import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
alignFile = new JPredFile(inFile, type);
((JPredFile) alignFile).removeNonSequences();
}
- else if (format.equals("PDB"))
- {
-
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- type);
- ((StructureFile) alignFile).setDbRefType(format);
- }
- else if (format.equalsIgnoreCase("mmCIF"))
+ else if (format.equals("PDB") || format.equalsIgnoreCase("mmCIF"))
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+ alignFile = new JmolParser(inFile, type);
((StructureFile) alignFile).setDbRefType(format);
}
else if (format.equals("STH"))
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
}
else
{
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))