formatting

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

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index d8807e7..58cb3ac 100644 (file)
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -41,6 +41,7 @@ import compbio.metadata.WrongParameterException;
 public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
 {
   Jws2Instance service;
+
   @SuppressWarnings("unchecked")
   protected SequenceAnnotation aaservice;
 
@@ -84,7 +85,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
    * reconfigure and restart the AAConsClient. This method will spawn a new
    * thread that will wait until any current jobs are finished, modify the
    * parameters and restart the conservation calculation with the new values.
-   *
+   * 
    * @param newpreset
    * @param newarguments
    */
@@ -128,7 +129,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     int serverErrorsLeft = 3;
 
     String rslt = "JOB NOT DEFINED";
-    StringBuffer msg=new StringBuffer();
+    StringBuffer msg = new StringBuffer();
     try
     {
       if (checkDone())
@@ -151,7 +152,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         guiProgress.setProgressBar("JABA " + getServiceActionText(),
                 progressId = System.currentTimeMillis());
       }
-      if (preset == null && arguments==null)
+      if (preset == null && arguments == null)
       {
         rslt = aaservice.analize(seqs);
       }
@@ -310,19 +311,22 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
       if (ap != null)
       {
         calcMan.workerComplete(this);
-        if (guiProgress != null && progressId!=-1)
+        if (guiProgress != null && progressId != -1)
         {
           guiProgress.setProgressBar("", progressId);
         }
         ap.paintAlignment(true);
       }
-      if (msg.length()>0)
+      if (msg.length() > 0)
       {
         // TODO: stash message somewhere in annotation or alignment view.
         // code below shows result in a text box popup
-        /* jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-        cap.setText(msg.toString());
-        jalview.gui.Desktop.addInternalFrame(cap, "Job Status for "+getServiceActionText(), 600, 400); */
+        /*
+         * jalview.gui.CutAndPasteTransfer cap = new
+         * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
+         * jalview.gui.Desktop.addInternalFrame(cap,
+         * "Job Status for "+getServiceActionText(), 600, 400);
+         */
       }
     }
 
@@ -352,8 +356,11 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
   protected boolean bySequence = false;
 
   Map<String, SequenceI> seqNames;
+
   boolean[] gapMap;
+
   int realw;
+
   public List<FastaSequence> getInputSequences(AlignmentI alignment)
   {
     if (alignment == null || alignment.getWidth() <= 0
@@ -372,7 +379,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     {
       seqNames = new HashMap<String, SequenceI>();
     }
-    gapMap=new boolean[0];
+    gapMap = new boolean[0];
     for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
     {
       if (sq.getEnd() - sq.getStart() > minlen - 1)
@@ -386,25 +393,28 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         FastaSequence seq;
         if (submitGaps)
         {
-          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,sq.getSequenceAsString()));
-          if (gapMap==null || gapMap.length<seq.getSequence().length())
+          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+                  sq.getSequenceAsString()));
+          if (gapMap == null || gapMap.length < seq.getSequence().length())
           {
-            boolean[] tg=gapMap;
-            gapMap=new boolean[seq.getLength()];
+            boolean[] tg = gapMap;
+            gapMap = new boolean[seq.getLength()];
             System.arraycopy(tg, 0, gapMap, 0, tg.length);
-            for (int p=tg.length;p<gapMap.length;p++)
+            for (int p = tg.length; p < gapMap.length; p++)
             {
-              gapMap[p]=false; // init as a gap
+              gapMap[p] = false; // init as a gap
             }
           }
-          for (int apos:sq.gapMap()) {
-            gapMap[apos]=true; // aligned.
+          for (int apos : sq.gapMap())
+          {
+            gapMap[apos] = true; // aligned.
           }
-        } else {
-        seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
-                AlignSeq
-                        .extractGaps(jalview.util.Comparison.GapChars,
-                                sq.getSequenceAsString())));
+        }
+        else
+        {
+          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+                  AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                          sq.getSequenceAsString())));
         }
         if (seq.getSequence().length() > ln)
         {
@@ -415,7 +425,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     if (alignedSeqs && submitGaps)
     {
       realw = 0;
-      for (int i=0;i<gapMap.length;i++)
+      for (int i = 0; i < gapMap.length; i++)
       {
         if (gapMap[i])
         {
@@ -430,21 +440,24 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         FastaSequence sq = seqs.get(p);
         int l = sq.getSequence().length();
         // strip gapped columns
-        char[] padded = new char[realw],orig=sq.getSequence().toCharArray();
-        for (int i=0,pp=0;i<realw; pp++)
+        char[] padded = new char[realw], orig = sq.getSequence()
+                .toCharArray();
+        for (int i = 0, pp = 0; i < realw; pp++)
         {
           if (gapMap[pp])
           {
-            if (orig.length>pp)
+            if (orig.length > pp)
             {
-              padded[i++]=orig[pp];
-            } else {
-              padded[i++]='-';
-            }       
+              padded[i++] = orig[pp];
+            }
+            else
+            {
+              padded[i++] = '-';
+            }
           }
         }
         seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
-                  new String(padded)));
+                new String(padded)));
       }
     }
     return seqs;
@@ -452,7 +465,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
 
   /**
    * notify manager that we have started, and wait for a free calculation slot
-   *
+   * 
    * @return true if slot is obtained and work still valid, false if another
    *         thread has done our work for us.
    */