JAL-1668 added filtering and sorting capabilites

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

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 8bc9ebf..e00d9ac 100644 (file)
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -31,7 +31,7 @@ public class PDBRestClient
     PDBSearchRequest request = new PDBSearchRequest();
     request.setAllowEmptySeq(false);
     request.setResponseSize(100);
-    request.setSearchTarget("pfam_name");
+    request.setFieldToSearchBy("pfam_name");
     request.setSearchTerm("Lipoc*");
     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
     wantedFields.add(PDBDocField.MOLECULE_TYPE);
@@ -50,7 +50,7 @@ public class PDBRestClient
             Boolean.TRUE);
     Client client = Client.create(clientConfig);
 
-    String query = request.getSearchTarget()
+    String query = request.getFieldToSearchBy()
             + request.getSearchTerm()
             + ((request.isAllowEmptySeq()) ? ""
                     : " AND molecule_sequence:['' TO *]");
@@ -60,10 +60,10 @@ public class PDBRestClient
 
     String responseSize = (request.getResponseSize() == 0) ? "200" : String
             .valueOf(request.getResponseSize());
-    String sortParam = (request.getSortTarget() == null || request
-            .getSortTarget().trim().isEmpty()) ? ""
+    String sortParam = (request.getFieldToSortBy() == null || request
+            .getFieldToSortBy().trim().isEmpty()) ? ""
             : (request
-            .getSortTarget() + (request.isAscending() ? " asc" : " desc"));
+            .getFieldToSortBy() + (request.isAscending() ? " asc" : " desc"));
 
     WebResource webResource = client.resource(pdbSearchEndpoint)
             .queryParam("wt", "json").queryParam("fl", wantedFields)
@@ -87,7 +87,8 @@ public class PDBRestClient
       }
     }
     // System.out.println("--------------> " + responseString);
-    return parseResponse(responseString, request.getWantedFields());
+    return parseResponse(responseString, request.getWantedFields(),
+            request.getAssociatedSequence());
   }
 
   private String parseException(String jsonResponse)
@@ -112,7 +113,7 @@ public class PDBRestClient
 
   @SuppressWarnings("unchecked")
   private PDBSearchResponse parseResponse(String jsonResponse,
-          List<PDBDocField> wantedFields)
+          List<PDBDocField> wantedFields, String associatedSequence)
   {
     PDBSearchResponse searchResult = new PDBSearchResponse();
     List<PDBResponseSummary> result = null;
@@ -137,7 +138,8 @@ public class PDBRestClient
           JSONObject doc = docIter.next();
           // if (doc.get("molecule_sequence") != null)
           // {
-          result.add(searchResult.new PDBResponseSummary(doc, wantedFields));
+          result.add(searchResult.new PDBResponseSummary(doc, wantedFields,
+                  associatedSequence));
           // }
         }
         searchResult.setItemsFound(numFound);