From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 3 Aug 2020 13:07:03 +0000 (+0100)
Subject: JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create tests and IdentifyFile routi... 
X-Git-Tag: Release_2_11_2_0~34^2~8^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8550acbddfcf94dbacaae9738a4b6d4f68b16b02;p=jalview.git

JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create tests and IdentifyFile routine for this format
---

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index cb61740..4f0480d 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
@@ -243,6 +244,22 @@ public enum FileFormat implements FileFormatI
       return new PhylipFile();
     }
   },
+  GenBank("GenBank/ENA Flatfile","gb",false,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
@@ -407,8 +424,8 @@ public enum FileFormat implements FileFormatI
    * @param shortName
    * @param extensions
    *          comma-separated list of file extensions associated with the format
-   * @param isReadable
-   * @param isWritable
+   * @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)