Logger moved to prefs so that class not found error can be handled in main

[jalview.git] / src / jalview / ws / JPredClient.java

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 45d4bd1..9fe7e27 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -190,7 +190,7 @@ public class JPredClient
                 "Timed out when communicating with server\nTry again later.\n"));\r
           }\r
           if (result.getState()==0)\r
-            jalview.bin.Jalview.log.debug("Finished "+jobId);\r
+            jalview.bin.Cache.log.debug("Finished "+jobId);\r
           if (result.isRunning())\r
           {\r
             wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
@@ -317,7 +317,7 @@ public class JPredClient
             "JPredWS Client: Failed to submit the prediction (Possibly a server error - see below)\n" +\r
             e.getMessage() + "\n");\r
 \r
-        jalview.bin.Jalview.log.debug("Failed Submission",e);\r
+        jalview.bin.Cache.log.debug("Failed Submission",e);\r
       }\r
     }\r
 \r
@@ -370,20 +370,20 @@ public class JPredClient
 \r
       try\r
       {\r
-        jalview.bin.Jalview.log.debug("Parsing output from JNet job.");\r
+        jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
         // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
         jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
             getPredfile(),\r
             "Paste");\r
         SequenceI[] preds = prediction.getSeqsAsArray();\r
-        jalview.bin.Jalview.log.debug("Got prediction profile.");\r
+        jalview.bin.Cache.log.debug("Got prediction profile.");\r
         Alignment al;\r
         int FirstSeq; // the position of the query sequence in Alignment al\r
         boolean noMsa = true; // set if no MSA has been returned by JPred\r
 \r
         if ( (this.msa != null) && (result.getAligfile() != null))\r
         {\r
-          jalview.bin.Jalview.log.debug("Getting associated alignment.");\r
+          jalview.bin.Cache.log.debug("Getting associated alignment.");\r
           // we ignore the returned alignment if we only predicted on a single sequence\r
           String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
               "Paste");\r
@@ -520,7 +520,7 @@ public class JPredClient
          */\r
 \r
         wsInfo.setProgressText(OutputHeader);\r
-        jalview.bin.Jalview.log.debug("Finished parsing output.");\r
+        jalview.bin.Cache.log.debug("Finished parsing output.");\r
         AlignFrame af = new AlignFrame(al);\r
 \r
         Desktop.addInternalFrame(af, altitle,\r
@@ -529,8 +529,8 @@ public class JPredClient
       }\r
       catch (Exception ex)\r
       {\r
-        jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");\r
-        jalview.bin.Jalview.log.debug("Exception: ",ex);\r
+        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.");\r
+        jalview.bin.Cache.log.debug("Exception: ",ex);\r
       }\r
     }\r
   }\r