JAL-4020 class reformatting

[jalview.git] / schemas / jalview.xsd

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 109b83b..1d2235e 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -10,6 +10,11 @@
        Public License for more details. * * You should have received a copy of the 
        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:
+           xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+       Note this also generates code for included schemas
+-->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
        xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours"
        xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset"
@@ -21,6 +26,7 @@
                schemaLocation="JalviewUserColours.xsd" />
        <xs:import namespace="www.jalview.org/xml/wsparamset"
                schemaLocation="JalviewWsParamSet.xsd" />
+       <xs:element name="JalviewModel" type="jv:JalviewModel" />
        <xs:complexType name="JalviewModel">
                <xs:sequence>
                        <xs:element name="creationDate" type="xs:dateTime" />
@@ -457,6 +463,8 @@
                                                                </xs:documentation>
                                                        </xs:annotation>
                                                </xs:attribute>
+                                               <xs:attribute name="showComplementFeatures" type="xs:boolean" use="optional" default="false" />
+                                               <xs:attribute name="showComplementFeaturesOnTop" type="xs:boolean" use="optional" default="false" />
                                        </xs:complexType>
                                </xs:element>
                                <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
@@ -699,27 +707,21 @@
                        </xs:documentation>
                </xs:annotation>
                <xs:sequence>
-                       <xs:element name="details" type="xs:string">
-                               <xs:annotation>
-                                       <xs:documentation>
-                                               The text report of the calculation
-                                       </xs:documentation>
-                               </xs:annotation>
-                       </xs:element>
                        <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
+                       <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
                        <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
-                       <xs:element name="eigenMatrixD" type="jv:DoubleVector" />
-                       <xs:element name="eigenMatrixE" type="jv:DoubleVector" />
                </xs:sequence>
        </xs:complexType>
        <xs:complexType name="DoubleVector">
                <xs:sequence>
-                       <xs:element name="d" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
+                       <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
                </xs:sequence>
        </xs:complexType>
        <xs:complexType name="DoubleMatrix">
                <xs:sequence>
                        <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
+                       <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
+                       <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
                </xs:sequence>
                <xs:attribute name="rows"  type="xs:int" />
                <xs:attribute name="columns" type="xs:int" />