X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fpdb%2FPDBFTSPanel.java;h=c9d7676542d224f35897739f799a0b9d50eb75fb;hp=b944b9b7cf2add3be0b530007d90d397456c55ab;hb=1114062d7c3034db3387f46a860c0e334206ce49;hpb=a38b3fde2cbfbeebabb57de545c76cee63c9eb3d

diff --git a/src/jalview/fts/service/pdb/PDBFTSPanel.java b/src/jalview/fts/service/pdb/PDBFTSPanel.java
index b944b9b..c9d7676 100644
--- a/src/jalview/fts/service/pdb/PDBFTSPanel.java
+++ b/src/jalview/fts/service/pdb/PDBFTSPanel.java
@@ -21,36 +21,41 @@
 
 package jalview.fts.service.pdb;
 
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import javax.help.HelpSetException;
+
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
 import jalview.gui.SequenceFetcher;
 import jalview.util.MessageManager;
 
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-
 @SuppressWarnings("serial")
 public class PDBFTSPanel extends GFTSPanel
 {
   private static String defaultFTSFrameTitle = MessageManager
           .getString("label.pdb_sequence_fetcher");
 
-
-  private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+  private static Map<String, Integer> tempUserPrefs = new HashMap<>();
 
   private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
 
-  public PDBFTSPanel(SequenceFetcher seqFetcher)
+  private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH";
+
+  public PDBFTSPanel(SequenceFetcher fetcher)
   {
-    super();
+    super(fetcher);
     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
-    this.seqFetcher = seqFetcher;
-    this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
-            .getProgressIndicator();
+    this.seqFetcher = fetcher;
+    this.progressIndicator = (fetcher == null) ? null
+            : fetcher.getProgressIndicator();
   }
 
   @Override
@@ -87,24 +92,24 @@ public class PDBFTSPanel extends GFTSPanel
           request.setSearchTerm(searchTerm + ")");
           request.setOffSet(offSet);
           request.setWantedFields(wantedFields);
-          FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
+          FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
           FTSRestResponse resultList;
           try
           {
-            resultList = pdbRestCleint.executeRequest(request);
+            resultList = pdbRestClient.executeRequest(request);
           } catch (Exception e)
           {
             setErrorMessage(e.getMessage());
             checkForErrors();
+            setSearchInProgress(false);
             return;
           }
 
           if (resultList.getSearchSummary() != null
                   && resultList.getSearchSummary().size() > 0)
           {
-            getResultTable().setModel(
-                    FTSRestResponse.getTableModel(request,
-                            resultList.getSearchSummary()));
+            getResultTable().setModel(FTSRestResponse.getTableModel(request,
+                    resultList.getSearchSummary()));
             FTSRestResponse.configureTableColumn(getResultTable(),
                     wantedFields, tempUserPrefs);
             getResultTable().setVisible(true);
@@ -114,24 +119,21 @@ public class PDBFTSPanel extends GFTSPanel
           totalResultSetCount = resultList.getNumberOfItemsFound();
           resultSetCount = resultList.getSearchSummary() == null ? 0
                   : resultList.getSearchSummary().size();
-          String result = (resultSetCount > 0) ? MessageManager
-                  .getString("label.results") : MessageManager
-                  .getString("label.result");
+          String result = (resultSetCount > 0)
+                  ? MessageManager.getString("label.results")
+                  : MessageManager.getString("label.result");
 
           if (isPaginationEnabled() && resultSetCount > 0)
           {
-            updateSearchFrameTitle(defaultFTSFrameTitle
-                    + " - "
-                    + result
-                    + " "
-                    + totalNumberformatter.format((Number) (offSet + 1))
-                    + " to "
-                    + totalNumberformatter
-                            .format((Number) (offSet + resultSetCount))
-                    + " of "
-                    + totalNumberformatter
-                            .format((Number) totalResultSetCount) + " "
-                    + " (" + (endTime - startTime) + " milli secs)");
+            String f1 = totalNumberformatter
+                    .format(Integer.valueOf(offSet + 1));
+            String f2 = totalNumberformatter
+                    .format(Integer.valueOf(offSet + resultSetCount));
+            String f3 = totalNumberformatter
+                    .format(Integer.valueOf(totalResultSetCount));
+            updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+                    + " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
+                    + (endTime - startTime) + " milli secs)");
           }
           else
           {
@@ -174,8 +176,8 @@ public class PDBFTSPanel extends GFTSPanel
       foundSearchTerms = foundSearchTermsBuilder.toString();
       if (foundSearchTerms.contains(" OR "))
       {
-        foundSearchTerms = foundSearchTerms.substring(
-                targetField.length() + 1, endIndex);
+        foundSearchTerms = foundSearchTerms
+                .substring(targetField.length() + 1, endIndex);
       }
     }
     else if (enteredText.contains(":"))
@@ -191,12 +193,12 @@ public class PDBFTSPanel extends GFTSPanel
     // mainFrame.dispose();
     disableActionButtons();
     StringBuilder selectedIds = new StringBuilder();
-    HashSet<String> selectedIdsSet = new HashSet<String>();
+    HashSet<String> selectedIdsSet = new HashSet<>();
     int primaryKeyColIndex = 0;
     try
     {
-      primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
-              wantedFields, false);
+      primaryKeyColIndex = getFTSRestClient()
+              .getPrimaryKeyColumIndex(wantedFields, false);
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -205,8 +207,8 @@ public class PDBFTSPanel extends GFTSPanel
     String searchTerm = getTypedText();
     for (int summaryRow : selectedRows)
     {
-      String idStr = getResultTable().getValueAt(summaryRow,
-              primaryKeyColIndex).toString();
+      String idStr = getResultTable()
+              .getValueAt(summaryRow, primaryKeyColIndex).toString();
       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
     }
 
@@ -221,8 +223,7 @@ public class PDBFTSPanel extends GFTSPanel
     }
 
     String ids = selectedIds.toString();
-    // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
-    seqFetcher.getTextArea().setText(ids);
+    seqFetcher.setQuery(ids);
     Thread worker = new Thread(seqFetcher);
     worker.start();
     delayAndEnableActionButtons();
@@ -278,12 +279,32 @@ public class PDBFTSPanel extends GFTSPanel
     return tempUserPrefs;
   }
 
-
   @Override
   public String getCacheKey()
   {
     return PDB_FTS_CACHE_KEY;
   }
 
+  @Override
+  public String getAutosearchPreference()
+  {
+    return PDB_AUTOSEARCH;
+  }
 
-}
+  @Override
+  protected void showHelp()
+  {
+    try
+    {
+      Help.showHelpWindow(HelpId.PdbFts);
+    } catch (HelpSetException e1)
+    {
+      e1.printStackTrace();
+    }
+  }
+
+  public String getDbName()
+  {
+    return "PDB";
+  }
+}
\ No newline at end of file