*/
package jalview.ext.jmol;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+ setStructureFileType(getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
? PDBEntry.Type.MMCIF.toString()
: "PDB");
return validator;
}
-
+ PDBEntry.Type jmolFiletype=null;
+ /**
+ * resolve a jmol filetype string and update the jmolFiletype field accordingly
+ * @param jmolIdentifiedFileType
+ * @return true if filetype was identified as MMCIF, PDB
+ */
+ public boolean updateFileType(String jmolIdentifiedFileType)
+ {
+ if (jmolIdentifiedFileType == null
+ || jmolIdentifiedFileType.trim().equals(""))
+ {
+ return false;
+ }
+ if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) {
+ jmolFiletype = PDBEntry.Type.MMCIF;
+ return true;
+ }
+ if ("pdb".equalsIgnoreCase(jmolIdentifiedFileType))
+ {
+ jmolFiletype = PDBEntry.Type.PDB;
+ return true;
+ }
+ return false;
+ }
+
public void transformJmolModelToJalview(ModelSet ms) throws IOException
{
try
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
- String isMMCIF = (String) ms.getInfo(0, "fileType");
-
+ boolean isMMCIF = false;
+ String jmolFileType_String = (String) ms.getInfo(0, "fileType");
+ if (updateFileType(jmolFileType_String))
+ {
+ setStructureFileType(jmolFiletype.toString());
+ }
+
+ isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
+
if (pdbId == null)
{
setId(safeName(getDataName()));
{
setId(pdbId);
setPDBIdAvailable(true);
- alphaFoldModel = alphaFold.search(pdbId) && isMMCIF!=null && isMMCIF.equalsIgnoreCase("mmcif");
+ alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
tmpchain.atoms.addElement(tmpatom);
} else
{
- tmpchain = new PDBChain(getId(), tmpatom.chain,isAlphafoldModel());
+ String tempFString=null;
+ if (isAlphafoldModel())
+ {
+ tempFString = "Alphafold Reliability";
+ }
+
+ tmpchain = new PDBChain(getId(), tmpatom.chain,tempFString);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}