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 e18d6af..33d8c33 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -83,7 +83,7 @@ public class StructureChooser extends GStructureChooser
 
   private FTSRestRequest lastPdbRequest;
 
-  private FTSRestClientI pdbRestCleint;
+  private FTSRestClientI pdbRestClient;
 
   private String selectedPdbFileName;
 
@@ -217,7 +217,7 @@ public class StructureChooser extends GStructureChooser
   void fetchStructuresMetaData()
   {
     long startTime = System.currentTimeMillis();
-    pdbRestCleint = PDBFTSRestClient.getInstance();
+    pdbRestClient = PDBFTSRestClient.getInstance();
     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
             .getStructureSummaryFields();
 
@@ -239,7 +239,7 @@ public class StructureChooser extends GStructureChooser
       FTSRestResponse resultList;
       try
       {
-        resultList = pdbRestCleint.executeRequest(pdbRequest);
+        resultList = pdbRestClient.executeRequest(pdbRequest);
       } catch (Exception e)
       {
         e.printStackTrace();
@@ -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
           {
@@ -461,7 +473,7 @@ public class StructureChooser extends GStructureChooser
       public void run()
       {
         long startTime = System.currentTimeMillis();
-        pdbRestCleint = PDBFTSRestClient.getInstance();
+        pdbRestClient = PDBFTSRestClient.getInstance();
         lbl_loading.setVisible(true);
         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
                 .getStructureSummaryFields();
@@ -497,7 +509,7 @@ public class StructureChooser extends GStructureChooser
           FTSRestResponse resultList;
           try
           {
-            resultList = pdbRestCleint.executeRequest(pdbRequest);
+            resultList = pdbRestClient.executeRequest(pdbRequest);
           } catch (Exception e)
           {
             e.printStackTrace();
@@ -565,6 +577,8 @@ public class StructureChooser extends GStructureChooser
   @Override
   protected void pdbFromFile_actionPerformed()
   {
+    // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+    // works
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
@@ -1190,19 +1204,26 @@ public class StructureChooser extends GStructureChooser
             && !discoveredStructuresSet.isEmpty();
   }
 
+  protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this. 
+  // Doing a search for "1" or "1c" is valuable?
+  // Those work but are enormously slow.
+
   @Override
   protected void txt_search_ActionPerformed()
   {
+    String text = txt_search.getText().trim();
+       if (text.length() >= PDB_ID_MIN) 
     new Thread()
     {
-      @Override
+
+       @Override
       public void run()
       {
         errorWarning.setLength(0);
         isValidPBDEntry = false;
-        if (txt_search.getText().length() > 0)
+        if (text.length() > 0)
         {
-          String searchTerm = txt_search.getText().toLowerCase();
+          String searchTerm = text.toLowerCase();
           searchTerm = searchTerm.split(":")[0];
           // System.out.println(">>>>> search term : " + searchTerm);
           List<FTSDataColumnI> wantedFields = new ArrayList<>();
@@ -1213,12 +1234,12 @@ public class StructureChooser extends GStructureChooser
           pdbRequest.setWantedFields(wantedFields);
           pdbRequest.setSearchTerm(searchTerm + ")");
           pdbRequest.setAssociatedSequence(selectedSequence);
-          pdbRestCleint = PDBFTSRestClient.getInstance();
-          wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+          pdbRestClient = PDBFTSRestClient.getInstance();
+          wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
           FTSRestResponse resultList;
           try
           {
-            resultList = pdbRestCleint.executeRequest(pdbRequest);
+            resultList = pdbRestClient.executeRequest(pdbRequest);
           } catch (Exception e)
           {
             errorWarning.append(e.getMessage());