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

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

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index 5961fc3..3b56a70 100644 (file)
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -258,11 +259,11 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
           {
             if (cancelJob(rslt))
             {
-              System.err.println("Cancelled AACon job: " + rslt);
+              jalview.bin.Console.errPrintln("Cancelled AACon job: " + rslt);
             }
             else
             {
-              System.err.println("FAILED TO CANCEL AACon job: " + rslt);
+              jalview.bin.Console.errPrintln("FAILED TO CANCEL AACon job: " + rslt);
             }
 
           } catch (Exception x)
@@ -344,8 +345,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
         }
         if (collectAnnotationResultsFor(rslt))
         {
-          jalview.bin.Cache.log.debug("Updating result annotation from Job "
-                  + rslt + " at " + service.getUri());
+          Console.debug("Updating result annotation from Job " + rslt
+                  + " at " + service.getUri());
           updateResultAnnotation(true);
           ap.adjustAnnotationHeight();
         }
@@ -355,13 +356,13 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     catch (JobSubmissionException x)
     {
 
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "submission error with " + getServiceActionText() + " :");
       x.printStackTrace();
       calcMan.disableWorker(this);
     } catch (ResultNotAvailableException x)
     {
-      System.err.println("collection error:\nJob ID: " + rslt);
+      jalview.bin.Console.errPrintln("collection error:\nJob ID: " + rslt);
       x.printStackTrace();
       calcMan.disableWorker(this);
 
@@ -392,7 +393,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
         {
           guiProgress.setProgressBar("", progressId);
         }
-        ap.paintAlignment(true);
+        // TODO: may not need to paintAlignment again !
+        ap.paintAlignment(false, false);
       }
       if (msg.length() > 0)
       {
@@ -439,11 +441,11 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       String id = rslt;
       if (cancelJob(rslt))
       {
-        System.err.println("Cancelled job " + id);
+        jalview.bin.Console.errPrintln("Cancelled job " + id);
       }
       else
       {
-        System.err.println("Job " + id + " couldn't be cancelled.");
+        jalview.bin.Console.errPrintln("Job " + id + " couldn't be cancelled.");
       }
     } catch (Exception q)
     {
@@ -602,7 +604,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
   protected boolean checkDone()
   {
     calcMan.notifyStart(this);
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     while (!calcMan.notifyWorking(this))
     {
       if (calcMan.isWorking(this))
@@ -613,7 +615,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       {
         if (ap != null)
         {
-          ap.paintAlignment(false);
+          ap.paintAlignment(false, false);
         }
 
         Thread.sleep(200);