package MCview;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import java.io.IOException;
boolean predictSecondaryStructure, boolean externalSecStr)
{
super();
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+ externalSecStr);
}
- public PDBfile(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- String file, String protocol) throws IOException
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String dataObject, String protocol)
+ throws IOException
{
- super(false, file, protocol);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ super(false, dataObject, protocol);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
- public PDBfile(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr,
FileParse source) throws IOException
{
super(false, source);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
@Override
public void parse() throws IOException
{
+ setDbRefType(DBRefSource.PDB);
// TODO set the filename sensibly - try using data source name.
setId(safeName(getDataName()));
break;
}
if (line.indexOf("ATOM") == 0
- || (line.indexOf("HETATM") == 0 && !terFlag))
+ || (StructureImportSettings.isProcessHETATMs()
+ && line.indexOf("HETATM") == 0 && !terFlag))
{
terFlag = false;