<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:complexType>
				<xs:attributeGroup ref="jv:position" />
			</xs:complexType
		</xs:element>
		<xs:element name="pcaData" type="jv:PcaData" />
	</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: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="PcaData">
		<xs:annotation>
			<xs:documentation>
				The results of a PCA calculation
			</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="symmRow" maxOccurs="unbounded" type="jv:doubleVector">
				<xs:annotation>
					<xs:documentation>
						The rows of the computed symmetry matrix
					</xs:documentation>
				</xs:annotation>
			</xs:element>
			<xs:element name="eigenRow" maxOccurs="unbounded" type="jv:doubleVector">
				<xs:annotation>
					<xs:documentation>
						The rows of the computed eigenvector
					</xs:documentation>
				</xs:annotation>
			</xs:element>
			<xs:element name="dVector" type="jv:doubleVector" />
			<xs:element name="eVector" type="jv:doubleVector" />
			</xs:element>
		</xs:sequence>
	</xs:complexType>

	<xs:complexType name="PcaData" base="xs:string">
		<xs:annotation>
			<xs:documentation>
				A string holding space-delimited numeric values
			</xs:documentation>
		</xs:annotation>
	</xs:complexType>