protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
PDBEntry[] pdbs, SequenceI[][] seqsForPdbs, AlignmentPanel ap)
{
+ PDBEntry[] pdbsForFile = getUniquePdbFiles(pdbs);
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(ap, pdbs, ap.av.collateForPDB(pdbs));
+ sview = new AppJmol(ap, pdbsForFile, ap.av.collateForPDB(pdbsForFile));
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(pdbs, ap.av.collateForPDB(pdbs), ap);
+ sview = new ChimeraViewFrame(pdbsForFile,
+ ap.av.collateForPDB(pdbsForFile), ap);
}
else
{
return sview;
}
+ /**
+ * Convert the array of PDBEntry into an array with no filename repeated
+ *
+ * @param pdbs
+ * @return
+ */
+ static PDBEntry[] getUniquePdbFiles(PDBEntry[] pdbs)
+ {
+ if (pdbs == null)
+ {
+ return null;
+ }
+ List<PDBEntry> uniques = new ArrayList<PDBEntry>();
+ List<String> filesSeen = new ArrayList<String>();
+ for (PDBEntry entry : pdbs)
+ {
+ String file = entry.getFile();
+ if (file == null)
+ {
+ uniques.add(entry);
+ }
+ else if (!filesSeen.contains(file))
+ {
+ uniques.add(entry);
+ filesSeen.add(file);
+ }
+ }
+ return uniques.toArray(new PDBEntry[uniques.size()]);
+ }
+
protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
{