X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileFormat.java;h=00f2e5c73dff09cf10c616d6ac6c82bc199844a1;hb=c1e71094304dcd2b975c485416ec5e25cca30815;hp=4b33dbfba7d87f49d5932fa56286c81d870f78ac;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..00f2e5c 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -20,16 +20,17 @@
  */
 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)
+  Fasta("Fasta", "fa,fasta,mfa,fastq", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -91,7 +92,7 @@ public enum FileFormat implements FileFormatI
       return new PIRFile();
     }
   },
-  BLC("BLC", "BLC", true, true)
+  BLC("BLC", "blc", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -243,6 +244,37 @@ public enum FileFormat implements FileFormatI
       return new PhylipFile();
     }
   },
+  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)
+            throws IOException
+    {
+      // 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
@@ -276,6 +308,21 @@ public enum FileFormat implements FileFormatI
       return new FeaturesFile();
     }
   },
+  FeatureSettings("Jalview Feature Settings File", "fc", false, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return null;
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
   ScoreMatrix("Substitution matrix", "", false, false)
   {
     @Override
@@ -306,7 +353,7 @@ 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 +394,7 @@ 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)
@@ -371,7 +418,7 @@ public enum FileFormat implements FileFormatI
     @Override
     public boolean isIdentifiable()
     {
-      return false;
+      return true;
     }
   };
 
@@ -408,7 +455,10 @@ public enum FileFormat implements FileFormatI
    * @param extensions
    *          comma-separated list of file extensions associated with the format
    * @param isReadable
+   *          - can be recognised by IdentifyFile and imported with the given
+   *          reader
    * @param isWritable
+   *          - can be exported with the returned writer
    */
   private FileFormat(String shortName, String extensions,
           boolean isReadable, boolean isWritable)