/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.
- *
+ * 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/>.
+ * 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.ws.dbsources;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+import jalview.io.FormatAdapter;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
/**
protected abstract String getXFAMURL();
+ @Override
public abstract String getDbVersion();
abstract String getXfamSource();
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
// TODO: this is not a perfect implementation. We need to be able to add
// individual references to each sequence in each family alignment that's
// retrieved.
startQuery();
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
+ // TODO: trap HTTP 404 exceptions and return null
+ AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+ + queries.trim().toUpperCase() + getXFAMURLSUFFIX(),
+ jalview.io.FormatAdapter.URL, "STH");
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
return rcds;
}
-}
\ No newline at end of file
+ /**
+ * Pfam and Rfam provide alignments
+ */
+ @Override
+ public boolean isAlignmentSource()
+ {
+ return true;
+ }
+
+ /**
+ * default suffix to append the retrieval URL for this source.
+ *
+ * @return "" for most Xfam sources
+ */
+ public String getXFAMURLSUFFIX()
+ {
+ return "";
+ }
+
+}