From 7a4569721f8419ae7e040fc672421aabb0321e8b Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 14 Jun 2012 11:41:42 +0100
Subject: [PATCH] formatting

---
 src/jalview/ws/jws2/JabawsAlignCalcWorker.java |   35 +++++++++++++-----------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index 8eb83ee..1f5250a 100644
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -133,7 +133,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
       return;
     }
 
-    String rslt="JOB NOT DEFINED";
+    String rslt = "JOB NOT DEFINED";
 
     try
     {
@@ -242,7 +242,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
       calcMan.workerCannotRun(this);
     } catch (ResultNotAvailableException x)
     {
-      System.err.println("collection error:\nJob ID: "+rslt);
+      System.err.println("collection error:\nJob ID: " + rslt);
       x.printStackTrace();
       calcMan.workerCannotRun(this);
 
@@ -304,7 +304,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
 
     if (alignment == null || alignment.getWidth() <= 0
             || alignment.getSequences() == null
-//             || (alignedSeqs && !alignment.isAligned() && !submitGaps)
+            // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
             || alignment.isNucleotide() ? !nucleotidesAllowed
             : !proteinAllowed)
     {
@@ -313,7 +313,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
 
     int minlen = 10;
-    int ln=-1;
+    int ln = -1;
     if (bySequence)
     {
       seqNames = new HashMap<String, SequenceI>();
@@ -330,11 +330,11 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
           seqNames.put(newname, sq);
         }
         FastaSequence seq;
-        seqs.add(seq=new compbio.data.sequence.FastaSequence(newname,
+        seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
                 (submitGaps) ? sq.getSequenceAsString() : AlignSeq
                         .extractGaps(jalview.util.Comparison.GapChars,
                                 sq.getSequenceAsString())));
-        if (seq.getSequence().length()>ln)
+        if (seq.getSequence().length() > ln)
         {
           ln = seq.getSequence().length();
         }
@@ -343,20 +343,23 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     if (alignedSeqs && submitGaps)
     {
       // try real hard to return something submittable
-      // TODO: some of AAcons measures need a minimum of two or three amino acids at each position, and aacons doesn't gracefully degrade.
-      for (int p=0; p<seqs.size();p++)
+      // TODO: some of AAcons measures need a minimum of two or three amino
+      // acids at each position, and aacons doesn't gracefully degrade.
+      for (int p = 0; p < seqs.size(); p++)
       {
-        FastaSequence sq=seqs.get(p);
-        int l=sq.getSequence().length();
-        if (l<ln)
+        FastaSequence sq = seqs.get(p);
+        int l = sq.getSequence().length();
+        if (l < ln)
         {
-          char[] padded=new char[ln];
-          System.arraycopy(sq.getSequence().toCharArray(),0,padded,0,sq.getSequence().length());
-          while (l<ln)
+          char[] padded = new char[ln];
+          System.arraycopy(sq.getSequence().toCharArray(), 0, padded, 0, sq
+                  .getSequence().length());
+          while (l < ln)
           {
-            padded[l++]='-';
+            padded[l++] = '-';
           }
-          seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(), new String(padded)));
+          seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
+                  new String(padded)));
         }
       }
 
-- 
1.7.10.2