JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[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.bin.Cache;
+import jalview.bin.Console;
 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)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "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);
         }
 
@@ -229,9 +229,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           }
         } catch (Exception e)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "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;
@@ -250,9 +250,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           }
         } catch (Exception e)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "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);
         }
 
@@ -425,7 +425,7 @@ class SeqSearchWSThread 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);
           }
@@ -469,9 +469,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     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;
@@ -496,7 +496,7 @@ class SeqSearchWSThread 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
       {
@@ -514,7 +514,7 @@ class SeqSearchWSThread 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");
@@ -579,7 +579,7 @@ class SeqSearchWSThread 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);
@@ -616,7 +616,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
   {
     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