import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLEncoder;
+import java.util.Iterator;
public class Annotate3D
{
sb.append(cbuff[i]);
}
}
-
- FileParse fp = new InputStreamParser(
- jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
- .toString()), source.getDataName());
- AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
- return nal;
+ Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+ .getRNAMLForPDBFileAsString(sb.toString());
+ AlignmentI al=null;
+ while (r.hasNext())
+ {
+ FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+ AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+ if (al==null)
+ {
+ al = nal;
+ } else {
+ al.append(nal);
+ }
+ }
+ return al;
} catch (Throwable x)
{
if (x instanceof IOException)