*/
package jalview.ws.dbsources;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
*/
public abstract class Xfam extends DbSourceProxyImpl
{
-
public Xfam()
{
super();
}
- protected abstract String getXFAMURL();
+ /**
+ * the base URL for this Xfam-like service
+ *
+ * @return
+ */
+ protected abstract String getURLPrefix();
@Override
public abstract String getDbVersion();
// retrieved.
startQuery();
// TODO: trap HTTP 404 exceptions and return null
- String xfamUrl = getXFAMURL() + queries.trim().toUpperCase()
- + getXFAMURLSUFFIX();
+ String xfamUrl = getURL(queries);
if (Cache.log != null)
{
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
// getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
}
}
stopQuery();
return rcds;
}
+ String getURL(String queries)
+ {
+ return getURLPrefix() + "/family/" + queries.trim().toUpperCase(Locale.ROOT)
+ + getURLSuffix();
+ }
+
/**
* Pfam and Rfam provide alignments
*/
*
* @return "" for most Xfam sources
*/
- public String getXFAMURLSUFFIX()
+ public String getURLSuffix()
{
return "";
}