X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=c21721bf49f4202a6f1d92a01f162eab89a960d1;hb=d9c741ff46d3370f152d67b5ca8a24d217b6827e;hp=109b83b507819d9b9a7261bc75482d656126a3e2;hpb=d6815a9bc0fc9b9c1fe8e1871a4b0e9d7bd7a11f;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 109b83b..c21721b 100755
--- 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" />
@@ -287,6 +293,11 @@
 									</xs:attribute>
 								</xs:complexType>
 							</xs:element>
+							<xs:element name="hmmerProfile" minOccurs="0" type="xs:string">
+								<xs:annotation>
+									<xs:documentation>name of the project jar entry that holds the HMM file with the profile for the sequence</xs:documentation>
+								</xs:annotation>
+							</xs:element>
 						</xs:sequence>
 						<xs:attribute name="colour" type="xs:int" use="optional" />
 						<xs:attribute name="start" type="xs:int" use="required" />
@@ -457,6 +468,8 @@
 								</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 +712,21 @@
 			</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" />