import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
for (int i = 0; i < ids.size(); i++)
{
Sequence sequence = (Sequence) ids.get(i);
- System.out.println(sequence.getName());
+ jalview.bin.Console.outPrintln(sequence.getName());
BlastThread thread = new BlastThread(sequence);
thread.start();
}
}
- DBRefEntry[] entries = oldseq.getDBRefs();
- if (entries != null)
+ List<DBRefEntry> entries = oldseq.getDBRefs();
+ // BH 2019.01.25 check for 0-length was missing here
+ if (entries != null && entries.size() > 0)
{
oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
jalview.datamodel.DBRefSource.UNIPROT, "0",
- entries[0].getAccessionId()));
+ entries.get(0).getAccessionId()));
}
}
}
BlastThread(Sequence sequence)
{
- System.out.println("blasting for: " + sequence.getName());
+ jalview.bin.Console.outPrintln("blasting for: " + sequence.getName());
this.sequence = sequence;
}
else
{
Thread.sleep(10000);
- System.out.println("WSWuBlastClient: I'm alive "
+ jalview.bin.Console.outPrintln("WSWuBlastClient: I'm alive "
+ sequence.getName() + " " + jobid); // log.debug
}
} catch (Exception ex)
{
jobComplete = true;
jobsRunning--;
- System.err.println("WSWUBlastClient error:\n" + exp.toString());
+ jalview.bin.Console.errPrintln("WSWUBlastClient error:\n" + exp.toString());
exp.printStackTrace();
}
}