JAL-4366 JAL-728 simple hack to use 3di matrix when gecos-3di is enabled

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index db6e03f..611aa79 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -21,7 +21,7 @@
 package jalview.ws.jws2;
 
 import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -574,7 +574,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           {
             cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
                     + exc + "\n");
-            Cache.log.warn(
+            Console.warn(
                     "Exception whilst cancelling " + jobs[job].getJobId(),
                     exc);
           }
@@ -667,9 +667,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     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;
@@ -703,7 +703,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       {
         j.setSubmitted(true);
         j.setSubjobComplete(false);
-        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+        // jalview.bin.Console.outPrintln(WsURL + " Job Id '" + jobId + "'");
         return;
       }
       else
@@ -749,7 +749,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     } catch (Error e)
     {
       // 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.printStackTrace(System.err);
@@ -759,7 +759,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     } catch (Exception e)
     {
       // 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.printStackTrace(System.err);
@@ -811,7 +811,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
             } catch (Exception e)
             {
 
-              Cache.log.warn(
+              Console.warn(
                       "Exception when retrieving remaining Job progress data for job "
                               + msjob.getJobId() + " on server " + WsUrl);
               e.printStackTrace();
@@ -835,12 +835,12 @@ class MsaWSThread extends AWS2Thread implements WSClientI
             }
           } while (nunchanged > 0 && nexcept > 0);
 
-          if (Cache.log.isDebugEnabled())
+          if (Console.isDebugEnabled())
           {
-            System.out.println("Job Execution file for job: "
+            jalview.bin.Console.outPrintln("Job Execution file for job: "
                     + msjob.getJobId() + " on server " + WsUrl);
-            System.out.println(msjob.getStatus());
-            System.out.println("*** End of status");
+            jalview.bin.Console.outPrintln(msjob.getStatus());
+            jalview.bin.Console.outPrintln("*** End of status");
 
           }
           try
@@ -850,7 +850,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           {
             // job has failed for some reason - probably due to invalid
             // parameters
-            Cache.log.debug(
+            Console.debug(
                     "Results not available for finished job - marking as broken job.",
                     e);
             msjob.jobProgress.append(
@@ -859,7 +859,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
             msjob.setjobStatus(JobStatus.FAILED);
           } catch (Exception e)
           {
-            Cache.log.error("Couldn't get Alignment for job.", e);
+            Console.error("Couldn't get Alignment for job.", e);
             // TODO: Increment count and retry ?
             msjob.setjobStatus(JobStatus.UNDEFINED);
           }
@@ -887,7 +887,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     } catch (Exception ex)
     {
 
-      Cache.log.error(
+      Console.error(
               "Unexpected exception when processing results for " + alTitle,
               ex);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
@@ -986,7 +986,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     else
     {
       // TODO 2.9.x feature
-      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