+/*
+ * 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.URI;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import java.util.Objects;
import javax.ws.rs.core.MediaType;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.api.StructureFTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
-import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
-import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
URI uri = webResource.getURI();
- System.out.println(uri.toString());
+ jalview.bin.Console.outPrintln(uri.toString());
// Execute the REST request
ClientResponse clientResponse;
return searchResult;
}
- private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
+ private static FTSData getFTSData(
+ Map<String, Object> tdbJsonStructureSummary,
FTSRestRequest tdbRequest)
{
String primaryKey = null;
summaryRowData[0] = associatedSequence;
colCounter = 1;
}
-
+ Map<String, Object> tdbJsonStructure = (Map<String, Object>) tdbJsonStructureSummary
+ .get("summary");
for (FTSDataColumnI field : displayFields)
{
String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
? " "
: tdbJsonStructure.get(field.getCode()).toString();
- // System.out.println("Field : " + field + " Data : " + fieldData);
+ // jalview.bin.Console.outPrintln("Field : " + field + " Data : " +
+ // fieldData);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
} catch (Exception e)
{
// e.printStackTrace();
- System.out.println("offending value:" + fieldData + fieldData);
+ jalview.bin.Console
+ .outPrintln("offending value:" + fieldData + fieldData);
}
}
}
private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
+ @Override
public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
{
if (allDefaultDisplayedStructureDataColumns == null