X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=358f0a16a2b5b26c14a611752948adc3beb2f4c9;hb=917e04d030979250a29886d8fe5a630ff2ae8d54;hp=72a327355aab5ff695b59b341095413061e7d130;hpb=e66214d1c10dd62afb50ea6a6e6952ae9cb0cc38;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 72a3273..358f0a1 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 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, 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"/>
@@ -26,6 +43,17 @@
 																<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:extension>
 														</xs:simpleContent>
 													</xs:complexType>
@@ -40,14 +68,14 @@
 						<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 +90,15 @@
 						<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">
@@ -94,11 +131,23 @@
 						<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="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="xpos" type="xs:int"/>
 						<xs:attribute name="ypos" type="xs:int"/>
 						<xs:attribute name="width" type="xs:int"/>
@@ -114,6 +163,13 @@
 						<xs:attribute name="textCol1" type="xs:int"/>
 						<xs:attribute name="textCol2" type="xs:int"/>
 						<xs:attribute name="textColThreshold" type="xs:int"/>
+						<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">
@@ -143,6 +199,9 @@
 						<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:element>
 				<xs:element name="FeatureSettings" minOccurs="0">
@@ -154,7 +213,20 @@
 									<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>