X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=resources%2Fembl_mapping.xml;h=01b921afb71e79a7c63f9875ce4b0b44109d1959;hb=eb5e0ce96aa9936a540b4d99a57cc2e5df3704f0;hp=515925604ba740567ee5cc2e99c51597be1c2809;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml
index 5159256..01b921a 100644
--- a/resources/embl_mapping.xml
+++ b/resources/embl_mapping.xml
@@ -1,111 +1,128 @@
 <?xml version="1.0"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-  Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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/>.
+ * 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.
 -->
 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">
 <!--
 	History: Originally created from EMBL_common_V1.0
 	Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd
+	Updated May 2016 for EMBL XML 1.2 JAL-2113 JAL-2114
+	  see ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
+	  see http://www.ebi.ac.uk/ena/submit/data-formats
 	-->
 	<class name="jalview.datamodel.xdb.embl.EmblFile">
-		<map-to xml="EMBL_Services"/>
+		<map-to xml="ROOT"/>
 		<field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
 			<bind-xml name="entry"/>
 		</field>
-		
 		<field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
 			<bind-xml name="Error"/>
 		</field>
 	</class>
 	<class name="jalview.datamodel.xdb.embl.EmblEntry">
-		<map-to xml="entry"/>
 		<field name="accession" type="string">
-			<bind-xml location="accession" node="attribute"/>
+			<bind-xml name="accession" node="attribute"/>
 		</field>
-		<field name="lastUpdated" type="string">
-			<bind-xml location="last-updated" node="attribute"/>
+		<!-- 
+		    in EMBL XML 1.2 sequence/@version became entry/version 
+		    entry/@version became entry/@entryVersion
+		-->
+		<field name="sequenceVersion" type="string">
+			<bind-xml name="version" node="attribute"/>
 		</field>
-		<field name="version" type="string">
-			<bind-xml location="version" node="attribute"/>
+		<field name="entryVersion" type="string">
+			<bind-xml name="entryVersion" node="attribute"/>
+		</field>
+		<field name="dataClass" type="string">
+			<bind-xml name="dataClass" node="attribute"/>
+		</field>
+		<field name="taxonomicDivision" type="string">
+			<bind-xml name="taxonomicDivision" node="attribute"/>
+		</field>
+		<field name="moleculeType" type="string">
+			<bind-xml name="moleculeType" node="attribute"/>
+		</field>
+		<field name="sequenceLength" type="string">
+			<bind-xml name="sequenceLength" node="attribute"/>
+		</field>
+		<field name="topology" type="string">
+			<bind-xml name="topology" node="attribute" location="type"/>
+		</field>
+		<field name="firstPublicDate" type="string">
+			<bind-xml name="firstPublic" node="attribute"/>
 		</field>
-		
-		<field name="rCreated" type="string">
-			<bind-xml location="releaseCreated" node="attribute"/>
+		<field name="firstPublicRelease" type="string">
+			<bind-xml name="firstPublicRelease" node="attribute"/>
 		</field>
-		<field name="rLastUpdated" type="string">
-			<bind-xml location="releaseLastUpdated" node="attribute"/>
+		<field name="lastUpdatedDate" type="string">
+			<bind-xml name="lastUpdated" node="attribute"/>
 		</field>
-		<field name="desc" type="string">
+		<field name="lastUpdatedRelease" type="string">
+			<bind-xml name="lastUpdatedRelease" node="attribute"/>
+		</field>
+		<field name="description" type="string">
 			<bind-xml name="description" node="element"/>
 		</field>
-		<field name="Keywords" type="string" collection="vector">
+		<field name="keywords" type="string" collection="vector">
 			<bind-xml name="keyword" node="element"/>
 		</field>
 		<field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
 			<bind-xml name="feature"/>
 		</field>
 		<field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
-			<bind-xml name="dbreference" />
+			<bind-xml name="xref" />
 		</field>
 		<field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
-			<bind-xml name="sequence"/> <!-- location="sequence" node="element"/ -->
+			<bind-xml name="sequence"/>
 		</field>
 	</class>
 	<class name="jalview.datamodel.xdb.embl.EmblSequence">
-		<map-to xml="sequence"/>
-		<field name="type" type="string">
-			<bind-xml name="type" node="attribute" location="type"/>
-		</field>
-		<field name="version" type="string">
-			<bind-xml name="version" node="attribute" location="version"/>
-		</field>
 		<field name="sequence" type="string">
 			<bind-xml node="text"/>
 		</field>
 	</class>
 	<class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
-		<map-to xml="feature"/>
 		<field name="name" type="string">
 			<bind-xml name="name" node="attribute"/>
 		</field>
+		<field name="location" type="string">
+			<bind-xml name="location" node="attribute"/>
+		</field>
 		<field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
-			<bind-xml name="dbreference" node="element"/>
+			<bind-xml name="xref" node="element"/>
 		</field>
 		<field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
 			<bind-xml name="qualifier"/>
 		</field>					
-		<field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">
-			<bind-xml name="location"/>
-		</field>
 	</class>
 	<class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
-		<field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->
-			<bind-xml name="primary" node="attribute"/>
+		<field name="accessionId" type="java.lang.String">
+			<bind-xml name="id" node="attribute"/>
 		</field>
-		<field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->
+		<field name="source" type="java.lang.String"> 
 			<bind-xml name="db" node="attribute"/>
 		</field>
-		<field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->
-			<bind-xml name="secondary" node="attribute"/>
+		<field name="version" type="string">
+			<bind-xml name="secondaryId" node="attribute"/>
 		</field>
 	</class>
 	<class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
-		<map-to xml="Qualifier"/>
 		<field name="name">
 			<bind-xml name="name" node="attribute"/>
 		</field>
@@ -116,43 +133,4 @@
 			<bind-xml name="value" node="element"/>
 		</field>
 	</class>
-	<class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
-		<map-to xml="location"/>
-		<field name="locationType" type="string">
-			<bind-xml name="type" node="attribute"/>
-		</field>
-		<field name="locationComplement" type="boolean">
-			<bind-xml name="complement" node="attribute"/>
-		</field>
-		<field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
-			<bind-xml name="locationElement"/>
-		</field>
-	</class>
-	<class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
-		<map-to xml="locationElement"/>
-		<field name="type" type="string">
-			<bind-xml name="type" node="attribute"/>
-		</field>
-		<field name="accession" type="string">
-			<bind-xml name="accession" node="attribute"/>			
-		</field>
-		<field name="version" type="string">
-			<bind-xml name="version" node="attribute"/>
-		</field>
-		<field name="complement" type="boolean">
-			<bind-xml name="complement"/>
-		</field>
-		<field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
-			<bind-xml name="basePosition" node="element"/>
-		</field>
-	</class>
-	<class name="jalview.datamodel.xdb.embl.BasePosition">
-		<map-to xml="basePosition"/>
-		<field name="type">
-			<bind-xml name="type" node="attribute"/>
-		</field>
-		<field name="pos">
-			<bind-xml node="text"/>
-		</field>
-	</class>
 </mapping>