+/*
+ * 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.threedbeacons;
+import java.net.HttpURLConnection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
+import javax.swing.SwingUtilities;
+
+import jalview.bin.Console;
+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.FormatAdapter;
import jalview.util.MessageManager;
@SuppressWarnings("serial")
public class TDBeaconsFTSPanel extends GFTSPanel
-{
+{
private static String defaultFTSFrameTitle = MessageManager
- .getString("label.threedb_sequence_fetcher");
+ .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)
{
- super(fetcher);
- pageLimit = TDBeaconsFTSRestClient.getInstance().getDefaultResponsePageSize();
+ // 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();
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(allowEmptySequence);
request.setResponseSize(100);
- request.setFieldToSearchBy("(" + searchTarget + ":");
- request.setSearchTerm(searchTerm + ")");
+ // expect it to be uniprot accesssion
+ request.setSearchTerm(searchTerm + ".json");
request.setOffSet(offSet);
request.setWantedFields(wantedFields);
- FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient.getInstance();
+ FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient
+ .getInstance();
FTSRestResponse resultList;
try
{
if (isPaginationEnabled() && resultSetCount > 0)
{
- String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
+ String f1 = totalNumberformatter
+ .format(Integer.valueOf(offSet + 1));
String f2 = totalNumberformatter
.format(Integer.valueOf(offSet + resultSetCount));
String f3 = totalNumberformatter
}
}.start();
}
-
+
@Override
public void okAction()
{
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<>();
+ final HashSet<String> selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
{
String idStr = getResultTable()
.getValueAt(summaryRow, primaryKeyColIndex).toString();
- selectedIdsSet.add(searchTerm);
+ selectedIdsSet.add(idStr);
}
for (String idStr : paginatorCart)
{
- selectedIdsSet.add(searchTerm);
+ selectedIdsSet.add(idStr);
}
for (String selectedId : selectedIdsSet)
selectedIds.append(selectedId).append(";");
}
- String ids = selectedIds.toString();
- seqFetcher.setQuery(ids);
- Thread worker = new Thread(seqFetcher);
- worker.start();
+ 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)
+ {
+ Console.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()
{
protected void showHelp()
{
System.out.println("No help implemented yet.");
-
+
+ }
+
+ public static String decodeSearchTerm(String enteredText)
+ {
+ // no multiple query support yet
+ return enteredText;
}
+ public String getDbName()
+ {
+ return "3D-Beacons";
+ }
}
git://source.jalview.org / jalview.git / blobdiff