JAL-3081 schema and binding class changes to save annotation sort order

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 07dee98..777afa3 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -11,7 +11,7 @@
        GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>. 
        * The Jalview Authors are detailed in the 'AUTHORS' file. -->
 <!-- 
-       Java JAXB binding classes are generated by running command line tool xjc:
+       Java JAXB binding classes are generated by running JDK command line tool xjc:
            xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
        Note this also generates code for included schemas
 -->
@@ -418,6 +418,8 @@
                                                <xs:attribute name="followSelection" type="xs:boolean"
                                                        use="optional" default="true" />
                                                <xs:attribute name="showAnnotation" type="xs:boolean" />
+                                               <xs:attribute name="showAutocalcAbove" type="xs:boolean" />
+                                               <xs:attribute name="sortAnnotationsBy" type="xs:string" />
                                                <xs:attribute name="centreColumnLabels" type="xs:boolean"
                                                        use="optional" default="false" />
                                                <xs:attribute name="showGroupConservation" type="xs:boolean"

diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index ed57edc..e45675d 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: 2019.11.07 at 02:47:42 PM GMT 
 //
 
 
@@ -187,6 +187,8 @@ import javax.xml.datatype.XMLGregorianCalendar;
  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showAutocalcAbove" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="sortAnnotationsBy" type="{http://www.w3.org/2001/XMLSchema}string" />
  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
@@ -292,8 +294,8 @@ import javax.xml.datatype.XMLGregorianCalendar;
  *                     &lt;/element>
  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
  *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
@@ -3106,8 +3108,8 @@ public class JalviewModel {
      *         &lt;/element>
      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
      *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
@@ -3162,14 +3164,6 @@ public class JalviewModel {
         protected Boolean showLabels;
         @XmlAttribute(name = "linkToAllViews")
         protected Boolean linkToAllViews;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
         @XmlAttribute(name = "includeGaps")
         protected Boolean includeGaps;
         @XmlAttribute(name = "matchGaps")
@@ -3178,6 +3172,14 @@ public class JalviewModel {
         protected Boolean includeGappedColumns;
         @XmlAttribute(name = "denominateByShortestLength")
         protected Boolean denominateByShortestLength;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
         /**
          * Gets the value of the sequencePoint property.
@@ -3526,195 +3528,195 @@ public class JalviewModel {
         }
 
         /**
-         * Gets the value of the width property.
+         * Gets the value of the includeGaps property.
          * 
          * @return
          *     possible object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public Integer getWidth() {
-            return width;
+        public Boolean isIncludeGaps() {
+            return includeGaps;
         }
 
         /**
-         * Sets the value of the width property.
+         * Sets the value of the includeGaps property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public void setWidth(Integer value) {
-            this.width = value;
+        public void setIncludeGaps(Boolean value) {
+            this.includeGaps = value;
         }
 
         /**
-         * Gets the value of the height property.
+         * Gets the value of the matchGaps property.
          * 
          * @return
          *     possible object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public Integer getHeight() {
-            return height;
+        public Boolean isMatchGaps() {
+            return matchGaps;
         }
 
         /**
-         * Sets the value of the height property.
+         * Sets the value of the matchGaps property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public void setHeight(Integer value) {
-            this.height = value;
+        public void setMatchGaps(Boolean value) {
+            this.matchGaps = value;
         }
 
         /**
-         * Gets the value of the xpos property.
+         * Gets the value of the includeGappedColumns property.
          * 
          * @return
          *     possible object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public Integer getXpos() {
-            return xpos;
+        public Boolean isIncludeGappedColumns() {
+            return includeGappedColumns;
         }
 
         /**
-         * Sets the value of the xpos property.
+         * Sets the value of the includeGappedColumns property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public void setXpos(Integer value) {
-            this.xpos = value;
+        public void setIncludeGappedColumns(Boolean value) {
+            this.includeGappedColumns = value;
         }
 
         /**
-         * Gets the value of the ypos property.
+         * Gets the value of the denominateByShortestLength property.
          * 
          * @return
          *     possible object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public Integer getYpos() {
-            return ypos;
+        public Boolean isDenominateByShortestLength() {
+            return denominateByShortestLength;
         }
 
