JAL-2909 Bam file parsing with insertions, first pass

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 686cd83..73775cf 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -28,8 +28,9 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
-import jalview.datamodel.UniprotFile;
+import jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.datamodel.xdb.uniprot.UniprotFile;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 import java.io.InputStream;
@@ -208,7 +209,7 @@ public class Uniprot extends DbSourceProxyImpl
     sequence.setDescription(getUniprotEntryDescription(entry));
 
     final String dbVersion = getDbVersion();
-    ArrayList<DBRefEntry> dbRefs = new ArrayList<DBRefEntry>();
+    ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
     for (String accessionId : entry.getAccession())
     {
       DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
@@ -218,7 +219,7 @@ public class Uniprot extends DbSourceProxyImpl
       dbRefs.add(dbRef);
     }
 
-    Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
+    Vector<PDBEntry> onlyPdbEntries = new Vector<>();
     for (PDBEntry pdb : entry.getDbReference())
     {
       DBRefEntry dbr = new DBRefEntry();
@@ -261,16 +262,17 @@ public class Uniprot extends DbSourceProxyImpl
 
         }
       }
-
     }
 
     sequence.setPDBId(onlyPdbEntries);
     if (entry.getFeature() != null)
     {
-      for (SequenceFeature sf : entry.getFeature())
+      for (UniprotFeature uf : entry.getFeature())
       {
-        sf.setFeatureGroup("Uniprot");
-        sequence.addSequenceFeature(sf);
+        SequenceFeature copy = new SequenceFeature(uf.getType(),
+                uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+        copy.setStatus(uf.getStatus());
+        sequence.addSequenceFeature(copy);
       }
     }
     for (DBRefEntry dbr : dbRefs)
@@ -308,23 +310,18 @@ public class Uniprot extends DbSourceProxyImpl
   /**
    *
    * @param entry
-   *          UniportEntry
+   *          UniprotEntry
    * @return The accession id(s) and name(s) delimited by '|'.
    */
   public static String getUniprotEntryId(UniprotEntry entry)
   {
     StringBuilder name = new StringBuilder(32);
-    // name.append("UniProt/Swiss-Prot");
-    // use 'canonicalised' name for optimal id matching
-    name.append(DBRefSource.UNIPROT);
-    for (String accessionId : entry.getAccession())
-    {
-      name.append(BAR_DELIMITER);
-      name.append(accessionId);
-    }
     for (String n : entry.getName())
     {
-      name.append(BAR_DELIMITER);
+      if (name.length() > 0)
+      {
+        name.append(BAR_DELIMITER);
+      }
       name.append(n);
     }
     return name.toString();