<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
<xs:element name="structureState" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:simpleContent>
- <xs:extension base="xs:string">
+ <xs:extension base="xs:string">
+ <xs:attributeGroup ref="jv:swingwindow"/>
<xs:attribute name="visible" type="xs:boolean"/>
- <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
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>
</xs:extension>
- </xs:simpleContent>
+ </xs:simpleContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
+ <xs:attributeGroup ref="jv:swingwindow"/>
<xs:attribute name="conservationSelected" type="xs:boolean"/>
<xs:attribute name="pidSelected" type="xs:boolean"/>
<xs:attribute name="bgColour" type="xs:string"/>
<xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
- <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="startRes" type="xs:int"/>
<xs:attribute name="startSeq" type="xs:int"/>
<xs:attribute name="fontName" type="xs:string"/>
</xs:documentation>
</xs:annotation>
</xs:attribute>
- </xs:complexType>
+ </xs:complexType>
</xs:element>
<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
</xs:element>
<xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence minOccurs="0">
- <xs:element name="title" type="xs:string"/>
- <xs:element name="newick" type="xs:string"/>
- </xs:sequence>
- <xs:attribute name="width" type="xs:int"/>
- <xs:attribute name="height" type="xs:int"/>
- <xs:attribute name="xpos" type="xs:int"/>
- <xs:attribute name="ypos" type="xs:int"/>
- <xs:attribute name="fontName" type="xs:string"/>
- <xs:attribute name="fontSize" type="xs:int"/>
- <xs:attribute name="fontStyle" type="xs:int"/>
- <xs:attribute name="threshold" type="xs:float"/>
- <xs:attribute name="showBootstrap" type="xs:boolean"/>
- <xs:attribute name="showDistances" type="xs:boolean"/>
- <xs:attribute name="markUnlinked" type="xs:boolean"/>
- <xs:attribute name="fitToWindow" type="xs:boolean"/>
- <xs:attribute name="currentTree" type="xs:boolean"/>
- <xs:attribute name="id" type="xs:ID" use="optional">
- <xs:annotation><xs:documentation>Tree ID added for binding tree visualization settings to vamsas document trees in jalview 2.4.1</xs:documentation></xs:annotation>
- </xs:attribute>
- </xs:complexType>
+ <xs:sequence minOccurs="0">
+ <xs:element name="title" type="xs:string"/>
+ <xs:element name="newick" type="xs:string"/>
+ </xs:sequence>
+ <xs:attribute name="fontName" type="xs:string"/>
+ <xs:attribute name="fontSize" type="xs:int"/>
+ <xs:attribute name="fontStyle" type="xs:int"/>
+ <xs:attribute name="threshold" type="xs:float"/>
+ <xs:attribute name="showBootstrap" type="xs:boolean"/>
+ <xs:attribute name="showDistances" type="xs:boolean"/>
+ <xs:attribute name="markUnlinked" type="xs:boolean"/>
+ <xs:attribute name="fitToWindow" type="xs:boolean"/>
+ <xs:attribute name="currentTree" type="xs:boolean"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation><xs:documentation>Tree ID added for binding tree visualization settings to vamsas document trees in jalview 2.4.1</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attributeGroup ref="jv:swingwindow"/>
+ </xs:complexType>
</xs:element>
<xs:element name="FeatureSettings" minOccurs="0">
<xs:complexType>
<xs:attribute name="type" type="xs:string" use="optional"/>
<xs:attribute name="file" type="xs:string"/>
</xs:complexType>
+ <!--
+ <xs:complexType name="reportWindow">
+ <xs:annotation>
+ <xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:string" use="required"/>
+ <xs:attribute name="type" type="xs:string" use="optional"/>
+ <xs:attribute name="file" type="xs:string" use="optional"/>
+ </xs:complexType>
+ -->
+ <xs:attributeGroup name="swingwindow">
+ <xs:annotation>
+ <xs:documentation>
+ base attributes for windows displayed in Jalview desktop.
+ </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="width" type="xs:int"/>
+ <xs:attribute name="height" type="xs:int"/>
+ <xs:attribute name="xpos" type="xs:int"/>
+ <xs:attribute name="ypos" type="xs:int"/>
+ </xs:attributeGroup>
</xs:schema>
git://source.jalview.org / jalview.git / blobdiff