/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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
// retrieved.
startQuery();
// TODO: trap HTTP 404 exceptions and return null
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
+ 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++)
{
return rcds;
}
+ /**
+ * 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 "";
+ }
+
}