import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
String vamsasId;
- DBRefEntryI sourceDBRef;
-
DBRefEntry[] dbrefs;
RNA rna;
}
if (dbrefs==null || dbrefs.length==0)
{
- return Arrays.asList(new DBRefEntry[0]);
+ return Collections.emptyList();
}
synchronized (dbrefs)
{
List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
- DBRefEntry tmp[] = new DBRefEntry[1], res[] = null;
+ DBRefEntry[] tmp = new DBRefEntry[1];
for (DBRefEntry ref : dbrefs)
{
if (!ref.isPrimary())
{
// PDB dbrefs imply there should be a PDBEntry associated
// TODO: tighten PDB dbrefs
- // formally imply Jalview has actually downlaoded and
+ // formally imply Jalview has actually downloaded and
// parsed the pdb file. That means there should be a cached file
// handle on the PDBEntry, and a real mapping between sequence and
// extracted sequence from PDB file
PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
- if (pdbentry != null && pdbentry.getType() != null
- && pdbentry.getType().equalsIgnoreCase("PDB"))
+ if (pdbentry != null && pdbentry.getFile() != null)
{
primaries.add(ref);
}
}
// check standard protein or dna sources
tmp[0] = ref;
- res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+ DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
if (res != null && res[0] == tmp[0])
{
primaries.add(ref);