X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=7511ad2f1b4f57561c5122ab93be0fbc1b477a8a;hb=1cb2d001bec9aac0da55fe770b40f034c4b071ff;hp=f60bb6a7f708583b293a3845dabdf5413b3d1eaf;hpb=0c5212bb1f000b06c01d71e67242efd74cfbc3b9;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index f60bb6a..7511ad2 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" />
@@ -293,6 +299,7 @@
 						<xs:attribute name="end" type="xs:int" use="required" />
 						<xs:attribute name="id" type="xs:string" use="required" />
 						<xs:attribute name="hidden" type="xs:boolean" />
+						<xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
@@ -430,6 +437,7 @@
 						<xs:attribute name="fontName" type="xs:string" />
 						<xs:attribute name="fontSize" type="xs:int" />
 						<xs:attribute name="fontStyle" type="xs:int" />
+						<xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
 						<xs:attribute name="viewName" type="xs:string" />
 						<xs:attribute name="sequenceSetId" type="xs:string" />
 						<xs:attribute name="gatheredViews" type="xs:boolean" />
@@ -498,6 +506,18 @@
 						<xs:sequence>
 							<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
+									<xs:sequence>
+									    <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+										    	<xs:annotation>
+										    		<xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
+										    	</xs:annotation>
+									    </xs:element> 
+			    			  		   		<xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
+										    	<xs:annotation>
+										    		<xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
+										    	</xs:annotation>
+										</xs:element>
+								  	</xs:sequence>
 									<xs:attribute name="type" type="xs:string" use="required" />
 									<xs:attribute name="colour" type="xs:int" use="required" />
 									<xs:attribute name="display" type="xs:boolean"
@@ -513,6 +533,7 @@
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
+									<xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
 									<xs:attribute name="threshold" type="xs:float"
 										use="optional">
 										<xs:annotation>
@@ -557,6 +578,11 @@
 			<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 				<xs:complexType>
 					<xs:attribute name="key" type="xs:string" use="required" />
+					<xs:attribute name="key2" type="xs:string" use="optional">
+						<xs:annotation>
+							<xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
 					<xs:attribute name="value" type="xs:string" use="required" />
 				</xs:complexType>
 			</xs:element>