X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=7585758f2d14a0b5588acdd56800de91e593b2d9;hb=eb9c652416a69e6db0531e956dd2011012eac898;hp=9aff348f7cfaa9721a676e8dd62d3ba07f55f10b;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 9aff348..7585758 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,13 @@
  */
 package jalview.io;
 
-import java.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-
-import jalview.datamodel.*;
+import java.io.IOException;
 
 /**
  * DOCUMENT ME!
@@ -79,7 +82,7 @@ public class FastaFile extends AlignFile
     StringBuffer sb = new StringBuffer();
     boolean firstLine = true;
 
-    String line,uline;
+    String line, uline;
     Sequence seq = null;
 
     boolean annotation = false;
@@ -141,23 +144,24 @@ 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.