--- /dev/null
+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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff