Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..2ffe577 100644 (file)
--- 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 +371,26 @@ 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();
     }
   };
 
+
   private boolean writable;
 
   private boolean readable;