xrefs retrieved from Uniprot

[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 8e7893f..65141f8 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -149,9 +149,12 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
             name.append(en2.nextElement());\r
           }\r
 \r
-          if (entry.getProtein() != null)\r
+          if (entry.getProtein()!=null && entry.getProtein().getName()!=null)\r
           {\r
-            name.append(" " + entry.getProtein().getName().elementAt(0));\r
+              for (int nm=0,nmSize=entry.getProtein().getName().size(); nm<nmSize;nm++)\r
+              {\r
+                name.append(" " + entry.getProtein().getName().elementAt(nm));\r
+              }\r
           }\r
 \r
           result.append(name + "\n"\r
@@ -193,11 +196,17 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
       Enumeration e = entry.getDbReference().elements();\r
       Vector onlyPdbEntries = new Vector();\r
+      Vector dbxrefs = new Vector();\r
       while (e.hasMoreElements())\r
       {\r
         PDBEntry pdb = (PDBEntry) e.nextElement();\r
         if (!pdb.getType().equals("PDB"))\r
         {\r
+          DBRefEntry dbr = new DBRefEntry();\r
+          dbr.setSource(pdb.getType());\r
+          dbr.setAccessionId(pdb.getId());\r
+          dbr.setVersion(DBRefSource.UNIPROT+":"+getDbVersion());\r
+          dbxrefs.addElement(dbr);\r
           continue;\r
         }\r
 \r
@@ -217,6 +226,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
                 new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()\r
                         .toString()));\r
       }\r
+      en2 = dbxrefs.elements();\r
+      while (en2.hasMoreElements())\r
+      {\r
+     // we always add as uniprot if we retrieved from uniprot or uniprot name\r
+        sq.addDBRef((DBRefEntry) en2.nextElement());\r
+                    \r
+      }\r
       sq.setPDBId(onlyPdbEntries);\r
       if (entry.getFeature() != null)\r
       {\r
@@ -249,6 +265,6 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   }\r
   public String getDbName()\r
   {\r
-    return getDbSource();\r
+    return "Uniprot"; // getDbSource();\r
   }\r
 }\r