JAL-1517 source formatting

[jalview.git] / src / jalview / ws / jws2 / JabawsCalcWorker.java

diff --git a/src/jalview/ws/jws2/JabawsCalcWorker.java b/src/jalview/ws/jws2/JabawsCalcWorker.java
index add8bd5..5223c52 100644 (file)
--- a/src/jalview/ws/jws2/JabawsCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsCalcWorker.java
@@ -57,11 +57,16 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
 {
 
   protected Jws2Instance service;
+
   @SuppressWarnings("unchecked")
   protected SequenceAnnotation aaservice;
+
   protected ScoreManager scoremanager;
+
   protected WsParamSetI preset;
+
   protected List<Argument> arguments;
+
   protected IProgressIndicator guiProgress;
 
   public JabawsCalcWorker(AlignViewportI alignViewport,
@@ -100,7 +105,8 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
    * @param newpreset
    * @param newarguments
    */
-  public void updateParameters(final WsParamSetI newpreset, final List<Argument> newarguments)
+  public void updateParameters(final WsParamSetI newpreset,
+          final List<Argument> newarguments)
   {
     preset = newpreset;
     arguments = newarguments;
@@ -135,9 +141,9 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
       return;
     }
     long progressId = -1;
-  
+
     int serverErrorsLeft = 3;
-  
+
     String rslt = "JOB NOT DEFINED";
     StringBuffer msg = new StringBuffer();
     try
@@ -146,15 +152,16 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
       {
         return;
       }
-      List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
-              .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
-  
+      List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(
+              alignViewport.getAlignment(),
+              bySequence ? alignViewport.getSelectionGroup() : null);
+
       if (seqs == null)
       {
         calcMan.workerComplete(this);
         return;
       }
-  
+
       AlignmentAnnotation[] aa = alignViewport.getAlignment()
               .getAlignmentAnnotation();
       if (guiProgress != null)
@@ -175,7 +182,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
         {
           throw new JobSubmissionException(
                   "Invalid parameter set. Check Jalview implementation.", x);
-  
+
         }
       }
       boolean finished = false;
@@ -201,12 +208,12 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
             {
               System.err.println("FAILED TO CANCEL AACon job: " + rslt);
             }
-  
+
           } catch (Exception x)
           {
-  
+
           }
-  
+
           return;
         }
         long cpos;
@@ -222,7 +229,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
               stats = aaservice.pullExecStatistics(rslt, rpos);
             } catch (Exception x)
             {
-  
+
               if (x.getMessage().contains(
                       "Position in a file could not be negative!"))
               {
@@ -259,7 +266,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
             rpos = stats.getNextPosition();
           }
         } while (stats != null && rpos > cpos);
-  
+
         if (!finished && status.equals(JobStatus.FAILED))
         {
           try
@@ -291,10 +298,10 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
         }
       }
     }
-  
+
     catch (JobSubmissionException x)
     {
-  
+
       System.err.println("submission error with " + getServiceActionText()
               + " :");
       x.printStackTrace();
@@ -304,18 +311,18 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
       System.err.println("collection error:\nJob ID: " + rslt);
       x.printStackTrace();
       calcMan.workerCannotRun(this);
-  
+
     } catch (OutOfMemoryError error)
     {
       calcMan.workerCannotRun(this);
-  
+
       // consensus = null;
       // hconsensus = null;
       ap.raiseOOMWarning(getServiceActionText(), error);
     } catch (Exception x)
     {
       calcMan.workerCannotRun(this);
-  
+
       // consensus = null;
       // hconsensus = null;
       System.err
@@ -323,7 +330,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
       x.printStackTrace();
     } finally
     {
-  
+
       calcMan.workerComplete(this);
       if (ap != null)
       {
@@ -346,7 +353,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
          */
       }
     }
-  
+
   }
 
