JAL-3210 Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index d4d077f..33d8c33 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -322,6 +322,11 @@ public class StructureChooser extends GStructureChooser
     boolean isUniProtRefsFound = false;
     StringBuilder queryBuilder = new StringBuilder();
     Set<String> seqRefs = new LinkedHashSet<>();
+    
+    /*
+     * note PDBs as DBRefEntry so they are not duplicated in query
+     */
+    Set<String> pdbids = new HashSet<>();
 
     if (seq.getAllPDBEntries() != null
             && queryBuilder.length() < MAX_QLENGTH)
@@ -330,17 +335,20 @@ public class StructureChooser extends GStructureChooser
       {
         if (isValidSeqName(entry.getId()))
         {
-          queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
-                  .append(" OR ");
+          String id = entry.getId().toLowerCase();
+          queryBuilder.append("pdb_id:").append(id).append(" OR ");
           isPDBRefsFound = true;
+          pdbids.add(id);
         }
       }
     }
 
-    if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
+    List<DBRefEntry> refs = seq.getDBRefs();
+    if (refs != null && refs.size() != 0)
     {
-      for (DBRefEntry dbRef : seq.getDBRefs())
+      for (int ib = 0, nb = refs.size(); ib < nb; ib++)
       {
+         DBRefEntry dbRef = refs.get(ib);
         if (isValidSeqName(getDBRefId(dbRef))
                 && queryBuilder.length() < MAX_QLENGTH)
         {
@@ -355,9 +363,13 @@ public class StructureChooser extends GStructureChooser
           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
           {
 
-            queryBuilder.append("pdb_id:")
-                    .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
-            isPDBRefsFound = true;
+            String id = getDBRefId(dbRef).toLowerCase();
+            if (!pdbids.contains(id))
+            {
+              queryBuilder.append("pdb_id:").append(id).append(" OR ");
+              isPDBRefsFound = true;
+              pdbids.add(id);
+            }
           }
           else
           {