*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.io.FormatAdapter;
import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
+
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
* to an alignment TODO: create interface to pass alignment properties and tree
{
super();
// all extensions of this PFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
+ addDbSourceProperty(DBRefSource.DOMAINDB);
+ addDbSourceProperty(DBRefSource.ALIGNMENTDB);
}
/*
* this doesn't work - DbSource is key for the hash of DbSourceProxy instances
* - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
* 'alignment' source - means proxy is higher level than a sequence source.
- * return jalview.datamodel.DBRefSource.PFAM; }
+ * return DBRefSource.PFAM; }
*/
/*
// 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,
+ AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+ + queries.trim().toUpperCase(), FormatAdapter.URL,
"STH");
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
+new DBRefEntry(DBRefSource.PFAM,
// getDbSource(),
getDbVersion(), queries.trim().toUpperCase()));
- if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
+ if (!getDbSource().equals(DBRefSource.PFAM))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(
new DBRefEntry(getDbSource(), getDbVersion(), queries
public String getXfamSource()
{
- return jalview.datamodel.DBRefSource.PFAM;
+ return DBRefSource.PFAM;
}
}