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)
- throws IOException
+ boolean externalSecStr, String dataObject,
+ DataSourceType sourceType) throws IOException
{
- super(false, dataObject, protocol);
+ super(false, dataObject, sourceType);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
}
@Override
- public String print()
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_pdb_file"));
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
} catch (NumberFormatException ex)
{
if (line != null)
public static String relocateCalcId(String calcId,
Hashtable<String, String> alreadyLoadedPDB) throws Exception
{
- int s = CALC_ID_PREFIX.length(), end = calcId
- .indexOf(CALC_ID_PREFIX, s);
+ int s = CALC_ID_PREFIX.length(),
+ end = calcId.indexOf(CALC_ID_PREFIX, s);
String between = calcId.substring(s, end - 1);
return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ calcId.substring(end);