+/*
+ * 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.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.Console;
import jalview.datamodel.AlignmentI;
import jalview.fts.api.FTSDataColumnI;
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;
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) )
+ // 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)
}
} catch (Exception x)
{
- Console.warn(
- "Couldn't retrieve 3d-beacons model for uniprot id"
- + searchTerm + " : " + tdbURL,
- x);
+ Console.warn("Couldn't retrieve 3d-beacons model for uniprot id"
+ + searchTerm + " : " + tdbURL, x);
}
}
seqFetcher.parseResult(allSeqs,
@Override
protected void showHelp()
{
- System.out.println("No help implemented yet.");
+ jalview.bin.Console.outPrintln("No help implemented yet.");
}
// no multiple query support yet
return enteredText;
}
+
+ public String getDbName()
+ {
+ return "3D-Beacons";
+ }
}