From 3bf07ba3afb39cea37a1e3eb32da7d498a1fd901 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 28 May 2007 11:15:40 +0000
Subject: [PATCH] prototype DBRef and Feature Type semantics (for annotating
 coding regions and distinguishing between DNA and peptide
 sequence databases)

---
 src/jalview/datamodel/DBRefSource.java        |    4 ++++
 src/jalview/datamodel/FeatureProperties.java  |   24 ++++++++++++++++++++++++
 src/jalview/datamodel/xdb/embl/EmblEntry.java |    7 ++++++-
 3 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 src/jalview/datamodel/FeatureProperties.java

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index aaf0ada..9e394bb 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -44,4 +44,8 @@ public class DBRefSource
    * PFAM ID
    */
   public static String PFAM = "PFAM";
+  /**
+   * List of databases whose sequences might have coding regions annotated
+   */
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS};
 }
diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
new file mode 100644
index 0000000..7eadf7b
--- /dev/null
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -0,0 +1,24 @@
+package jalview.datamodel;
+
+/**
+ * A set of feature property constants used by jalview
+ * @author JimP
+ *
+ */
+public class FeatureProperties
+{
+
+  public static final String EXONPOS = "exon number";
+  public static final String EXONPRODUCT = "product";
+  /**
+   * lookup feature type for a particular database to see if its a coding region feature
+   * @param dbrefsource
+   * @param string
+   * @return
+   */
+  public static boolean isCodingFeature(String dbrefsource, String type)
+  {
+    return ((dbrefsource==null || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL))
+            && type.equalsIgnoreCase("CDS"));
+  }
+}
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index e6c7197..a22eff7 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,6 +1,8 @@
 package jalview.datamodel.xdb.embl;
 
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -414,7 +416,7 @@ public class EmblEntry
               ;
           }
         }
-        if (feature.getName().equalsIgnoreCase("CDS"))
+        if (FeatureProperties.isCodingFeature(DBRefSource.EMBL, "CDS"))
         {
           // extract coding region(s)
           jalview.datamodel.Mapping map = null;
@@ -502,6 +504,8 @@ public class EmblEntry
               sf.setFeatureGroup(jalview.datamodel.DBRefSource.EMBL);
               sf.setDescription("Exon " + (1 + xint) + " for protein '"
                       + prname + "' EMBLCDS:" + prid);
+              sf.setValue(FeatureProperties.EXONPOS, new Integer(1+xint));
+              sf.setValue(FeatureProperties.EXONPRODUCT, prname);
               if (vals != null && vals.size() > 0)
               {
                 Enumeration kv = vals.elements();
@@ -523,6 +527,7 @@ public class EmblEntry
               DBRefEntry ref = (DBRefEntry) dbr.next();
               ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
                       .getSource()));
+              // Hard code the kind of protein product accessions that EMBL cite
               if (ref.getSource().equals(
                       jalview.datamodel.DBRefSource.UNIPROT))
               {
-- 
1.7.10.2