import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import java.io.IOException;
}
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String file, String protocol)
+ boolean externalSecStr, String dataObject, String protocol)
throws IOException
{
- super(false, file, protocol);
+ super(false, dataObject, protocol);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
break;
}
if (line.indexOf("ATOM") == 0
- || (line.indexOf("HETATM") == 0 && !terFlag))
+ || (StructureImportSettings.isProcessHETATMs()
+ && line.indexOf("HETATM") == 0 && !terFlag))
{
terFlag = false;