import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.util.MessageManager;
}
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String dataObject, String protocol)
+ boolean externalSecStr, String dataObject,
+ DataSourceType sourceType)
throws IOException
{
- super(false, dataObject, protocol);
+ super(false, dataObject, sourceType);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr,
- FileParse source) throws IOException
+ boolean externalSecStr, FileParse source) throws IOException
{
super(false, source);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
}
@Override
- public String print()
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
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.