- <xs:attribute name="xpos" type="xs:int"/>
- <xs:attribute name="ypos" type="xs:int"/>
- <xs:attribute name="width" type="xs:int"/>
- <xs:attribute name="height" type="xs:int"/>
+ <xs:attribute name="viewId" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>additional identifier which properly disambiguates
+ the structure view from any other view with the same attributes. This is not an ID,
+ because it is possible to have many references to the same physical structure view
+ from different sequences in an alignment. A structureState element citing the same
+ viewId will appear for each instance.</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="alignwithAlignPanel" type="xs:boolean" use="optional" default="true">
+ <xs:annotation>
+ <xs:documentation>
+ Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7).
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="colourwithAlignPanel" type="xs:boolean" use="optional" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ Flag set if the alignment panel containing this JSeq should be included in those used to colour its associated sequences in this structureState(since Jalview 2.7).
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="colourByJmol" type="xs:boolean" use="optional" default="true">
+ <xs:annotation><xs:documentation>
+ Flag set if the structure display is coloured by the Jmol state, rather than by one or more linked alignment views.
+ </xs:documentation></xs:annotation></xs:attribute>
+