apply jalview code style

[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 63872f5..98f2645 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -100,8 +100,8 @@ class JPredThread extends JWS1Thread implements WSClientI
       jalview.bin.Cache.log.debug("Parsing output from JNet job.");
       // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
       // "File");
-      jalview.io.JPredFile prediction = new jalview.io.JPredFile(result
-              .getPredfile(), "Paste");
+      jalview.io.JPredFile prediction = new jalview.io.JPredFile(
+              result.getPredfile(), "Paste");
       SequenceI[] preds = prediction.getSeqsAsArray();
       jalview.bin.Cache.log.debug("Got prediction profile.");
 
@@ -110,8 +110,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         jalview.bin.Cache.log.debug("Getting associated alignment.");
         // we ignore the returned alignment if we only predicted on a single
         // sequence
-        String format = new jalview.io.IdentifyFile().Identify(result
-                .getAligfile(), "Paste");
+        String format = new jalview.io.IdentifyFile().Identify(
+                result.getAligfile(), "Paste");
 
         if (jalview.io.FormatAdapter.isValidFormat(format))
         {
@@ -180,8 +180,8 @@ class JPredThread extends JWS1Thread implements WSClientI
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
-        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al
-                .getSequenceAt(FirstSeq), SequenceInfo))
+        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+                al.getSequenceAt(FirstSeq), SequenceInfo))
         {
           throw (new Exception(
                   "Couldn't recover sequence properties for JNet Query sequence!"));
@@ -352,8 +352,8 @@ class JPredThread extends JWS1Thread implements WSClientI
     {
       super();
       this.predMap = delMap;
-      String sq = AlignSeq.extractGaps(Comparison.GapChars, seq
-              .getSequenceAsString());
+      String sq = AlignSeq.extractGaps(Comparison.GapChars,
+              seq.getSequenceAsString());
       if (sq.length() >= 20)
       {
         this.SequenceInfo = SequenceInfo;
@@ -470,14 +470,12 @@ class JPredThread extends JWS1Thread implements WSClientI
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       if (e.getMessage().indexOf("Exception") > -1)
       {
-        wsInfo
-                .setStatus(j.getJobnum(),
-                        WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        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");
+        wsInfo.setStatus(j.getJobnum(),
+                WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        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("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
                         + e.getMessage() + "\n");
@@ -492,8 +490,8 @@ class JPredThread extends JWS1Thread implements WSClientI
                 "Failed to submit the prediction:\n" + e.getMessage()
                         + wsInfo.getProgressText());
 
-        jalview.bin.Cache.log.debug("Failed Submission of job " + j.getJobnum(),
-                e);
+        jalview.bin.Cache.log.debug(
+                "Failed Submission of job " + j.getJobnum(), e);
 
       }
       j.setAllowedServerExceptions(-1);
@@ -585,7 +583,8 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             jalview.bin.Cache.log.error(
                     "JNet Client: JPred Annotation Parse Error", e);
-            wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+            wsInfo.setStatus(j.getJobnum(),
+                    WebserviceInfo.STATE_STOPPED_ERROR);
             wsInfo.appendProgressText(j.getJobnum(), OutputHeader + "\n"
                     + j.result.getStatus()
                     + "\nInvalid JNet job result data!\n" + e.getMessage());
@@ -646,7 +645,7 @@ class JPredThread extends JWS1Thread implements WSClientI
 
   public void pollJob(AWsJob job) throws Exception
   {
-    ((JPredJob)job).result = server.getresult(job.getJobId());
+    ((JPredJob) job).result = server.getresult(job.getJobId());
   }
 
   public boolean isCancellable()