X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=cc8b1e9ca9835a311cc7d1fef74c7c6ff78e06b8;hb=1ce0262fabd88d6bf4ac6e2ef3d6253561baf18c;hp=72a327355aab5ff695b59b341095413061e7d130;hpb=e66214d1c10dd62afb50ea6a6e6952ae9cb0cc38;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 72a3273..cc8b1e9 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,4 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+ * 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.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+-->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
 		<xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
 	<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
@@ -20,14 +37,39 @@
 												<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
+																		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>	
+																
 															</xs:extension>
-														</xs:simpleContent>
+												    </xs:simpleContent>
 													</xs:complexType>
 												</xs:element>
 											</xs:sequence>
@@ -40,14 +82,14 @@
 						<xs:attribute name="colour" type="xs:int" use="optional"/>
 						<xs:attribute name="start" type="xs:int" use="required"/>
 						<xs:attribute name="end" type="xs:int" use="required"/>
-						<xs:attribute name="id" type="xs:int" use="required"/>
+						<xs:attribute name="id" type="xs:string" use="required"/>
 						<xs:attribute name="hidden" type="xs:boolean"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="seq" type="xs:int" maxOccurs="unbounded"/>
+							<xs:element name="seq" type="xs:string" maxOccurs="unbounded"/>
 						</xs:sequence>
 						<xs:attribute name="start" type="xs:int"/>
 						<xs:attribute name="end" type="xs:int"/>
@@ -62,6 +104,15 @@
 						<xs:attribute name="textCol1" type="xs:int"/>
 						<xs:attribute name="textCol2" type="xs:int"/>
 						<xs:attribute name="textColThreshold" type="xs:int"/>
+						<xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
+						<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean" use="optional" default="true"/>
+						<xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
+						<xs:attribute name="showSequenceLogo" type="xs:boolean" use="optional" default="false"/>
+						<xs:attribute name="id" type="xs:string" use="optional"><xs:annotation>
+						<xs:documentation>
+						Optional sequence group ID (only needs to be unique for this alignment)
+						</xs:documentation>
+						</xs:annotation></xs:attribute>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="Viewport" maxOccurs="unbounded">
@@ -84,6 +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"/>
@@ -94,15 +146,23 @@
 						<xs:attribute name="rightAlignIds" type="xs:boolean"/>
 						<xs:attribute name="showText" type="xs:boolean"/>
 						<xs:attribute name="showColourText" type="xs:boolean"/>
+						<xs:attribute name="showUnconserved" type="xs:boolean" use="optional" default="false"/>
 						<xs:attribute name="showBoxes" type="xs:boolean"/>
 						<xs:attribute name="wrapAlignment" type="xs:boolean"/>
 						<xs:attribute name="renderGaps" type="xs:boolean"/>
 						<xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
+						<xs:attribute name="showNPfeatureTooltip" type="xs:boolean" use="optional"/>
+						<xs:attribute name="showDbRefTooltip" type="xs:boolean" use="optional"/>
+						<xs:attribute name="followHighlight" type="xs:boolean" use="optional" default="true"/>
+						<xs:attribute name="followSelection" type="xs:boolean" use="optional" default="true"/>
 						<xs:attribute name="showAnnotation" 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="centreColumnLabels" type="xs:boolean" use="optional" default="false"/>
+						<xs:attribute name="showGroupConservation" type="xs:boolean" use="optional" default="false"/>
+						<xs:attribute name="showGroupConsensus" type="xs:boolean" use="optional" default="false"/>
+						<xs:attribute name="showConsensusHistogram" type="xs:boolean" use="optional" default="true"/>
+						<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="startRes" type="xs:int"/>
 						<xs:attribute name="startSeq" type="xs:int"/>
 						<xs:attribute name="fontName" type="xs:string"/>
@@ -114,7 +174,14 @@
 						<xs:attribute name="textCol1" type="xs:int"/>
 						<xs:attribute name="textCol2" type="xs:int"/>
 						<xs:attribute name="textColThreshold" type="xs:int"/>
-					</xs:complexType>
+						<xs:attribute name="id" type="xs:ID" use="optional">
+							<xs:annotation>
+								<xs:documentation>
+									unique id used by jalview to synchronize between stored and instantiated views
+								</xs:documentation>
+							</xs:annotation>
+						</xs:attribute>
+          </xs:complexType>
 				</xs:element>
 				<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
@@ -126,24 +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: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>
@@ -154,7 +221,20 @@
 									<xs:attribute name="colour" type="xs:int" use="required"/>
 									<xs:attribute name="display" type="xs:boolean" use="required"/>
 									<xs:attribute name="order" type="xs:float" use="optional"/>
-								</xs:complexType>
+									<xs:attribute name="mincolour" type="xs:int" use="optional">
+									<xs:annotation><xs:documentation>Optional minimum colour for graduated feature colour</xs:documentation>
+									</xs:annotation></xs:attribute>
+									<xs:attribute name="threshold" type="xs:float" use="optional">
+									<xs:annotation><xs:documentation>threshold value for graduated feature colour</xs:documentation>
+									</xs:annotation></xs:attribute>
+									<xs:attribute name="threshstate" type="xs:int" use="optional">
+									<xs:annotation><xs:documentation>threshold type for graduated feature colour</xs:documentation>
+									</xs:annotation></xs:attribute>
+									<xs:attribute name="max" type="xs:float" use="optional"/>
+									<xs:attribute name="min" type="xs:float" use="optional"/>
+									<xs:attribute name="colourByLabel" type="xs:boolean" use="optional"/>
+									<xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
+							</xs:complexType>
 							</xs:element>
 							<xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
@@ -198,4 +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>