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JAL-4308 reduce number of refs to 5, always have canonical reference first.
[jalview.git]
/
src
/
jalview
/
io
/
WSWUBlastClient.java
diff --git
a/src/jalview/io/WSWUBlastClient.java
b/src/jalview/io/WSWUBlastClient.java
index
d526a31
..
c7c90f4
100755
(executable)
--- a/
src/jalview/io/WSWUBlastClient.java
+++ b/
src/jalview/io/WSWUBlastClient.java
@@
-32,6
+32,7
@@
import jalview.util.MessageManager;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.StringTokenizer;
import java.util.Vector;
@@
-83,7
+84,7
@@
public class WSWUBlastClient
for (int i = 0; i < ids.size(); i++)
{
Sequence sequence = (Sequence) ids.get(i);
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();
BlastThread thread = new BlastThread(sequence);
thread.start();
@@
-175,12
+176,13
@@
public class WSWUBlastClient
}
}
}
}
- 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",
{
oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
jalview.datamodel.DBRefSource.UNIPROT, "0",
- entries[0].getAccessionId()));
+ entries.get(0).getAccessionId()));
}
}
}
}
}
}
@@
-247,7
+249,7
@@
public class WSWUBlastClient
BlastThread(Sequence sequence)
{
BlastThread(Sequence sequence)
{
- System.out.println("blasting for: " + sequence.getName());
+ jalview.bin.Console.outPrintln("blasting for: " + sequence.getName());
this.sequence = sequence;
}
this.sequence = sequence;
}
@@
-274,7
+276,7
@@
public class WSWUBlastClient
else
{
Thread.sleep(10000);
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)
+ sequence.getName() + " " + jobid); // log.debug
}
} catch (Exception ex)
@@
-313,7
+315,7
@@
public class WSWUBlastClient
{
jobComplete = true;
jobsRunning--;
{
jobComplete = true;
jobsRunning--;
- System.err.println("WSWUBlastClient error:\n" + exp.toString());
+ jalview.bin.Console.errPrintln("WSWUBlastClient error:\n" + exp.toString());
exp.printStackTrace();
}
}
exp.printStackTrace();
}
}