X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=6e5de81d6efd865e0277435d082e35b2cab7b6bb;hb=7a2f4e9ee4119f0369743e7996bcebbb6ab46f9e;hp=2db0ded1682df40d00c8420c7e2518188486c5cb;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 2db0ded..6e5de81 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -6,21 +6,22 @@
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
 import java.io.*;
 
-
 import jalview.datamodel.*;
 
 /**
@@ -77,7 +78,7 @@ public class FastaFile extends AlignFile
     StringBuffer sb = new StringBuffer();
     boolean firstLine = true;
 
-    String line,uline;
+    String line, uline;
     Sequence seq = null;
 
     boolean annotation = false;
@@ -139,23 +140,24 @@ public class FastaFile extends AlignFile
       seqs.addElement(seq);
     }
   }
+
   private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
   {
     Annotation[] anots = new Annotation[sb.length()];
     char cb;
-    for (int i=0;i<anots.length;i++)
+    for (int i = 0; i < anots.length; i++)
     {
       char cn = sb.charAt(i);
       if (cn != ' ')
       {
-        anots[i] = new Annotation(""+cn, null,
-              ' ', Float.NaN);
+        anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
       }
     }
     AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
             .substring(2), seq.getDescription(), anots);
     return aa;
   }
+
   /**
    * called by AppletFormatAdapter to generate an annotated alignment, rather
    * than bare sequences.