X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FThreeDBStructureChooserQuerySource.java;h=9e4ee21ec8915b7f730baebe36be6a8912c80a3f;hb=d654b1f014790b7ae25e6eec631847170a930987;hp=9b6d8e872393a3e2d83c9a294c73e194bf403462;hpb=9018c06add8548b4921a4c21f21a1b85a0bea1de;p=jalview.git

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index 9b6d8e8..9e4ee21 100644
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui.structurechooser;
 
 import java.util.ArrayList;
@@ -12,6 +32,7 @@ import java.util.Set;
 
 import javax.swing.JTable;
 
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
@@ -23,6 +44,7 @@ import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
 import jalview.jbgui.FilterOption;
 
@@ -43,8 +65,6 @@ public class ThreeDBStructureChooserQuerySource
 
   private static final String FILTER_SOURCE_PREFIX = "only_";
 
-  private static int MAX_QLENGTH = 7820;
-
   protected FTSRestRequest lastTdbRequest;
 
   protected FTSRestClientI tdbRestClient;
@@ -74,19 +94,9 @@ public class ThreeDBStructureChooserQuerySource
 
   public String buildQuery(SequenceI seq)
   {
-    boolean isPDBRefsFound = false;
-    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<>();
-
     List<DBRefEntry> refs = seq.getDBRefs();
     int ib = checkUniprotRefs(refs);
-    if (ib>-1)
+    if (ib > -1)
     {
       return getDBRefId(refs.get(ib));
     }
@@ -95,8 +105,10 @@ public class ThreeDBStructureChooserQuerySource
 
   /**
    * Searches DBRefEntry for uniprot refs
+   * 
    * @param seq
-   * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of Uniprot canonical DBRefEntry 
+   * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of
+   *         Uniprot canonical DBRefEntry
    */
   public static int checkUniprotRefs(List<DBRefEntry> refs)
   {
@@ -128,7 +140,6 @@ public class ThreeDBStructureChooserQuerySource
    */
   static boolean isValidSeqName(String seqName)
   {
-    // System.out.println("seqName : " + seqName);
     String ignoreList = "pdb,uniprot,swiss-prot";
     if (seqName.length() < 3)
     {
@@ -138,7 +149,7 @@ public class ThreeDBStructureChooserQuerySource
     {
       return false;
     }
-    seqName = seqName.toLowerCase();
+    seqName = seqName.toLowerCase(Locale.ROOT);
     for (String ignoredEntry : ignoreList.split(","))
     {
       if (seqName.contains(ignoredEntry))
@@ -180,13 +191,14 @@ public class ThreeDBStructureChooserQuerySource
     {
       FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
       resultList = tdbRestClient.executeRequest(tdbRequest);
-      
+
       lastTdbRequest = tdbRequest;
-      if (resultList!=null)
+      if (resultList != null)
       { // Query the PDB and add additional metadata
         FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
                 getPDBQuerySource(), resultList);
-        FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+
+        resultList = joinResponses(resultList, pdbResponse);
       }
       return resultList;
     }
@@ -249,11 +261,12 @@ public class ThreeDBStructureChooserQuerySource
   {
     if (tdbEntries != null && lastTdbRequest != null)
     {
-      int prov_idx = lastTdbRequest.getFieldIndex("Provider");
-      boolean hasPDBe=false;
-      for (FTSData row : tdbEntries)
+      boolean hasPDBe = false;
+      for (FTSData _row : tdbEntries)
       {
-        String provider = (String) row.getSummaryData()[prov_idx];
+        // tdb returns custom object
+        TDB_FTSData row = (TDB_FTSData) _row;
+        String provider = (String) row.getProvider();
         FilterOption providerOpt = new FilterOption(
                 "3DB Provider - " + provider,
                 FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
@@ -263,21 +276,24 @@ public class ThreeDBStructureChooserQuerySource
           tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
           if ("PDBe".equalsIgnoreCase(provider))
           {
-            hasPDBe=true;
+            hasPDBe = true;
           }
         }
       }
       if (!hasPDBe)
       {
         // remove the PDBe options from the available filters
-        int op=0;
-        while (op<xtantOptions.size())
+        int op = 0;
+        while (op < xtantOptions.size())
         {
           FilterOption filter = xtantOptions.get(op);
-          if (filter.getQuerySource() instanceof PDBStructureChooserQuerySource)
+          if (filter
+                  .getQuerySource() instanceof PDBStructureChooserQuerySource)
           {
             xtantOptions.remove(op);
-          } else {
+          }
+          else
+          {
             op++;
           }
         }
@@ -367,8 +383,7 @@ public class ThreeDBStructureChooserQuerySource
     int urlColumnIndex = restable.getColumn("Url").getModelIndex();
     int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
     int humanUrl = restable.getColumn("Page URL").getModelIndex();
-    int categoryColumnIndex = restable.getColumn("Model Category")
-            .getModelIndex();
+    int modelformat = restable.getColumn("Model Format").getModelIndex();
     final int up_start_idx = restable.getColumn("Uniprot Start")
             .getModelIndex();
     final int up_end_idx = restable.getColumn("Uniprot End")
@@ -405,6 +420,8 @@ public class ThreeDBStructureChooserQuerySource
               .toString();
       String modelPage = humanUrl < 1 ? null
               : (String) restable.getValueAt(row, humanUrl);
+      String strucFormat = restable.getValueAt(row, modelformat).toString();
+
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
               refSeqColIndex);
       selectedSeqsToView.add(selectedSeq);
@@ -418,11 +435,16 @@ public class ThreeDBStructureChooserQuerySource
       {
         pdbEntry = new PDBEntry();
         pdbEntry.setId(pdbIdStr);
-        boolean hasCif = urlStr.toLowerCase(Locale.ENGLISH).endsWith("cif");
-        boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH)
-                .contains("pdb");
-        pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF
-                : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
+        pdbEntry.setAuthoritative(true);
+        try
+        {
+          pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
+        } catch (Exception q)
+        {
+          Console.warn("Unknown filetype for 3D Beacons Model from: "
+                  + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+        }
+
         if (!"PDBe".equalsIgnoreCase(typeColumn))
         {
           pdbEntry.setRetrievalUrl(urlStr);
@@ -452,7 +474,7 @@ public class ThreeDBStructureChooserQuerySource
 
   public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
   {
-    List<String> pdbIds = new ArrayList<String>();
+    Set<String> pdbIds = new HashSet<String>();
     int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
     int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
     for (FTSData row : upResponse.getSearchSummary())
@@ -513,7 +535,6 @@ public class ThreeDBStructureChooserQuerySource
             : -1;
     int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
 
-    List<FTSData> joinedRows = new ArrayList<FTSData>();
     for (final FTSData row : upResponse.getSearchSummary())
     {
       String id = (String) row.getSummaryData()[idx_modelId];
@@ -547,4 +568,22 @@ public class ThreeDBStructureChooserQuerySource
     return upResponse;
   }
 
+  public TDB_FTSData getFTSDataFor(JTable restable, int selectedRow,
+          Collection<FTSData> discoveredStructuresSet)
+  {
+    int idColumnIndex = restable.getColumn("Model id").getModelIndex();
+
+    String modelId = (String) restable.getValueAt(selectedRow,
+            idColumnIndex);
+    for (FTSData row : discoveredStructuresSet)
+    {
+      if (row instanceof TDB_FTSData
+              && ((TDB_FTSData) row).getModelId().equals(modelId))
+      {
+        return ((TDB_FTSData) row);
+      }
+    }
+    return null;
+  }
+
 }
\ No newline at end of file