05 100644 (file)
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -2,7 +2,7 @@
 // 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: 2018.12.20 at 11:47:26 AM GMT 
+// Generated on: 2019.07.10 at 12:10:00 PM BST 
 //
 
 
@@ -96,6 +96,7 @@ import javax.xml.datatype.XMLGregorianCalendar;
  *                         &lt;/complexContent>
  *                       &lt;/complexType>
  *                     &lt;/element>
+ *                     &lt;element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
  *                   &lt;/sequence>
  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
@@ -208,6 +209,8 @@ import javax.xml.datatype.XMLGregorianCalendar;
  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  *                 &lt;/restriction>
  *               &lt;/complexContent>
  *             &lt;/complexType>
@@ -1943,6 +1946,7 @@ public class JalviewModel {
      *             &lt;/complexContent>
      *           &lt;/complexType>
      *         &lt;/element>
+     *         &lt;element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
      *       &lt;/sequence>
      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
@@ -1962,7 +1966,8 @@ public class JalviewModel {
         "features",
         "pdbids",
         "hiddenSequences",
-        "rnaViewer"
+        "rnaViewer",
+        "hmmerProfile"
     })
     public static class JSeq {
 
@@ -1974,6 +1979,8 @@ public class JalviewModel {
         protected List<Integer> hiddenSequences;
         @XmlElement(namespace = "www.jalview.org")
         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
+        @XmlElement(namespace = "www.jalview.org")
+        protected String hmmerProfile;
         @XmlAttribute(name = "colour")
         protected Integer colour;
         @XmlAttribute(name = "start", required = true)
@@ -2104,6 +2111,30 @@ public class JalviewModel {
         }
 
         /**
+         * Gets the value of the hmmerProfile property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getHmmerProfile() {
+            return hmmerProfile;
+        }
+
+        /**
+         * Sets the value of the hmmerProfile property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setHmmerProfile(String value) {
+            this.hmmerProfile = value;
+        }
+
+        /**
          * Gets the value of the colour property.
          * 
          * @return
@@ -4808,6 +4839,8 @@ public class JalviewModel {
      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
      *     &lt;/restriction>
      *   &lt;/complexContent>
      * &lt;/complexType>
@@ -4914,6 +4947,10 @@ public class JalviewModel {
         protected String id;
         @XmlAttribute(name = "complementId")
         protected String complementId;
+        @XmlAttribute(name = "showComplementFeatures")
+        protected Boolean showComplementFeatures;
+        @XmlAttribute(name = "showComplementFeaturesOnTop")
+        protected Boolean showComplementFeaturesOnTop;
         @XmlAttribute(name = "width")
         protected Integer width;
         @XmlAttribute(name = "height")
@@ -6034,6 +6071,62 @@ public class JalviewModel {
         }
 
         /**
+         * Gets the value of the showComplementFeatures property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeatures() {
+            if (showComplementFeatures == null) {
+                return false;
+            } else {
+                return showComplementFeatures;
+            }
+        }
+
+        /**
+         * Sets the value of the showComplementFeatures property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeatures(Boolean value) {
+            this.showComplementFeatures = value;
+        }
+
+        /**
+         * Gets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeaturesOnTop() {
+            if (showComplementFeaturesOnTop == null) {
+                return false;
+            } else {
+                return showComplementFeaturesOnTop;
+            }
+        }
+
+        /**
+         * Sets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeaturesOnTop(Boolean value) {
+            this.showComplementFeaturesOnTop = value;
+        }
+
+        /**
          * Gets the value of the width property.
          * 
          * @return