From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 26 Oct 2005 14:22:55 +0000 (+0000)
Subject: Used for sequence feature mapping
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=41886e56255f40c3eb2ff4e3fad8e21b4e1b0040;p=jalview.git

Used for sequence feature mapping
---

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
new file mode 100755
index 0000000..de1e8f0
--- /dev/null
+++ b/resources/uniprot_mapping.xml
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<!DOCTYPE mapping PUBLIC "-//EXOLAB/Castor Object Mapping DTD Version 1.0//EN" "http://castor.exolab.org/mapping.dtd">
+<mapping>
+	<class name="jalview.datamodel.UniprotFile">
+                 <map-to xml="uniprot"/>               
+                 <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry"  collection="vector">
+		      <bind-xml name="entry"/>
+		 </field>		
+        </class>
+		 
+	 <class name="jalview.datamodel.UniprotEntry">
+	      <field name="name" type="string"/>
+	      <field name="accession" type="string"/>
+	      <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
+	      	<bind-xml name="sequence"/> 
+	       </field>
+	       <field name="features" type="jalview.datamodel.SequenceFeature" collection="vector">
+	       	  <bind-xml name="feature"/>
+	       </field>
+	       
+	 </class>
+	 
+	 
+	 <class name="jalview.datamodel.SequenceFeature">
+	 	<field name="type">
+	 		<bind-xml name="type" node="attribute"/>
+	 	</field>
+	 	<field name="description">
+			 <bind-xml name="description" node="attribute"/>
+	 	</field>
+	 	<field name="status">
+			<bind-xml name="status" node="attribute"/>
+	 	</field>
+	 	<field name="position">
+	 	 <bind-xml name="position" node="attribute" location="location/position"/>
+	 	 </field>
+		<field name="begin">
+		 <bind-xml name="position" node="attribute" location="location/begin"/>
+	 	 </field>
+		<field name="end">
+		 <bind-xml name="position" node="attribute" location="location/end"/>
+	 	 </field>
+	 </class>
+	
+          <class name="jalview.datamodel.UniprotSequence">
+		     <field name="content" type="string">
+		        <bind-xml name="sequence" node="text"/>
+		     </field>
+	 </class>
+
+</mapping>