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JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance...
[jalview.git]
/
src
/
jalview
/
ws
/
jws1
/
MsaWSThread.java
diff --git
a/src/jalview/ws/jws1/MsaWSThread.java
b/src/jalview/ws/jws1/MsaWSThread.java
index
006f014
..
727f5be
100644
(file)
--- a/
src/jalview/ws/jws1/MsaWSThread.java
+++ b/
src/jalview/ws/jws1/MsaWSThread.java
@@
-21,7
+21,7
@@
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
@@
-410,7
+410,7
@@
class MsaWSThread extends JWS1Thread implements WSClientI
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
@@
-453,9
+453,9
@@
class MsaWSThread extends JWS1Thread implements WSClientI
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
"Tried to submit an already submitted job " + j.getJobId());
}
return;
@@
-479,7
+479,7
@@
class MsaWSThread extends JWS1Thread implements WSClientI
j.setJobId(jobsubmit.getJobId());
j.setSubmitted(true);
j.setSubjobComplete(false);
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
{
}
else
{
@@
-497,7
+497,7
@@
class MsaWSThread extends JWS1Thread implements WSClientI
{
// TODO: JBPNote catch timeout or other fault types explicitly
// For unexpected errors
{
// 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");
+ "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ "When contacting Server:" + WsUrl + "\n" + e.toString()
+ "\n");
@@
-542,11
+542,11
@@
class MsaWSThread extends JWS1Thread implements WSClientI
&& jobs[j].hasResults())
{
results++;
&& jobs[j].hasResults())
{
results++;
- // if (Cache.log.isDebugEnabled())
+ // if (Cache.isDebugEnabled())
// {
// {
- // System.out.println("Job lob for job
+ // jalview.bin.Console.outPrintln("Job lob for job
// "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
// "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
- // System.out.println(jobs[j].getStatus());
+ // jalview.bin.Console.outPrintln(jobs[j].getStatus());
// }
vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result)
// }
vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result)
@@
-571,7
+571,7
@@
class MsaWSThread extends JWS1Thread implements WSClientI
} catch (Exception ex)
{
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
@@
-709,7
+709,7
@@
class MsaWSThread extends JWS1Thread implements WSClientI
}
else
{
}
else
{
- System.out.println("MERGE WITH OLD FRAME");
+ jalview.bin.Console.outPrintln("MERGE WITH OLD FRAME");
// TODO: modify alignment in original frame, replacing old for new
// alignment using the commands.EditCommand model to ensure the update can
// be undone
// TODO: modify alignment in original frame, replacing old for new
// alignment using the commands.EditCommand model to ensure the update can
// be undone