         /**
-         * Sets the value of the ypos property.
+         * Sets the value of the denominateByShortestLength property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Integer }
+         *     {@link Boolean }
          *     
          */
-        public void setYpos(Integer value) {
-            this.ypos = value;
+        public void setDenominateByShortestLength(Boolean value) {
+            this.denominateByShortestLength = value;
         }
 
         /**
-         * Gets the value of the includeGaps property.
+         * Gets the value of the width property.
          * 
          * @return
          *     possible object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public Boolean isIncludeGaps() {
-            return includeGaps;
+        public Integer getWidth() {
+            return width;
         }
 
         /**
-         * Sets the value of the includeGaps property.
+         * Sets the value of the width property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public void setIncludeGaps(Boolean value) {
-            this.includeGaps = value;
+        public void setWidth(Integer value) {
+            this.width = value;
         }
 
         /**
-         * Gets the value of the matchGaps property.
+         * Gets the value of the height property.
          * 
          * @return
          *     possible object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public Boolean isMatchGaps() {
-            return matchGaps;
+        public Integer getHeight() {
+            return height;
         }
 
         /**
-         * Sets the value of the matchGaps property.
+         * Sets the value of the height property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public void setMatchGaps(Boolean value) {
-            this.matchGaps = value;
+        public void setHeight(Integer value) {
+            this.height = value;
         }
 
         /**
-         * Gets the value of the includeGappedColumns property.
+         * Gets the value of the xpos property.
          * 
          * @return
          *     possible object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public Boolean isIncludeGappedColumns() {
-            return includeGappedColumns;
+        public Integer getXpos() {
+            return xpos;
         }
 
         /**
-         * Sets the value of the includeGappedColumns property.
+         * Sets the value of the xpos property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public void setIncludeGappedColumns(Boolean value) {
-            this.includeGappedColumns = value;
+        public void setXpos(Integer value) {
+            this.xpos = value;
         }
 
         /**
-         * Gets the value of the denominateByShortestLength property.
+         * Gets the value of the ypos property.
          * 
          * @return
          *     possible object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public Boolean isDenominateByShortestLength() {
-            return denominateByShortestLength;
+        public Integer getYpos() {
+            return ypos;
         }
 
         /**
-         * Sets the value of the denominateByShortestLength property.
+         * Sets the value of the ypos property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public void setDenominateByShortestLength(Boolean value) {
-            this.denominateByShortestLength = value;
+        public void setYpos(Integer value) {
+            this.ypos = value;
         }
 
 
@@ -4787,6 +4789,8 @@ public class JalviewModel {
      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showAutocalcAbove" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="sortAnnotationsBy" type="{http://www.w3.org/2001/XMLSchema}string" />
      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
@@ -4869,6 +4873,10 @@ public class JalviewModel {
         protected Boolean followSelection;
         @XmlAttribute(name = "showAnnotation")
         protected Boolean showAnnotation;
+        @XmlAttribute(name = "showAutocalcAbove")
+        protected Boolean showAutocalcAbove;
+        @XmlAttribute(name = "sortAnnotationsBy")
+        protected String sortAnnotationsBy;
         @XmlAttribute(name = "centreColumnLabels")
         protected Boolean centreColumnLabels;
         @XmlAttribute(name = "showGroupConservation")
@@ -5498,6 +5506,54 @@ public class JalviewModel {
         }
 
         /**
+         * Gets the value of the showAutocalcAbove property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowAutocalcAbove() {
+            return showAutocalcAbove;
+        }
+
+        /**
+         * Sets the value of the showAutocalcAbove property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowAutocalcAbove(Boolean value) {
+            this.showAutocalcAbove = value;
+        }
+
+        /**
+         * Gets the value of the sortAnnotationsBy property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSortAnnotationsBy() {
+            return sortAnnotationsBy;
+        }
+
+        /**
+         * Sets the value of the sortAnnotationsBy property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSortAnnotationsBy(String value) {
+            this.sortAnnotationsBy = value;
+        }
+
+        /**
          * Gets the value of the centreColumnLabels property.
          * 
          * @return