X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=5fd2bab696038e37a994518adeebfb9575b428b6;hb=3ec49f04ac668312e8eb3e963c52df6797fea89f;hp=e32427dd60c86e63aee3dc8185adc71c55574d92;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index e32427d..5fd2bab 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,24 +1,28 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
-  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-  
-  This program 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 2
-  of the License, or (at your option) any later version.
-  
-  This program 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 this program; if not, write to the Free Software
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
-
 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
+<!-- 
+	Java JAXB binding classes are generated by running command line tool xjc:
+ 	    xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ 	Note this also generates code for included schemas
+-->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
 	<xs:complexType name="VAMSAS">
 		<xs:sequence>
@@ -99,6 +103,11 @@
 							</xs:element>
 						</xs:choice>
 					</xs:sequence>
+					<xs:attribute name="mappingType" type="xs:string" use="optional">
+						<xs:annotation>
+							<xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
 				</xs:extension>
 			</xs:complexContent>	
 		</xs:complexType>
@@ -157,6 +166,20 @@
 								<xs:attribute name="source" type="xs:string"/>
 								<xs:attribute name="version" type="xs:string"/>
 								<xs:attribute name="accessionId" type="xs:string"/>
+								<xs:attribute name="locus" type="xs:boolean" default="false">
+									<xs:annotation>
+										<xs:documentation>
+											true for gene locus mapping, source=species, version=assembly, accession=chromosome
+										</xs:documentation>
+									</xs:annotation>
+								</xs:attribute>
+								<xs:attribute name="canonical" type="xs:boolean" default="false">
+									<xs:annotation>
+										<xs:documentation>
+											true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
+										</xs:documentation>
+									</xs:annotation>
+								</xs:attribute>
 							</xs:complexType>
 						</xs:element>
 					</xs:sequence>
@@ -167,6 +190,13 @@
 							</xs:documentation>
 						</xs:annotation>
 					</xs:attribute>
+					<xs:attribute name="biotype" type="xs:string" use="optional">
+						<xs:annotation>
+							<xs:documentation>
+								Biotype of the sequence (if known)
+							</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
 				</xs:extension>
 			</xs:complexContent>
 		</xs:complexType>
@@ -174,26 +204,62 @@
 	<xs:element name="Annotation">
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
-				<xs:element name="label" type="xs:string"/>
-				<xs:element name="description" type="xs:string" minOccurs="0"/>
+				<xs:element ref="vamsas:annotationElement" minOccurs="0"
+					maxOccurs="unbounded" />
+				<xs:element name="label" type="xs:string" />
+				<xs:element name="description" type="xs:string"
+					minOccurs="0" />
 				<xs:element name="thresholdLine" minOccurs="0">
 					<xs:complexType>
-						<xs:attribute name="label" type="xs:string"/>
-						<xs:attribute name="value" type="xs:float"/>
-						<xs:attribute name="colour" type="xs:int"/>
+						<xs:attribute name="label" type="xs:string" />
+						<xs:attribute name="value" type="xs:float" />
+						<xs:attribute name="colour" type="xs:int" />
+					</xs:complexType>
+				</xs:element>
+				<xs:element name="contactmatrix" type="vamsas:MatrixType"
+					maxOccurs="unbounded" minOccurs="0">
+				</xs:element>
+				<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:attribute name="name" type="xs:string" />
+						<xs:attribute name="value" type="xs:string" />
 					</xs:complexType>
 				</xs:element>
 			</xs:sequence>
-			<xs:attribute name="graph" type="xs:boolean" use="required"/>
-			<xs:attribute name="graphType" type="xs:int" use="optional"/>
-			<xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
-			<xs:attribute name="graphColour" type="xs:int" use="optional"/>
-			<xs:attribute name="graphGroup" type="xs:int" use="optional"/>
-			<xs:attribute name="id" type="xs:string" use="optional"/>
-			<xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
-			<xs:attribute name="score" type="xs:double" use="optional"/>
-			<xs:attribute name="visible" type="xs:boolean" use="optional"/>
+			<xs:attribute name="graph" type="xs:boolean" use="required" />
+			<xs:attribute name="graphType" type="xs:int" use="optional" />
+			<xs:attribute name="sequenceRef" type="xs:string"
+				use="optional" />
+			<xs:attribute name="groupRef" type="xs:string"
+				use="optional" />
+			<xs:attribute name="graphColour" type="xs:int"
+				use="optional" />
+			<xs:attribute name="graphGroup" type="xs:int"
+				use="optional" />
+			<xs:attribute name="graphHeight" type="xs:int" use="optional">
+			<xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
+			<xs:attribute name="id" type="xs:string" use="optional" />
+			<xs:attribute name="scoreOnly" type="xs:boolean"
+				use="optional" default="false" />
+			<xs:attribute name="score" type="xs:double" use="optional" />
+			<xs:attribute name="visible" type="xs:boolean"
+				use="optional" />
+			<xs:attribute name="centreColLabels" type="xs:boolean"
+				use="optional" />
+			<xs:attribute name="scaleColLabels" type="xs:boolean"
+				use="optional" />
+			<xs:attribute name="showAllColLabels" type="xs:boolean"
+				use="optional" />
+
+
+			<xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
+			<xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
+			</xs:annotation></xs:attribute>
+			<xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
+			<xs:annotation><xs:documentation>is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores</xs:documentation></xs:annotation></xs:attribute>
+			<xs:attribute name="calcId" type="xs:string" use="optional">
+			<xs:annotation><xs:documentation>Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system.</xs:documentation></xs:annotation>
+			</xs:attribute>
 		</xs:complexType>
 	</xs:element>	
 	<xs:element name="SequenceSet">
@@ -245,4 +311,14 @@
 		<xs:attribute name="id" type="xs:string"/>
 		<xs:attribute name="description" type="xs:string"/>
 	</xs:complexType>
+	<xs:complexType name="MatrixType">
+	<xs:simpleContent><xs:extension base="xs:string">
+	<xs:attribute name="id" type="xs:string"/>
+	<xs:attribute name="type" type="xs:string" use="required"/>
+	<xs:attribute name="rows" type="xs:integer" use="required"/>
+	<xs:attribute name="cols" type="xs:integer" use="required"/>
+	</xs:extension>
+	</xs:simpleContent>
+	</xs:complexType>
+	
 </xs:schema>