}
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to parse the annotation file associated with the alignment.");
- System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ jalview.bin.Console.errPrintln(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
}
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to parse the Features file associated with the alignment.");
- System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ jalview.bin.Console.errPrintln(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
jalview.io.NewickFile nf = null;
}
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to parse the treeFile associated with the alignment.");
- System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ jalview.bin.Console.errPrintln(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
j.setJobId(jobsubmit.getJobId());
j.setSubmitted(true);
j.setSubjobComplete(false);
- // System.out.println(WsURL + " Job Id '" + jobId + "'");
+ // jalview.bin.Console.outPrintln(WsURL + " Job Id '" + jobId + "'");
}
else
{
{
// TODO: JBPNote catch timeout or other fault types explicitly
// For unexpected errors
- System.err.println(WebServiceName
+ jalview.bin.Console.errPrintln(WebServiceName
+ "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ "When contacting Server:" + WsUrl + "\n" + e.toString()
+ "\n");
{
if (!newFrame)
{
- System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+ jalview.bin.Console.errPrintln("MERGE WITH OLD FRAME NOT IMPLEMENTED");
return;
}
// each subjob is an independent alignment for the moment