X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fthreedbeacons%2FTDBeaconsFTSPanel.java;fp=src%2Fjalview%2Ffts%2Fservice%2Fthreedbeacons%2FTDBeaconsFTSPanel.java;h=7fa6aa5e50f79e7c17361cc70fa6c68682639f4b;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=0000000000000000000000000000000000000000;hpb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;p=jalview.git

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
new file mode 100644
index 0000000..7fa6aa5
--- /dev/null
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
@@ -0,0 +1,280 @@
+package jalview.fts.service.threedbeacons;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import javax.swing.SwingUtilities;
+
+import org.json.JSONArray;
+import org.json.JSONObject;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+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.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.SequenceFetcher;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
+@SuppressWarnings("serial")
+public class TDBeaconsFTSPanel extends GFTSPanel
+{
+  private static String defaultFTSFrameTitle = MessageManager
+          .getString("label.pdb_sequence_fetcher");
+
+  private static Map<String, Integer> tempUserPrefs = new HashMap<>();
+
+  private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";
+
+  private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
+
+  private static HttpURLConnection connection;
+
+  public TDBeaconsFTSPanel(SequenceFetcher fetcher)
+  {
+    // no ID retrieval option for TD Beacons just now
+    super(null);
+    pageLimit = TDBeaconsFTSRestClient.getInstance()
+            .getDefaultResponsePageSize();
+    this.seqFetcher = fetcher;
+    this.progressIndicator = (fetcher == null) ? null
+            : fetcher.getProgressIndicator();
+  }
+
+  @Override
+  public void searchAction(boolean isFreshSearch)
+  {
+    mainFrame.requestFocusInWindow();
+    if (isFreshSearch)
+    {
+      offSet = 0;
+    }
+    new Thread()
+    {
+      @Override
+      public void run()
+      {
+        reset();
+        boolean allowEmptySequence = false;
+        if (getTypedText().length() > 0)
+        {
+          setSearchInProgress(true);
+          long startTime = System.currentTimeMillis();
+
+          String searchTarget = ((FTSDataColumnI) cmb_searchTarget
+                  .getSelectedItem()).getCode();
+          wantedFields = TDBeaconsFTSRestClient.getInstance()
+                  .getAllDefaultDisplayedFTSDataColumns();
+          String searchTerm = getTypedText(); // to add : decodeSearchTerm
+
+          FTSRestRequest request = new FTSRestRequest();
+          request.setAllowEmptySeq(allowEmptySequence);
+          request.setResponseSize(100);
+          // expect it to be uniprot accesssion
+          request.setSearchTerm(searchTerm + ".json");
+          request.setOffSet(offSet);
+          request.setWantedFields(wantedFields);
+          FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient
+                  .getInstance();
+          FTSRestResponse resultList;
+          try
+          {
+            resultList = tdbRestClient.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()));
+            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)
+          {
+            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
+          {
+            updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+                    + resultSetCount + " " + result + " ("
+                    + (endTime - startTime) + " milli secs)");
+          }
+
+          setSearchInProgress(false);
+          refreshPaginatorState();
+          updateSummaryTableSelections();
+        }
+        txt_search.updateCache();
+      }
+    }.start();
+  }
+
+  @Override
+  public void okAction()
+  {
+    // mainFrame.dispose();
+    disableActionButtons();
+    StringBuilder selectedIds = new StringBuilder();
+    final HashSet<String> selectedIdsSet = new HashSet<>();
+    int primaryKeyColIndex = 0;
+    try
+    {
+      primaryKeyColIndex = getFTSRestClient()
+              .getPrimaryKeyColumIndex(wantedFields, false);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    int[] selectedRows = getResultTable().getSelectedRows();
+    String searchTerm = getTypedText();
+    for (int summaryRow : selectedRows)
+    {
+      String idStr = getResultTable()
+              .getValueAt(summaryRow, primaryKeyColIndex).toString();
+      selectedIdsSet.add(idStr);
+    }
+
+    for (String idStr : paginatorCart)
+    {
+      selectedIdsSet.add(idStr);
+    }
+
+    for (String selectedId : selectedIdsSet)
+    {
+      selectedIds.append(selectedId).append(";");
+    }
+
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        AlignmentI allSeqs = null;
+        FormatAdapter fl = new jalview.io.FormatAdapter();
+        for (String tdbURL : selectedIdsSet)
+        {
+          try
+          {
+            // retrieve the structure via its URL
+            AlignmentI tdbAl = fl.readFile(tdbURL, DataSourceType.URL,
+                    FileFormat.MMCif);
+
+            // TODO: pad structure according to its Uniprot Start so all line up w.r.t. the Uniprot reference sequence
+            // TODO: give the structure a sensible name (not the giant URL *:o) )
+            if (tdbAl != null)
+            {
+              if (allSeqs != null)
+              {
+                allSeqs.append(tdbAl);
+              }
+              else
+              {
+                allSeqs = tdbAl;
+              }
+            }
+          } catch (Exception x)
+          {
+            Cache.log.warn(
+                    "Couldn't retrieve 3d-beacons model for uniprot id"
+                            + searchTerm + " : " + tdbURL,
+                    x);
+          }
+        }
+        seqFetcher.parseResult(allSeqs,
+                "3D-Beacons models for " + searchTerm, FileFormat.MMCif,
+                null);
+
+      }
+    });
+    delayAndEnableActionButtons();
+  }
+
+  @Override
+  public FTSRestClientI getFTSRestClient()
+  {
+    return TDBeaconsFTSRestClient.getInstance();
+  }
+
+  @Override
+  public String getFTSFrameTitle()
+  {
+    return defaultFTSFrameTitle;
+  }
+
+  @Override
+  public boolean isPaginationEnabled()
+  {
+    return true;
+  }
+
+  @Override
+  public Map<String, Integer> getTempUserPrefs()
+  {
+    return tempUserPrefs;
+  }
+
+  @Override
+  public String getCacheKey()
+  {
+    return THREEDB_FTS_CACHE_KEY;
+  }
+
+  @Override
+  public String getAutosearchPreference()
+  {
+    return THREEDB_AUTOSEARCH;
+  }
+
+  @Override
+  protected void showHelp()
+  {
+    System.out.println("No help implemented yet.");
+
+  }
+
+  public static String decodeSearchTerm(String enteredText)
+  {
+    // no multiple query support yet
+    return enteredText;
+  }
+}