X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=1d2235ed1a7663d0997592d703f2ac24b515d4d1;hb=e1435f3be030f94fdeb82d122ebe27bd5956041c;hp=e5058c6007f1a465ce3aef66182e38b6463bd30e;hpb=e33dce78f446dd3ba3d83d82731e42c70c0d2cb5;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index e5058c6..1d2235e 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" />
@@ -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">
@@ -496,6 +504,50 @@
 						<xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
 					</xs:complexType>
 				</xs:element>
+				<xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:sequence>
+							<xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
+								<xs:complexType>
+									<xs:attribute name="sequenceRef" type="xs:string" />
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="axis" minOccurs="3" maxOccurs="3">
+								<xs:annotation>
+									<xs:documentation>
+										endpoints of X, Y and Z axes in that order
+									</xs:documentation>
+								</xs:annotation>
+								<xs:complexType>
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="seqPointMin">
+								<xs:complexType>
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="seqPointMax">
+								<xs:complexType>
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="pcaData" type="jv:PcaDataType" />
+						</xs:sequence>
+						<xs:attribute name="title" type="xs:string" />
+						<xs:attribute name="scoreModelName" type="xs:string" />
+						<xs:attribute name="xDim" type="xs:int" />
+						<xs:attribute name="yDim" type="xs:int" />
+						<xs:attribute name="zDim" type="xs:int" />
+						<xs:attribute name="bgColour" type="xs:int" />
+						<xs:attribute name="scaleFactor" type="xs:float" />
+						<xs:attribute name="showLabels" type="xs:boolean" />
+						<xs:attribute name="linkToAllViews" type="xs:boolean" />
+						<xs:attributeGroup ref="jv:SimilarityParams" />
+						<xs:attributeGroup ref="jv:swingwindow" />
+					</xs:complexType>
+				</xs:element>
 				<xs:element name="FeatureSettings" minOccurs="0">
 					<xs:complexType>
 						<xs:sequence>
@@ -632,5 +684,46 @@
 		<xs:attribute name="predefinedColours" type="xs:boolean"
 			use="optional" />
 	</xs:complexType>
-
+	<xs:attributeGroup name="SimilarityParams">
+		<xs:annotation>
+			<xs:documentation>
+				parameters that condition a similarity score calculation
+			</xs:documentation>
+		</xs:annotation>
+		<xs:attribute name="includeGaps" type="xs:boolean" />
+		<xs:attribute name="matchGaps" type="xs:boolean" />
+		<xs:attribute name="includeGappedColumns" type="xs:boolean" />
+		<xs:attribute name="denominateByShortestLength" type="xs:boolean" />
+	</xs:attributeGroup>
+	<xs:attributeGroup name="position">
+		<xs:attribute name="xPos" type="xs:float" />
+		<xs:attribute name="yPos" type="xs:float" />
+		<xs:attribute name="zPos" type="xs:float" />
+	</xs:attributeGroup>
+	<xs:complexType name="PcaDataType">
+		<xs:annotation>
+			<xs:documentation>
+				The results of a PCA calculation
+			</xs:documentation>
+		</xs:annotation>
+		<xs:sequence>
+			<xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
+			<xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
+			<xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
+		</xs:sequence>
+	</xs:complexType>
+	<xs:complexType name="DoubleVector">
+		<xs:sequence>
+			<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" />
+	</xs:complexType>
 </xs:schema>