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 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,
- FileParse source) throws IOException
+ 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()));
Atom tmpatom = new Atom(line);
try
{
- tmpchain = findChain(tmpatom.chain);
+ tmpchain = findChain(tmpatom.chain);
if (tmpatom.resNumIns.trim().equals(lastID))
{
// phosphorylated protein - seen both CA and P..
markCalcIds();
}
-
-
/**
* Process a parsed chain to construct and return a Sequence, and add it to
* the list of sequences parsed.