protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
throws Exception
{
- // System.out.println("this is a PDB format and RNA sequence");
+ // jalview.bin.Console.outPrintln("this is a PDB format and RNA sequence");
// note: we use reflection here so that the applet can compile and run
// without the HTTPClient bits and pieces needed for accessing Annotate3D
// web service
processPdbFileWithAnnotate3d(rnaSequences);
} catch (Exception x)
{
- System.err.println("Exceptions when dealing with RNA in pdb file");
+ jalview.bin.Console.errPrintln("Exceptions when dealing with RNA in pdb file");
x.printStackTrace();
}
processWithJmolParser(proteinSequences, true);
} catch (Exception x)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exceptions from Jmol when processing data in pdb file");
x.printStackTrace();
}