From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 5 Nov 2021 16:51:37 +0000 (+0000)
Subject: JAL-3829 format and tidy up unused code
X-Git-Tag: Release_2_11_2_0~24^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=37762f10a4836b6f80bf2b31b77b431dd38da68e

JAL-3829 format and tidy up unused code
---

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index ffc6c66..2890a01 100644
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -4,7 +4,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Comparator;
-import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
@@ -12,6 +11,7 @@ import java.util.Set;
 
 import javax.swing.JTable;
 
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
@@ -44,8 +44,6 @@ public class ThreeDBStructureChooserQuerySource
 
   private static final String FILTER_SOURCE_PREFIX = "only_";
 
-  private static int MAX_QLENGTH = 7820;
-
   protected FTSRestRequest lastTdbRequest;
 
   protected FTSRestClientI tdbRestClient;
@@ -75,19 +73,9 @@ 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));
     }
@@ -96,8 +84,10 @@ 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)
   {
@@ -129,7 +119,6 @@ public class ThreeDBStructureChooserQuerySource
    */
   static boolean isValidSeqName(String seqName)
   {
-    // System.out.println("seqName : " + seqName);
     String ignoreList = "pdb,uniprot,swiss-prot";
     if (seqName.length() < 3)
     {
@@ -181,13 +170,14 @@ 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;
     }
@@ -250,8 +240,7 @@ public class ThreeDBStructureChooserQuerySource
   {
     if (tdbEntries != null && lastTdbRequest != null)
     {
-      int prov_idx = lastTdbRequest.getFieldIndex("Provider");
-      boolean hasPDBe=false;
+      boolean hasPDBe = false;
       for (FTSData _row : tdbEntries)
       {
         // tdb returns custom object
@@ -266,21 +255,24 @@ 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++;
           }
         }
@@ -371,8 +363,6 @@ public class ThreeDBStructureChooserQuerySource
     int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
     int humanUrl = restable.getColumn("Page URL").getModelIndex();
     int modelformat = restable.getColumn("Model Format").getModelIndex();
-    int categoryColumnIndex = restable.getColumn("Model Category")
-            .getModelIndex();
     final int up_start_idx = restable.getColumn("Uniprot Start")
             .getModelIndex();
     final int up_end_idx = restable.getColumn("Uniprot End")
@@ -523,7 +513,6 @@ 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];
@@ -561,13 +550,15 @@ public class ThreeDBStructureChooserQuerySource
           Collection<FTSData> discoveredStructuresSet)
   {
     int idColumnIndex = restable.getColumn("Model id").getModelIndex();
-    
-    String modelId = (String) restable.getValueAt(selectedRow, idColumnIndex);
-    for (FTSData row:discoveredStructuresSet)
+
+    String modelId = (String) restable.getValueAt(selectedRow,
+            idColumnIndex);
+    for (FTSData row : discoveredStructuresSet)
     {
-      if (row instanceof TDB_FTSData && ((TDB_FTSData)row).getModelId().equals(modelId))
+      if (row instanceof TDB_FTSData
+              && ((TDB_FTSData) row).getModelId().equals(modelId))
       {
-        return ((TDB_FTSData)row);
+        return ((TDB_FTSData) row);
       }
     }
     return null;