X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fuimodel%2FPDBRestRequest.java;h=24f38d1dc1c770cba7d8b59a2319123403070624;hb=239d28bd8c08790bbc513a09b2b869fff862f63f;hp=2b9a7f3476b5052619f7d767d0ea3e0fc8567830;hpb=fd235cc7542d6e308e054a8a76580a6c511ae631;p=jalview.git

diff --git a/src/jalview/ws/uimodel/PDBRestRequest.java b/src/jalview/ws/uimodel/PDBRestRequest.java
index 2b9a7f3..24f38d1 100644
--- a/src/jalview/ws/uimodel/PDBRestRequest.java
+++ b/src/jalview/ws/uimodel/PDBRestRequest.java
@@ -21,7 +21,8 @@
 
 package jalview.ws.uimodel;
 
-
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceI;
 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
 
 import java.util.Collection;
@@ -40,16 +41,18 @@ public class PDBRestRequest
 
   private String fieldToSortBy;
 
-  private String associatedSequence;
+  private SequenceI associatedSequence;
 
   private boolean allowEmptySequence;
 
+  private boolean allowUnpublishedEntries = Cache.getDefault(
+          "ALLOW_UNPUBLISHED_PDB_QUERYING", false);
+
   private int responseSize;
 
   private boolean isSortAscending;
 
-  private Collection<PDBDocField> wantedFields;// = new
-                                               // Collection<PDBDocField>();
+  private Collection<PDBDocField> wantedFields;
 
   public String getFieldToSearchBy()
   {
@@ -117,14 +120,37 @@ public class PDBRestRequest
     return isSortAscending;
   }
 
-  public String getAssociatedSequence()
+  public SequenceI getAssociatedSequence()
   {
     return associatedSequence;
   }
 
-  public void setAssociatedSequence(String associatedSequence)
+  public void setAssociatedSequence(SequenceI associatedSequence)
   {
     this.associatedSequence = associatedSequence;
   }
 
+  public String getQuery()
+  {
+    return fieldToSearchBy + searchTerm
+            + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]")
+            + (isAllowUnpublishedEntries() ? "" : " AND status:REL");
+  }
+
+  public String toString()
+  {
+    return "Query : " + getQuery() + " sort field: " + fieldToSortBy
+            + " isAsc: " + isAscending() + " Associated Seq : "
+            + associatedSequence;
+  }
+
+  public boolean isAllowUnpublishedEntries()
+  {
+    return allowUnpublishedEntries;
+  }
+
+  public void setAllowUnpublishedEntries(boolean allowUnpublishedEntries)
+  {
+    this.allowUnpublishedEntries = allowUnpublishedEntries;
+  }
 }