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JAL-629 Fix --structureimage and options
[jalview.git]
/
src
/
jalview
/
ws
/
jws1
/
SeqSearchWSThread.java
diff --git
a/src/jalview/ws/jws1/SeqSearchWSThread.java
b/src/jalview/ws/jws1/SeqSearchWSThread.java
index
c0dcf67
..
805f64c
100644
(file)
--- a/
src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/
src/jalview/ws/jws1/SeqSearchWSThread.java
@@
-22,7
+22,7
@@
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
import jalview.api.FeatureColourI;
import jalview.analysis.AlignSeq;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
@@
-212,9
+212,9
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to parse the annotation file associated with the alignment.");
"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);
}
e.printStackTrace(System.err);
}
@@
-229,9
+229,9
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to parse the Features file associated with the alignment.");
"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;
e.printStackTrace(System.err);
}
jalview.io.NewickFile nf = null;
@@
-250,9
+250,9
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to parse the treeFile associated with the alignment.");
"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);
}
e.printStackTrace(System.err);
}
@@
-425,7
+425,7
@@
class SeqSearchWSThread 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.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
@@
-469,9
+469,9
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
{
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
{
- if (Cache.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
{
- Cache.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
"Tried to submit an already submitted job " + j.getJobId());
}
return;
@@
-496,7
+496,7
@@
class SeqSearchWSThread 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
{
@@
-514,7
+514,7
@@
class SeqSearchWSThread 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");
@@
-579,7
+579,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
} catch (Exception ex)
{
} catch (Exception ex)
{
- Cache.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);
@@
-616,7
+616,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
{
if (!newFrame)
{
{
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
return;
}
// each subjob is an independent alignment for the moment