+ if (afclient.isValidReference(pdbid))
+ {
+ pdbseq = afclient.getSequenceRecords(pdbid,
+ processingEntry.getRetrievalUrl());
+ }
+ else
+ {
+ if (processingEntry.hasRetrievalUrl())
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbid, "UTF-8")
+ .replace("%", "__");
+
+ // retrieve from URL to new local tmpfile
+ File tmpFile = File.createTempFile(safePDBId,
+ "." + (PDBEntry.Type.MMCIF.toString().equals(
+ processingEntry.getType().toString()) ? "cif"
+ : "pdb"));
+ String fromUrl = processingEntry.getRetrievalUrl();
+ UrlDownloadClient.download(fromUrl, tmpFile);
+
+ // may not need this check ?
+ String file = tmpFile.getAbsolutePath();
+ if (file != null)
+ {
+ pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,
+ tmpFile, pdbid, null, null, null);
+ }
+ }
+ else
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ }
+ }