X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=a042dee94a97fcba75fa665e3c81fde8df73b1ca;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=a239625f401fa20035072d4ce7bef46264c2192e;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index a239625..a042dee 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -22,7 +22,7 @@ package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -119,17 +119,17 @@ 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()
@@ -235,8 +235,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alhidden = HiddenColumns.propagateInsertions(profileseq, al,
-                    input);
+            alhidden = al.propagateInsertions(profileseq, input);
           }
         }
       }
@@ -462,7 +461,7 @@ 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
@@ -481,11 +480,11 @@ class JPredThread extends JWS1Thread implements WSClientI
         wsInfo.setProgressText(j.getJobnum(),
                 "Failed to submit the prediction. (Just close the window)\n"
                         + "It is most likely that there is a problem with the server.\n");
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "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
       {
@@ -496,8 +495,7 @@ 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);
@@ -524,7 +522,7 @@ 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);
@@ -578,9 +576,9 @@ 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;
@@ -593,8 +591,7 @@ 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(),
@@ -653,7 +650,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
         else
         {
-          Cache.log.info("Append results onto existing alignment.");
+          Console.info("Append results onto existing alignment.");
         }
       }
     }