X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileFormat.java;h=b7df731d19ff7164a2ae36355dc226de754907cb;hb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;hp=4b33dbfba7d87f49d5932fa56286c81d870f78ac;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..b7df731 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -306,7 +306,7 @@ public enum FileFormat implements FileFormatI
       else
       {
         StructureImportSettings.setShowSeqFeatures(true);
-        return new MCview.PDBfile(
+        return new mc_view.PDBfile(
                 StructureImportSettings.isVisibleChainAnnotation(),
                 StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),
@@ -347,7 +347,7 @@ public enum FileFormat implements FileFormatI
       return true;
     }
   },
-  Jalview("Jalview", "jar,jvp", true, true)
+  Jalview("Jalview", "jvp, jar", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -371,10 +371,40 @@ public enum FileFormat implements FileFormatI
     @Override
     public boolean isIdentifiable()
     {
-      return false;
+      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;