   @Override
@@ -360,32 +367,42 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
   public abstract String getServiceActionText();
 
   protected boolean submitGaps = true;
+
   protected boolean alignedSeqs = true;
+
   protected boolean nucleotidesAllowed = false;
+
   protected boolean proteinAllowed = false;
+
   /**
    * record sequences for mapping result back to afterwards
    */
   protected boolean bySequence = false;
+
   protected Map<String, SequenceI> seqNames;
+
   protected boolean[] gapMap;
+
   int realw;
-  int start,end;
 
-  public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
+  int start, end;
+
+  public List<FastaSequence> getInputSequences(AlignmentI alignment,
+          AnnotatedCollectionI inputSeqs)
   {
     if (alignment == null || alignment.getWidth() <= 0
-            || alignment.getSequences() == null
-            || alignment.isNucleotide() ? !nucleotidesAllowed
+            || alignment.getSequences() == null || alignment.isNucleotide() ? !nucleotidesAllowed
             : !proteinAllowed)
     {
       return null;
     }
-    if (inputSeqs==null || inputSeqs.getWidth()<=0 || inputSeqs.getSequences()==null || inputSeqs.getSequences().size()<1)
+    if (inputSeqs == null || inputSeqs.getWidth() <= 0
+            || inputSeqs.getSequences() == null
+            || inputSeqs.getSequences().size() < 1)
     {
       inputSeqs = alignment;
     }
-    
+
     List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
 
     int minlen = 10;
@@ -395,13 +412,14 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
       seqNames = new HashMap<String, SequenceI>();
     }
     gapMap = new boolean[0];
-    start=inputSeqs.getStartRes();
-    end=inputSeqs.getEndRes();
-    
+    start = inputSeqs.getStartRes();
+    end = inputSeqs.getEndRes();
 
     for (SequenceI sq : ((List<SequenceI>) inputSeqs.getSequences()))
     {
-      if (bySequence ? sq.findPosition(end+1) -sq.findPosition(start+1) > minlen - 1 : sq.getEnd() - sq.getStart() > minlen - 1)
+      if (bySequence ? sq.findPosition(end + 1)
+              - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
+              - sq.getStart() > minlen - 1)
       {
         String newname = SeqsetUtils.unique_name(seqs.size() + 1);
         // make new input sequence with or without gaps
@@ -433,7 +451,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
         {
           seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
                   AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
-                          sq.getSequenceAsString(start,end+1))));
+                          sq.getSequenceAsString(start, end + 1))));
         }
         if (seq.getSequence().length() > ln)
         {
@@ -504,7 +522,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
         {
           ap.paintAlignment(false);
         }
-  
+
         Thread.sleep(200);
       } catch (Exception ex)
       {
@@ -519,8 +537,9 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
     return false;
   }
 
-  protected void createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String calcId,
-          int alWidth, Score scr)
+  protected void createAnnotationRowsForScores(
+          List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
+          Score scr)
   {
     // simple annotation row
     AlignmentAnnotation annotation = alignViewport.getAlignment()
@@ -533,7 +552,8 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
     }
   }
 
-  protected AlignmentAnnotation createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String typeName,
+  protected AlignmentAnnotation createAnnotationRowsForScores(
+          List<AlignmentAnnotation> ourAnnot, String typeName,
           String calcId, SequenceI dseq, int base, Score scr)
   {
     System.out.println("Creating annotation on dseq:" + dseq.getStart()
@@ -553,8 +573,8 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
     return annotation;
   }
 
-  private void constructAnnotationFromScore(AlignmentAnnotation annotation, int base,
-          int alWidth, Score scr)
+  private void constructAnnotationFromScore(AlignmentAnnotation annotation,
+          int base, int alWidth, Score scr)
   {
     Annotation[] elm = new Annotation[alWidth];
     Iterator<Float> vals = scr.getScores().iterator();
@@ -589,7 +609,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
       }
       elm[i] = new Annotation("", "" + val, ' ', val);
     }
-  
+
     annotation.annotations = elm;
     annotation.belowAlignment = true;
     if (x < 0)
@@ -621,7 +641,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
         }
       }
       our.clear();
-  
+
       ap.adjustAnnotationHeight();
     }
   }