Submissions for secondary structure prediction are now filtered to remove empty seque...

[jalview.git] / resources / uniprot_mapping.xml

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index de1e8f0..d6961aa 100755 (executable)
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -1,5 +1,4 @@
 <?xml version="1.0"?>\r
-<!DOCTYPE mapping PUBLIC "-//EXOLAB/Castor Object Mapping DTD Version 1.0//EN" "http://castor.exolab.org/mapping.dtd">\r
 <mapping>\r
        <class name="jalview.datamodel.UniprotFile">\r
                  <map-to xml="uniprot"/>               \r
@@ -9,27 +8,31 @@
         </class>\r
                 \r
         <class name="jalview.datamodel.UniprotEntry">\r
-             <field name="name" type="string"/>\r
-             <field name="accession" type="string"/>\r
+               <field name="name" type="string" collection="vector"/>\r
+               <field name="accession" type="string" collection="vector"/>\r
+               <field name="proteinName" type="string" collection="vector">\r
+                       <bind-xml name="name" location="entry/protein"/>\r
+               </field>\r
+               \r
+             \r
              <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">\r
                <bind-xml name="sequence"/> \r
               </field>\r
-              <field name="features" type="jalview.datamodel.SequenceFeature" collection="vector">\r
-                 <bind-xml name="feature"/>\r
-              </field>\r
-              \r
+              <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>\r
+              <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>\r
+                      \r
         </class>\r
         \r
         \r
         <class name="jalview.datamodel.SequenceFeature">\r
                <field name="type">\r
-                       <bind-xml name="type" node="attribute"/>\r
+                       <bind-xml node="attribute"/>\r
                </field>\r
                <field name="description">\r
-                        <bind-xml name="description" node="attribute"/>\r
+                        <bind-xml node="attribute"/>\r
                </field>\r
                <field name="status">\r
-                       <bind-xml name="status" node="attribute"/>\r
+                       <bind-xml node="attribute"/>\r
                </field>\r
                <field name="position">\r
                 <bind-xml name="position" node="attribute" location="location/position"/>\r
@@ -47,5 +50,22 @@
                        <bind-xml name="sequence" node="text"/>\r
                     </field>\r
         </class>\r
+        \r
+        <class name="jalview.datamodel.PDBEntry">\r
+               <field name="type"><bind-xml node="attribute"/></field>\r
+               <field name="id"><bind-xml node="attribute"/></field>\r
+               <field name="property" collection="hashtable">\r
+                       <bind-xml name="property">\r
+                          <class name="org.exolab.castor.mapping.MapItem">\r
+                             <field name="key">\r
+                               <bind-xml name="type" node="attribute"/>\r
+                             </field>\r
+                             <field name="value">\r
+                               <bind-xml node="attribute"/>\r
+                               </field>\r
+                          </class>\r
+                       </bind-xml>\r
+               </field>\r
+        </class>\r
 \r
 </mapping>\r