*/
package jalview.ws.dbsources;
-import jalview.bin.Cache;
+import java.util.Locale;
+
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.io.DataSourceType;
*/
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)
- {
- Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
- }
+ Console.debug("XFAM URL for retrieval is: " + xfamUrl);
- AlignmentI rcds = new FormatAdapter().readFile(xfamUrl ,
+ AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
DataSourceType.URL, FileFormat.Stockholm);
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
- // getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ // getDbSource(),
+ 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()));
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
+ 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 "";
}