apply jalview code style

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

diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index 5c21d0a..3eca137 100644 (file)
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -123,8 +123,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
         // for
         // any
         // subjob
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils
-                .SeqCharacterHash(seqs[i]));
+        SeqNames.put(newname,
+                jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
         if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
         {
           seqarray[n] = new vamsas.objects.simple.Sequence();
@@ -139,8 +139,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
           if (seqs[i].getEnd() >= seqs[i].getStart())
           {
             empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
-                    .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
-                            .getSequenceAsString());
+                    .extractGaps(jalview.util.Comparison.GapChars,
+                            seqs[i].getSequenceAsString());
           }
           emptySeqs.add(new String[]
           { newname, empty });
@@ -360,9 +360,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
         }
         if (njobs > 0)
         {
-          wsinfo
-                  .setProgressName("region " + jobs[j].getJobnum(),
-                          jobs[j].getJobnum());
+          wsinfo.setProgressName("region " + jobs[j].getJobnum(),
+                  jobs[j].getJobnum());
         }
         wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
       }
@@ -416,7 +415,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
             cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
                     + exc + "\n");
             Cache.log.warn(
-                    "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+                    "Exception whilst cancelling " + jobs[job].getJobId(),
+                    exc);
           }
           wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
                   + cancelledMessage + "\n");
@@ -433,9 +433,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     {
       if (!jobComplete)
       {
-        wsInfo
-                .setProgressText(OutputHeader
-                        + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+        wsInfo.setProgressText(OutputHeader
+                + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
       }
     }
   }
@@ -505,13 +504,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI
                       + e.toString() + "\n");
       j.setAllowedServerExceptions(0);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo
-              .appendProgressText(
-                      j.getJobnum(),
-                      "Failed to submit sequences for alignment.\n"
-                              + "It is most likely that there is a problem with the server.\n"
-                              + "Just close the window\n");
+      wsInfo.setStatus(j.getJobnum(),
+              WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.appendProgressText(
+              j.getJobnum(),
+              "Failed to submit sequences for alignment.\n"
+                      + "It is most likely that there is a problem with the server.\n"
+                      + "Just close the window\n");
 
       // e.printStackTrace(); // TODO: JBPNote DEBUG
     }
@@ -526,8 +525,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
     for (int i = 0, j = seqs.length; i < j; i++)
     {
-      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
-              .getSeq());
+      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+              seqs[i].getSeq());
     }
 
     return msa;
@@ -546,13 +545,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI
                 && jobs[j].hasResults())
         {
           results++;
-          //if (Cache.log.isDebugEnabled())
-         // {
-         //   System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
-         //   System.out.println(jobs[j].getStatus());
-         // }
+          // if (Cache.log.isDebugEnabled())
+          // {
+          // System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
+          // System.out.println(jobs[j].getStatus());
+          // }
 
-          vamsas.objects.simple.Alignment valign =  ((MsaResult)((MsaWSJob) jobs[j]).result)
+          vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result)
                   .getMsa();
           if (valign != null)
           {
@@ -561,12 +560,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI
             String[] lines = valign.getMethod();
             for (int line = 0; line < lines.length; line++)
             {
-              wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n");
+              wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line]
+                      + "\n");
             }
             // JBPNote The returned files from a webservice could be
             // hidden behind icons in the monitor window that,
             // when clicked, pop up their corresponding data
-            
+
           }
         }
       }
@@ -695,8 +695,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
           }
           for (int i = 0, l = alorders.size(); i < l; i++)
           {
-            af.addSortByOrderMenuItem(WebServiceName
-                    + ((String) names.get(i)) + " Ordering",
+            af.addSortByOrderMenuItem(
+                    WebServiceName + ((String) names.get(i)) + " Ordering",
                     (AlignmentOrder) alorders.get(i));
           }
         }