X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=cc8b1e9ca9835a311cc7d1fef74c7c6ff78e06b8;hb=20c48abe18f05c2802d7e59e1efb227547a4165d;hp=8ba8b4bbbc913e5fc628203208a23a744f2a2edf;hpb=022166d52c42285e0d414f6f3f7c550f4ab65974;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 8ba8b4b..cc8b1e9 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,7 +1,7 @@
 <?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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -37,12 +37,9 @@
 												<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
@@ -59,17 +56,20 @@
 																</xs:documentation>
 																</xs:annotation>
 																</xs:attribute>
-																<xs:attribute name="colourwithAlignPanel" type="xs:boolean" use="optional" default="true">
+																<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>
@@ -135,6 +135,7 @@
 								</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"/>
@@ -162,10 +163,6 @@
 						<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"/>
@@ -184,7 +181,7 @@
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
-					</xs:complexType>
+          </xs:complexType>
 				</xs:element>
 				<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
@@ -196,27 +193,24 @@
 				</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>
@@ -284,4 +278,27 @@
 		<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>