From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 3 Jun 2014 15:25:24 +0000 (+0100)
Subject: JAL-690 JAL-1503 update file types/extensions in Jalview file browser
X-Git-Tag: Release_2_8_1~4^2~3^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f4a19df4f13209eeff28e1c2ad1a770310dc3b98;p=jalview.git

JAL-690 JAL-1503 update file types/extensions in Jalview file browser
---

diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java
index 0dcc7c2..03d7c59 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -30,15 +30,23 @@ public class JalviewFileView extends FileView
 
   static
   {
+    // TODO: these names should come from the FormatAdapter lists for readable/writable extensions 
+    alignSuffix.put("amsa", "AMSA file");
     alignSuffix.put("fasta", "Fasta file");
     alignSuffix.put("fa", "Fasta file");
     alignSuffix.put("fastq", "Fasta file");
+    alignSuffix.put("mfa", "Fasta file");
     alignSuffix.put("blc", "BLC file");
     alignSuffix.put("msf", "MSF file");
     alignSuffix.put("pfam", "PFAM file");
     alignSuffix.put("aln", "Clustal file");
     alignSuffix.put("pir", "PIR file");
-    alignSuffix.put("jar", "Jalview file");
+    alignSuffix.put("jar", "Jalview Project file (old)");
+    alignSuffix.put("jvp", "Jalview Project file");
+    alignSuffix.put("amsa", "AMSA file");
+    alignSuffix.put("sto", "Stockholm File");
+    alignSuffix.put("stk", "Stockholm File");
+    alignSuffix.put("sto", "Stockholm File");
   }
 
   public String getTypeDescription(File f)