Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / ws / jws1 / JPredThread.java

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index b7b8e5f..06f80c4 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -23,7 +23,7 @@ package jalview.ws.jws1;
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
 import jalview.analysis.SeqsetUtils.SequenceInfo;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -121,17 +121,17 @@ class JPredThread extends JWS1Thread implements WSClientI
 
       JpredResult result = (JpredResult) this.result;
 
-      Cache.log.debug("Parsing output from JNet job.");
+      Console.debug("Parsing output from JNet job.");
       // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
       // "File");
       JPredFile prediction = new JPredFile(result.getPredfile(),
               DataSourceType.PASTE);
       SequenceI[] preds = prediction.getSeqsAsArray();
-      Cache.log.debug("Got prediction profile.");
+      Console.debug("Got prediction profile.");
 
       if ((this.msa != null) && (result.getAligfile() != null))
       {
-        Cache.log.debug("Getting associated alignment.");
+        Console.debug("Getting associated alignment.");
         // we ignore the returned alignment if we only predicted on a single
         // sequence
         FileFormatI format = new IdentifyFile()
@@ -463,7 +463,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         {
           job.setSubmitted(true);
           job.setSubjobComplete(false);
-          Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+          Console.info(WsUrl + " Job Id '" + job.getJobId() + "'");
         }
       }
       else
@@ -486,7 +486,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                 "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
                         + e.getMessage() + "\n");
 
-        jalview.bin.Cache.log.warn("Server Exception", e);
+        Console.warn("Server Exception", e);
       }
       else
       {
@@ -497,8 +497,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                         "info.failed_to_submit_prediction", new String[]
                         { e.getMessage(), wsInfo.getProgressText() }));
 
-        jalview.bin.Cache.log
-                .debug("Failed Submission of job " + j.getJobnum(), e);
+        Console.debug("Failed Submission of job " + j.getJobnum(), e);
 
       }
       j.setAllowedServerExceptions(-1);
@@ -525,7 +524,7 @@ class JPredThread extends JWS1Thread implements WSClientI
     } catch (Exception ex)
     {
 
-      Cache.log.error(
+      Console.error(
               "Unexpected exception when processing results for " + altitle,
               ex);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
@@ -579,9 +578,9 @@ class JPredThread extends JWS1Thread implements WSClientI
           msa = (j.msa != null) ? true : msa;
           try
           {
-            jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+            Console.debug("Parsing output of job " + jn);
             jobres = j.getResultSet();
-            jalview.bin.Cache.log.debug("Finished parsing output.");
+            Console.debug("Finished parsing output.");
             if (jobs.length == 1)
             {
               res = jobres;
@@ -594,8 +593,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             }
           } catch (Exception e)
           {
-            jalview.bin.Cache.log
-                    .error("JNet Client: JPred Annotation Parse Error", e);
+            Console.error("JNet Client: JPred Annotation Parse Error", e);
             wsInfo.setStatus(j.getJobnum(),
                     WebserviceInfo.STATE_STOPPED_ERROR);
             wsInfo.appendProgressText(j.getJobnum(),
@@ -654,7 +652,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
         else
         {
-          Cache.log.info("Append results onto existing alignment.");
+          Console.info("Append results onto existing alignment.");
         }
       }
     }