{
long progressSessionId = System.currentTimeMillis() * 3;
+ boolean inspectPdbEntry=false;
+ PDBEntry barepdbe=null;
+ if (tft==null || paeFilename==null)
+ {
+ for (SequenceI s:sequenceArray)
+ {
+ while (s.getDatasetSequence()!=null)
+ {
+ s = s.getDatasetSequence();
+ }
+ if (s.getAllPDBEntries()!=null)
+ {
+ for (PDBEntry p:s.getAllPDBEntries())
+ {
+ if (p.getFile()!=null && p.getFile().equals(pdbFile))
+ {
+ if (barepdbe==null)
+ {
+ barepdbe=new PDBEntry(p);
+ } else {
+ // todo - may need to copy and null the chaincode so we can do a faithful update
+ barepdbe.updateFrom(p);
+ }
+ }
+ }
+ }
+ }
+ if (barepdbe!=null)
+ {
+ if (barepdbe.hasTempFacType())
+ {
+ try {
+ tft = TFType.valueOf(barepdbe.getTempFacType().toUpperCase(Locale.ROOT));
+ } catch (IllegalArgumentException ia)
+ {
+ Console.warn("Ignoring unknown temperature factor type '"+barepdbe.getTempFacType()+"'");
+ }
+ }
+ }
+
+ }
/**
* do we extract and transfer annotation from 3D data ?
*/