Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_acro...

[jalview.git] / schemas / jalview.xsd

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 7511ad2..07dee98 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -499,6 +499,51 @@
                                                        </xs:annotation>
                                                </xs:attribute>
                                                <xs:attributeGroup ref="jv:swingwindow" />
+                                               <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">
@@ -637,5 +682,46 @@
                <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>