From ede7927272c6b59e01466d3120e834b26e021003 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 7 Sep 2018 14:19:28 +0100
Subject: [PATCH] JAL-3106 use .jvp as default

---
 help/html/releases.html               |    4 ++++
 src/jalview/io/FileFormat.java        |    2 +-
 src/jalview/io/JalviewFileFilter.java |   22 +++++++++++++---------
 3 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index 82ec15d..3dac399 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -152,6 +152,10 @@ li:before {
               treated as RNA secondary structure.
             </li>
             <li>
+              <!-- JAL-3106 -->.jvp should be used as default extension
+              (not .jar) when saving a jalview project file.
+            </li>
+            <li>
               <!-- JAL-3105 -->Mac Users: closing a window correctly
               transfers focus to previous window on OSX
             </li>
diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..e94e1ce 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -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)
diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index d59e88a..21f5b0f 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -21,8 +21,10 @@
 package jalview.io;
 
 import java.io.File;
-import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.Map;
 import java.util.StringTokenizer;
 
 import javax.swing.filechooser.FileFilter;
@@ -31,7 +33,7 @@ public class JalviewFileFilter extends FileFilter
 {
   public static Hashtable suffixHash = new Hashtable();
 
-  private Hashtable filters = null;
+  private Map<String, JalviewFileFilter> filters = null;
 
   private String description = "no description";
 
@@ -72,10 +74,11 @@ public class JalviewFileFilter extends FileFilter
 
   public String getAcceptableExtension()
   {
-    return filters.keys().nextElement().toString();
+    return filters.keySet().iterator().next().toString();
   }
 
   // takes account of the fact that database is a directory
+  @Override
   public boolean accept(File f)
   {
     if (f != null)
@@ -87,7 +90,7 @@ public class JalviewFileFilter extends FileFilter
         return true;
       }
 
-      if ((extension != null) && (filters.get(getExtension(f)) != null))
+      if ((extension != null) && (filters.get(extension) != null))
       {
         return true;
       }
@@ -118,13 +121,14 @@ public class JalviewFileFilter extends FileFilter
   {
     if (filters == null)
     {
-      filters = new Hashtable(5);
+      filters = new LinkedHashMap<>(5);
     }
 
     filters.put(extension.toLowerCase(), this);
     fullDescription = null;
   }
 
+  @Override
   public String getDescription()
   {
     if (fullDescription == null)
@@ -135,15 +139,15 @@ public class JalviewFileFilter extends FileFilter
                 : (description + " (");
 
         // build the description from the extension list
-        Enumeration extensions = filters.keys();
+        Iterator<String> extensions = filters.keySet().iterator();
 
         if (extensions != null)
         {
-          fullDescription += ("." + (String) extensions.nextElement());
+          fullDescription += ("." + extensions.next());
 
-          while (extensions.hasMoreElements())
+          while (extensions.hasNext())
           {
-            fullDescription += (", " + (String) extensions.nextElement());
+            fullDescription += (", " + extensions.next());
           }
         }
 
-- 
1.7.10.2