Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / io / FileFormat.java

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 1d240b2..6fe338c 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -244,7 +244,7 @@ public enum FileFormat implements FileFormatI
       return new PhylipFile();
     }
   },
-  GenBank("GenBank Flatfile", "gb", true, false)
+  GenBank("GenBank Flatfile", "gb, gbk", true, false)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -405,8 +405,38 @@ public enum FileFormat implements FileFormatI
     {
       return true;
     }
+  },
+  HMMER3("HMMER3", "hmm", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new HMMFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new HMMFile();
+    }
+  },   BSML("BSML", "bbb", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new BSMLFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
   };
 
+
   private boolean writable;
 
   private boolean readable;