X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniprotFTSPanel.java;h=88442de1877d06e88ea91797b8e45e5e674df590;hb=7b10124f09af29607ea0150726ad5d63da09fdaf;hp=51d773566219ddf464ccf0fdf006f59e66771fb4;hpb=007af0c9001900071f6d8e9214143f79e10f4938;p=jalview.git

diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index 51d7735..88442de 100644
--- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@ -1,47 +1,246 @@
+/*
+ * 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.fts.service.uniprot;
 
+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.SequenceFetcher;
 import jalview.util.MessageManager;
 
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
 @SuppressWarnings("serial")
 public class UniprotFTSPanel extends GFTSPanel
 {
 
+  private static String defaultFTSFrameTitle = MessageManager
+          .getString("label.uniprot_sequence_fetcher");
+
+
+  private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+
+  private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
 
   public UniprotFTSPanel(SequenceFetcher seqFetcher)
   {
+    super();
+    pageLimit = UniProtFTSRestClient.getInstance()
+            .getDefaultResponsePageSize();
     this.seqFetcher = seqFetcher;
-    this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+    this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
             .getProgressIndicator();
+    initCache();
   }
 
   @Override
-  public void txt_search_ActionPerformed()
+  public void searchAction(boolean isFreshSearch)
   {
-    // TODO Auto-generated method stub
+    if (isFreshSearch)
+    {
+      offSet = 0;
+    }
+    new Thread()
+    {
+      @Override
+      public void run()
+      {
+        reset();
+        String searchInput = getTypedText();
+        if (searchInput.length() > 0)
+        {
+          setSearchInProgress(true);
+          long startTime = System.currentTimeMillis();
+
+          String searchTarget = ((FTSDataColumnI) cmb_searchTarget
+                  .getSelectedItem()).getAltCode();
+
+          wantedFields = UniProtFTSRestClient.getInstance()
+                  .getAllDefaultDisplayedFTSDataColumns();
+          String searchTerm = decodeSearchTerm(getTypedText(),
+                  searchTarget);
+
+          FTSRestRequest request = new FTSRestRequest();
+          request.setFieldToSearchBy(searchTarget);
+          request.setSearchTerm(searchTerm);
+          request.setOffSet(offSet);
+          request.setWantedFields(wantedFields);
+          FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
+                  .getInstance();
+          FTSRestResponse resultList;
+          try
+          {
+            resultList = uniProtRestCleint.executeRequest(request);
+          } catch (Exception e)
+          {
+            e.printStackTrace();
+            setErrorMessage(e.getMessage());
+            checkForErrors();
+            return;
+          }
+
+          if (resultList.getSearchSummary() != null
+                  && resultList.getSearchSummary().size() > 0)
+          {
+            getResultTable().setModel(
+                    FTSRestResponse.getTableModel(request,
+                            resultList.getSearchSummary()));
+            FTSRestResponse.configureTableColumn(getResultTable(),
+                    wantedFields, tempUserPrefs);
+            getResultTable().setVisible(true);
+          }
+
+          long endTime = System.currentTimeMillis();
+          totalResultSetCount = resultList.getNumberOfItemsFound();
+          resultSetCount = resultList.getSearchSummary() == null ? 0
+                  : resultList.getSearchSummary().size();
+          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)");
+          }
+          else
+          {
+            updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+                    + resultSetCount + " " + result + " ("
+                    + (endTime - startTime) + " milli secs)");
+          }
+          setSearchInProgress(false);
+          refreshPaginatorState();
+          updateSummaryTableSelections();
+        }
+        updateCache();
+      }
+    }.start();
 
   }
 
-  @Override
-  public void btn_ok_ActionPerformed()
+  public String decodeSearchTerm(String enteredText, String targetField)
   {
-    // TODO Auto-generated method stub
+    int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
+            : targetField.length() + 1;
+    String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
+            : targetField + ":";
+    String foundSearchTerms = enteredText;
+    StringBuilder foundSearchTermsBuilder = new StringBuilder();
+    if (enteredText.contains(";"))
+    {
+      String[] searchTerms = enteredText.split(";");
+      for (String searchTerm : searchTerms)
+      {
+        foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
+                .append(" OR ");
+      }
+      int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
+      foundSearchTerms = foundSearchTermsBuilder.toString();
+      if (foundSearchTerms.contains(" OR "))
+      {
+        foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
+                endIndex);
+      }
+    }
+    return foundSearchTerms;
+  }
 
+  @Override
+  public boolean isPaginationEnabled()
+  {
+    return true;
   }
 
+  @Override
+  public void okAction()
+  {
+    disableActionButtons();
+    StringBuilder selectedIds = new StringBuilder();
+    HashSet<String> selectedIdsSet = new HashSet<String>();
+    int primaryKeyColIndex = 0;
+    try
+    {
+      primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
+              wantedFields, false);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    int[] selectedRows = getResultTable().getSelectedRows();
+    for (int summaryRow : selectedRows)
+    {
+      String idStr = getResultTable().getValueAt(summaryRow,
+              primaryKeyColIndex).toString();
+      selectedIdsSet.add(idStr);
+    }
+    selectedIdsSet.addAll(paginatorCart);
+    for (String selectedId : selectedIdsSet)
+    {
+      selectedIds.append(selectedId).append(";");
+    }
+
+    String ids = selectedIds.toString();
+    // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
+    seqFetcher.getTextArea().setText(ids);
+    Thread worker = new Thread(seqFetcher);
+    worker.start();
+    delayAndEnableActionButtons();
+  }
 
   @Override
   public FTSRestClientI getFTSRestClient()
   {
-    return UniProtRestClient.getInstance();
+    return UniProtFTSRestClient.getInstance();
   }
 
   @Override
   public String getFTSFrameTitle()
   {
-    return MessageManager.getString("label.uniprot_sequence_fetcher");
+    return defaultFTSFrameTitle;
+  }
+
+  @Override
+  public Map<String, Integer> getTempUserPrefs()
+  {
+    return tempUserPrefs;
   }
 
+  @Override
+  public String getCacheKey()
+  {
+    return UNIPROT_FTS_CACHE_KEY;
+  }
 }