From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 6 Dec 2005 12:08:56 +0000 (+0000)
Subject: After merge
X-Git-Tag: Release_2_07~48
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=010b61b99e344283e1042e0a15d7082128fa0311;p=jalview.git

After merge
---

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
new file mode 100755
index 0000000..d6961aa
--- /dev/null
+++ b/resources/uniprot_mapping.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<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" collection="vector"/>
+	 	<field name="accession" type="string" collection="vector"/>
+	      	<field name="proteinName" type="string" collection="vector">
+	      		<bind-xml name="name" location="entry/protein"/>
+	      	</field>
+	      	
+	      
+	      <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
+	      	<bind-xml name="sequence"/> 
+	       </field>
+	       <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
+	       <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
+	   	       
+	 </class>
+	 
+	 
+	 <class name="jalview.datamodel.SequenceFeature">
+	 	<field name="type">
+	 		<bind-xml node="attribute"/>
+	 	</field>
+	 	<field name="description">
+			 <bind-xml node="attribute"/>
+	 	</field>
+	 	<field name="status">
+			<bind-xml 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>
+	 
+	 <class name="jalview.datamodel.PDBEntry">
+	 	<field name="type"><bind-xml node="attribute"/></field>
+	 	<field name="id"><bind-xml node="attribute"/></field>
+	 	<field name="property" collection="hashtable">
+			<bind-xml name="property">
+			   <class name="org.exolab.castor.mapping.MapItem">
+			      <field name="key">
+				<bind-xml name="type" node="attribute"/>
+			      </field>
+			      <field name="value">
+			      	<bind-xml node="attribute"/>
+			      	</field>
+			   </class>
+			</bind-xml>
+		</field>
+	 </class>
+
+</mapping>