From 065fef732147eadd0453d4dbb9b8081ad4a1d301 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 15 Nov 2023 13:29:19 +0000
Subject: [PATCH] JAL-3836 Allow .ext.gz files to be recognised in the File
 Chooser if .ext is a recognised extension.

---
 src/jalview/io/JalviewFileFilter.java |   40 +++++++++++++++++++++++++--------
 src/jalview/io/JalviewFileView.java   |   20 +++++++----------
 2 files changed, 39 insertions(+), 21 deletions(-)

diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index 5e9a242..d9d609c 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -126,22 +126,44 @@ public class JalviewFileFilter extends FileFilter
     return false;
   }
 
-  public String getExtension(File f)
+  public static String getExtension(File f)
   {
-    if (f != null)
+    if (f == null)
+    {
+      return "";
+    }
+    String ext = getExtension(f.getName(), true, true);
+    return ext;
+  }
+
+  public static String getExtension(String filename, boolean ignoreGz,
+          boolean emptyStringForNoExtension)
+  {
+    if (filename == null)
     {
-      String filename = f.getName();
-      int i = filename.lastIndexOf('.');
+      return emptyStringForNoExtension ? "" : null;
+    }
+    int i = filename.lastIndexOf('.');
 
-      if ((i > 0) && (i < (filename.length() - 1)))
+    // i>0 as we don't consider a file ".hidden" to be an extension of "hidden"
+    // i<(filename.length()-1) since we don't consider a file "hi." to have an
+    // extension
+    if (i > 0 && i < (filename.length() - 1))
+    {
+      String ext = filename.substring(i + 1).toLowerCase(Locale.ROOT);
+      if (ignoreGz && ext.equals("gz"))
       {
-        return filename.substring(i + 1).toLowerCase(Locale.ROOT);
+        // don't allow .gz all the way down! (only one in fact)
+        return getExtension(filename.substring(0, i), false,
+                emptyStringForNoExtension);
+      }
+      else
+      {
+        return ext;
       }
-
-      ;
     }
 
-    return "";
+    return emptyStringForNoExtension ? "" : null;
   }
 
   public void addExtension(String extension)
diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java
index 5996781..d010013 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -20,20 +20,19 @@
  */
 package jalview.io;
 
-import java.util.Locale;
-
-import jalview.util.MessageManager;
-
 import java.io.File;
 import java.net.URL;
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.Locale;
 import java.util.Map;
 
 import javax.swing.Icon;
 import javax.swing.ImageIcon;
 import javax.swing.filechooser.FileView;
 
+import jalview.util.MessageManager;
+
 public class JalviewFileView extends FileView
 {
   private static Map<String, String> extensions;
@@ -131,16 +130,13 @@ public class JalviewFileView extends FileView
    */
   public static String getExtension(File f)
   {
-    String ext = null;
-    String s = f.getName();
-    int i = s.lastIndexOf('.');
-
-    if ((i > 0) && (i < (s.length() - 1)))
+    // don't set an icon for folders (that's flatlaf's job!)
+    if (f.isDirectory())
     {
-      ext = s.substring(i + 1).toLowerCase(Locale.ROOT);
+      return null;
     }
-
-    return ext;
+    // ignore .gz and want null for no extension
+    return JalviewFileFilter.getExtension(f.getName(), true, false);
   }
 
   /**
-- 
1.7.10.2