X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=c698a31b81963fe24ec8c3044ceaf6a10eb0fb15;hb=5fe8a7444f60733f195cd812e75d7e873e688880;hp=9c8cdf66cbee9608700d774d0d0299cce221bf9a;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 9c8cdf6..c698a31 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -20,14 +20,14 @@
  */
 package jalview.io;
 
+import java.io.IOException;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
-import java.io.IOException;
-
 /**
  * DOCUMENT ME!
  * 
@@ -69,7 +69,12 @@ public class FastaFile extends AlignFile
 
   public FastaFile(FileParse source) throws IOException
   {
-    super(source);
+    this(source, true);
+  }
+
+  public FastaFile(FileParse source, boolean closeData) throws IOException
+  {
+    super(true, source, closeData);
   }
 
   public FastaFile(SequenceI[] seqs)
@@ -164,8 +169,8 @@ public class FastaFile extends AlignFile
         anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
       }
     }
-    AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
-            .substring(2), seq.getDescription(), anots);
+    AlignmentAnnotation aa = new AlignmentAnnotation(
+            seq.getName().substring(2), seq.getDescription(), anots);
     return aa;
   }
 
@@ -180,8 +185,7 @@ public class FastaFile extends AlignFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      AlignmentAnnotation aa = annotations
-              .elementAt(i);
+      AlignmentAnnotation aa = annotations.elementAt(i);
       aa.setPadGaps(true, al.getGapCharacter());
       al.addAnnotation(aa);
     }