X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=c21b02c03b3b2e751d4248842f9a51633ce647d6;hb=refs%2Fheads%2Ffeatures%2FJAL-2446NCList;hp=d6188091491f83d54bfe6e4f4460883c91b44d40;hpb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index d618809..c21b02c 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -61,7 +61,8 @@ public class ClustalFile extends AlignFile
     boolean flag = false;
     boolean rna = false;
     boolean top = false;
-    StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
+    StringBuffer pssecstr = new StringBuffer(),
+            consstr = new StringBuffer();
     Vector headers = new Vector();
     Hashtable seqhash = new Hashtable();
     StringBuffer tempseq;
@@ -158,16 +159,15 @@ public class ClustalFile extends AlignFile
           }
 
           Sequence newSeq = parseId(headers.elementAt(i).toString());
-          newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
-                  .toString());
+          newSeq.setSequence(
+                  seqhash.get(headers.elementAt(i).toString()).toString());
 
           seqs.addElement(newSeq);
         }
         else
         {
-          System.err
-                  .println("Clustal File Reader: Can't find sequence for "
-                          + headers.elementAt(i));
+          System.err.println("Clustal File Reader: Can't find sequence for "
+                  + headers.elementAt(i));
         }
       }
       AlignmentAnnotation lastssa = null;
@@ -186,9 +186,8 @@ public class ClustalFile extends AlignFile
         AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
                 "secondary structure", consstr.toString());
         ssa.label = "Consensus Secondary Structure";
-        if (lastssa == null
-                || !lastssa.getRNAStruc().equals(
-                        ssa.getRNAStruc().replace('-', '.')))
+        if (lastssa == null || !lastssa.getRNAStruc()
+                .equals(ssa.getRNAStruc().replace('-', '.')))
         {
           annotations.addElement(ssa);
         }
@@ -236,8 +235,8 @@ public class ClustalFile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form(printId(s[j],
-                jvsuffix) + " "));
+        out.append(new Format("%-" + maxid + "s")
+                .form(printId(s[j], jvsuffix) + " "));
 
         int start = i * len;
         int end = start + len;