initial support for EMBL file parsing.

[jalview.git] / resources / embl_mapping.xml

diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml
new file mode 100644 (file)
index 0000000..7238e89
--- /dev/null
+++ b/resources/embl_mapping.xml
@@ -0,0 +1,135 @@
+<?xml version="1.0"?>\r
+<mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
+       xsi:schemaLocation="http://castor.exolab.org/ castor-mapping.xsd">\r
+       <!-- -->\r
+       <class name="jalview.datamodel.xdb.embl.EmblFile">\r
+               <map-to xml="EMBL_Services"/>\r
+               <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">\r
+                       <bind-xml name="entry"/>\r
+               </field>\r
+               \r
+               <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">\r
+                       <bind-xml name="Error"/>\r
+               </field>\r
+       </class>\r
+       <class name="jalview.datamodel.xdb.embl.EmblEntry">\r
+               <map-to xml="entry"/>\r
+               <field name="accession" type="string">
+                       <bind-xml location="accession" node="attribute"/>
+               </field>\r
+               <field name="lastUpdated" type="string">\r
+                       <bind-xml location="last-updated" node="attribute"/>\r
+               </field>\r
+               <field name="version" type="string">\r
+                       <bind-xml location="version" node="attribute"/>\r
+               </field>\r
+               \r
+               <field name="rCreated" type="string">\r
+                       <bind-xml location="releaseCreated" node="attribute"/>\r
+               </field>\r
+               <field name="rLastUpdated" type="string">\r
+                       <bind-xml location="releaseLastUpdated" node="attribute"/>\r
+               </field>\r
+               <field name="desc" type="string">
+                       <bind-xml name="description" node="element"/>
+               </field>\r
+               <field name="Keywords" type="string" collection="vector">\r
+                       <bind-xml name="keyword" node="element"/>\r
+               </field>\r
+               <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">\r
+                       <bind-xml location="sequence" node="element"/>\r
+               </field>\r
+               <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">\r
+                       <bind-xml name="feature"/>
+               </field>\r
+               <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
+                       <bind-xml name="dbreference" />\r
+               </field>\r
+       </class>\r
+       <class name="jalview.datamodel.xdb.embl.EmblSequence">
+               <map-to xml="sequence"/>\r
+               <field name="type" type="string">\r
+                       <bind-xml name="type" node="attribute" location="type"/>\r
+               </field>\r
+               <field name="version" type="string">\r
+                       <bind-xml name="version" node="attribute" location="version"/>\r
+               </field>\r
+               <field name="sequence" type="string">\r
+                       <bind-xml node="text"/>\r
+               </field>
+       </class>\r
+       <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
+               <map-to xml="feature"/>\r
+               <field name="name" type="string">
+                       <bind-xml name="name" node="attribute"/>
+               </field>\r
+               <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
+                       <bind-xml name="dbreference" node="element"/>
+               </field>\r
+               <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
+                       <bind-xml name="qualifier"/>\r
+               </field>                                        \r
+               <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
+                       <bind-xml name="location"/>\r
+               </field>\r
+       </class>\r
+       <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
+               <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->\r
+                       <bind-xml name="primary" node="attribute"/>\r
+               </field>\r
+               <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->\r
+                       <bind-xml name="db" node="attribute"/>\r
+               </field>\r
+               <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->\r
+                       <bind-xml name="secondary" node="attribute"/>\r
+               </field>\r
+       </class>\r
+       <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
+               <map-to xml="Qualifier"/>\r
+               <field name="name">\r
+                       <bind-xml name="name" node="attribute"/>\r
+               </field>\r
+               <field name="value">
+                       <bind-xml node="text"/>
+               </field>\r
+       </class>\r
+       <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
+               <map-to xml="location"/>\r
+               <field name="locationType" type="string">\r
+                       <bind-xml name="type" node="attribute"/>\r
+               </field>\r
+               <field name="locationComplement" type="boolean">\r
+                       <bind-xml name="complement" node="attribute"/>\r
+               </field>\r
+               <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
+                       <bind-xml name="locationElement"/>\r
+               </field>\r
+       </class>\r
+       <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
+               <map-to xml="locationElement"/>\r
+               <field name="type" type="string">\r
+                       <bind-xml name="type" node="attribute"/>\r
+               </field>\r
+               <field name="accession" type="string">\r
+                       <bind-xml name="accession" node="attribute"/>                   \r
+               </field>\r
+               <field name="version" type="string">\r
+                       <bind-xml name="version" node="attribute"/>\r
+               </field>\r
+               <field name="complement" type="boolean">\r
+                       <bind-xml name="complement"/>\r
+               </field>\r
+               <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
+                       <bind-xml name="basePosition" node="element"/>\r
+               </field>\r
+       </class>\r
+       <class name="jalview.datamodel.xdb.embl.BasePosition">
+               <map-to xml="basePosition"/>\r
+               <field name="type">
+                       <bind-xml name="type" node="attribute"/>
+               </field>\r
+               <field name="pos">
+                       <bind-xml node="text"/>\r
+               </field>\r
+       </class>\r
+</mapping>\r