package MCview;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
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 file, String protocol)
+ throws IOException
{
super(false, file, protocol);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ 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()));