X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=abfabb117344c24de767cc45f02a54baec4ed13e;hb=refs%2Fheads%2Fnew_feature%2FJAL-4019_ambiguous_base_colourscheme;hp=f061b4216f66834e2843cea1368f79daeecbd56d;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index f061b42..abfabb1 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,22 +1,28 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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>
@@ -97,6 +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>
@@ -155,6 +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>
@@ -165,6 +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>
@@ -184,6 +216,10 @@
 						<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" type="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 			</xs:sequence>
 			<xs:attribute name="graph" type="xs:boolean" use="required" />
 			<xs:attribute name="graphType" type="xs:int" use="optional" />
@@ -214,6 +250,11 @@
 			<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">
@@ -265,4 +306,49 @@
 		<xs:attribute name="id" type="xs:string"/>
 		<xs:attribute name="description" type="xs:string"/>
 	</xs:complexType>
+	<xs:complexType name="MatrixType">
+		<xs:sequence>
+			<xs:element name="elements" type="xs:string" minOccurs="1"
+				maxOccurs="1">
+				<xs:annotation>
+					<xs:documentation>serialised representation of matrix as one or
+						more sets of comma separated values</xs:documentation>
+				</xs:annotation>
+			</xs:element>
+			<xs:element name="groups" type="xs:string" minOccurs="0"
+				maxOccurs="unbounded">
+				<xs:annotation>
+					<xs:documentation>Comma separated series of BigIntegers formed from
+						bitsets defining partitions on the rows/columns of the matrix
+					</xs:documentation>
+				</xs:annotation>
+			</xs:element>
+			<xs:element name="newick" type="xs:string" minOccurs="0"
+				maxOccurs="unbounded">
+				<xs:annotation>
+					<xs:documentation>tree computed for this</xs:documentation>
+				</xs:annotation>
+			</xs:element>
+			<xs:element name="property" type="vamsas:property"
+				minOccurs="0" maxOccurs="unbounded" />
+		</xs:sequence>
+
+		<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:attribute name="treeMethod" type="xs:string"
+			use="optional" />
+		<xs:attribute name="cutHeight" type="xs:double"
+			use="optional" />
+		<xs:attribute name="id" type="xs:string" use="optional" />
+
+	</xs:complexType>
+	<xs:complexType name="property">
+		<xs:attribute name="name" type="xs:string" />
+		<xs:attribute name="value" type="xs:string" />
+	</xs:complexType>
+				
+	
 </xs:schema>