X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileFormat.java;h=6fe338ca902cd452180f53acadc1494127877c22;hb=49db0dff1da16c3355b43a41498c1fc93ef47e91;hp=4f0480dcb30a9b90574c598cb4de540df26732c6;hpb=8550acbddfcf94dbacaae9738a4b6d4f68b16b02;p=jalview.git

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4f0480d..6fe338c 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -20,14 +20,14 @@
  */
 package jalview.io;
 
+import java.io.IOException;
+
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 
-import java.io.IOException;
-
 public enum FileFormat implements FileFormatI
 {
   Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
@@ -244,7 +244,22 @@ public enum FileFormat implements FileFormatI
       return new PhylipFile();
     }
   },
-  GenBank("GenBank/ENA Flatfile","gb",false,false)
+  GenBank("GenBank Flatfile", "gb, gbk", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new GenBankFile(source, "GenBank");
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
+  Embl("ENA Flatfile", "txt", true, false)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -253,13 +268,13 @@ public enum FileFormat implements FileFormatI
       // Always assume we import from EMBL for now
       return new EmblFlatFile(source, DBRefSource.EMBL);
     }
+
     @Override
     public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null;
     }
-  }
-  ,
+  },
   Jnet("JnetFile", "", false, false)
   {
     @Override
@@ -390,8 +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;