Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...

[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 9ad936b..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;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 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");
-            Cache.warn(
+            Console.warn(
                     "Exception whilst cancelling " + jobs[job].getJobId(),
                     exc);
           }
@@ -453,9 +453,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     MsaWSJob j = (MsaWSJob) job;
     if (j.isSubmitted())
     {
-      if (Cache.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.debug(
+        Console.debug(
                 "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);
-        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+        // jalview.bin.Console.outPrintln(WsURL + " Job Id '" + jobId + "'");
       }
       else
       {
@@ -497,7 +497,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     {
       // 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");
@@ -544,9 +544,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
           results++;
           // if (Cache.isDebugEnabled())
           // {
-          // System.out.println("Job lob for job
+          // jalview.bin.Console.outPrintln("Job lob for job
           // "+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)
@@ -571,7 +571,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     } catch (Exception ex)
     {
 
-      Cache.error(
+      Console.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
     {
-      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