X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=3f890ba7293f7eabd9a11872e2d830d39c54c103;hb=d62b90cb6effb7b380e5f7d590691dd884b024cf;hp=9661d12dfe9faac3f0f550a45eaa2321e972aea4;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 9661d12..3f890ba 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,23 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel.xdb.embl;
 
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
@@ -26,11 +33,14 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-
+/**
+ * Data model for one entry returned from an EMBL query, as marshalled by a
+ * Castor binding file
+ * 
+ * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+ * 
+ * @see embl_mapping.xml
+ */
 public class EmblEntry
 {
   String accession;
@@ -47,13 +57,11 @@ public class EmblEntry
 
   String lastUpdated;
 
-  Vector keywords;
-
-  Vector refs;
+  Vector<String> keywords;
 
-  Vector dbRefs;
+  Vector<DBRefEntry> dbRefs;
 
-  Vector features;
+  Vector<EmblFeature> features;
 
   EmblSequence sequence;
 
@@ -77,7 +85,7 @@ public class EmblEntry
   /**
    * @return the dbRefs
    */
-  public Vector getDbRefs()
+  public Vector<DBRefEntry> getDbRefs()
   {
     return dbRefs;
   }
@@ -86,7 +94,7 @@ public class EmblEntry
    * @param dbRefs
    *          the dbRefs to set
    */
-  public void setDbRefs(Vector dbRefs)
+  public void setDbRefs(Vector<DBRefEntry> dbRefs)
   {
     this.dbRefs = dbRefs;
   }
@@ -111,7 +119,7 @@ public class EmblEntry
   /**
    * @return the features
    */
-  public Vector getFeatures()
+  public Vector<EmblFeature> getFeatures()
   {
     return features;
   }
@@ -120,7 +128,7 @@ public class EmblEntry
    * @param features
    *          the features to set
    */
-  public void setFeatures(Vector features)
+  public void setFeatures(Vector<EmblFeature> features)
   {
     this.features = features;
   }
@@ -128,7 +136,7 @@ public class EmblEntry
   /**
    * @return the keywords
    */
-  public Vector getKeywords()
+  public Vector<String> getKeywords()
   {
     return keywords;
   }
@@ -137,7 +145,7 @@ public class EmblEntry
    * @param keywords
    *          the keywords to set
    */
-  public void setKeywords(Vector keywords)
+  public void setKeywords(Vector<String> keywords)
   {
     this.keywords = keywords;
   }
@@ -160,23 +168,6 @@ public class EmblEntry
   }
 
   /**
-   * @return the refs
-   */
-  public Vector getRefs()
-  {
-    return refs;
-  }
-
-  /**
-   * @param refs
-   *          the refs to set
-   */
-  public void setRefs(Vector refs)
-  {
-    this.refs = refs;
-  }
-
-  /**
    * @return the releaseCreated
    */
   public String getRCreated()
@@ -188,7 +179,7 @@ public class EmblEntry
    * @param releaseCreated
    *          the releaseCreated to set
    */
-  public void setRcreated(String releaseCreated)
+  public void setRCreated(String releaseCreated)
   {
     this.rCreated = releaseCreated;
   }
@@ -423,9 +414,13 @@ public class EmblEntry
       { 1, dna.getLength() }, 1, 1));
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
+      {
         for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
                 .addDBRef((DBRefEntry) i.next()))
+        {
           ;
+        }
+      }
     }
     try
     {
@@ -438,7 +433,9 @@ public class EmblEntry
           {
             for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                     .addDBRef((DBRefEntry) dbr.next()))
+            {
               ;
+            }
           }
         }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
@@ -454,7 +451,9 @@ public class EmblEntry
             {
               for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                       .addDBRef((DBRefEntry) dbr.next()))
+              {
                 ;
+              }
             }
           }
         }
@@ -580,8 +579,10 @@ public class EmblEntry
       }
     }
     Sequence product = null;
+    DBRefEntry protEMBLCDS = null;
     exon = adjustForPrStart(prstart, exon);
-
+    boolean noProteinDbref=true;
+    
     if (prseq != null && prname != null && prid != null)
     {
       // extract proteins.
@@ -657,8 +658,14 @@ public class EmblEntry
           // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
           pcdnaref.setMap(new Mapping(mp));
           if (product != null)
+          {
             product.addDBRef(pcdnaref);
-
+            protEMBLCDS = new DBRefEntry(pcdnaref);
+            protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+            product.addDBRef(protEMBLCDS);
+            
+          }     
+          
         }
       }
       // add cds feature to dna seq - this may include the stop codon
@@ -669,18 +676,20 @@ public class EmblEntry
         sf.setEnd(exon[xint + 1]);
         sf.setType(feature.getName());
         sf.setFeatureGroup(sourceDb);
-        sf.setDescription("Exon " + (1 + (int) (xint / 2))
+        sf.setDescription("Exon " + (1 + xint / 2)
                 + " 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();
+          Enumeration kv = vals.keys();
           while (kv.hasMoreElements())
           {
             Object key = kv.nextElement();
             if (key != null)
+            {
               sf.setValue(key.toString(), vals.get(key));
+            }
           }
         }
         dna.addSequenceFeature(sf);
@@ -710,6 +719,7 @@ public class EmblEntry
                               + ref.getAccessionId());
             }
           }
+          noProteinDbref = false;
         }
         if (product != null)
         {
@@ -732,6 +742,33 @@ public class EmblEntry
         }
         dna.addDBRef(ref);
       }
+      if (noProteinDbref && product != null)
+      {
+        // add protein coding reference to dna sequence so xref matches
+        if (protEMBLCDS == null)
+        {
+          protEMBLCDS = new DBRefEntry();
+          protEMBLCDS.setAccessionId(prid);
+          protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+          protEMBLCDS.setVersion(getVersion());
+          protEMBLCDS
+                  .setMap(new Mapping(product, map.getMap().getInverse()));
+        }
+        product.addDBRef(protEMBLCDS);
+          
+        // Add converse mapping reference
+        if (map != null)
+        {
+          Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
+                  .getInverse());
+          DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
+          ncMap.setMap(pmap);
+          if (map.getTo() != null)
+          {
+            dna.addDBRef(ncMap);
+          }
+        }
+      }
     }
   }