From 5c49150fcafd9726b4814557332ae2f60c0c46a2 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Sun, 14 May 2023 12:22:02 +0100
Subject: [PATCH] JAL-629 add an {extension} substitution

---
 src/jalview/bin/argparser/ArgParser.java    |    9 +++++++++
 src/jalview/bin/argparser/ArgValuesMap.java |   22 ++++++++++++++++++----
 src/jalview/util/FileUtils.java             |   25 +++++++++++++++++++------
 3 files changed, 46 insertions(+), 10 deletions(-)

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 7132e89..2a3272c 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -81,6 +81,11 @@ public class ArgParser
   // the linked id substitution string used to use the idCounter
   private static final String LINKEDIDAUTOCOUNTER = "{n}";
 
+  // the linked id substitution string used to use the filename extension of
+  // --append
+  // or --open
+  private static final String LINKEDIDEXTENSION = "{extension}";
+
   // the linked id substitution string used to use the base filename of --append
   // or --open
   private static final String LINKEDIDBASENAME = "{basename}";
@@ -637,6 +642,10 @@ public class ArgParser
       {
         rest = rest.replace(LINKEDIDBASENAME, avm.getBasename());
       }
+      if (rest.contains(LINKEDIDEXTENSION))
+      {
+        rest = rest.replace(LINKEDIDEXTENSION, avm.getExtension());
+      }
       if (rest.contains(LINKEDIDDIRNAME))
       {
         rest = rest.replace(LINKEDIDDIRNAME, avm.getDirname());
diff --git a/src/jalview/bin/argparser/ArgValuesMap.java b/src/jalview/bin/argparser/ArgValuesMap.java
index 158041b..99a1ef6 100644
--- a/src/jalview/bin/argparser/ArgValuesMap.java
+++ b/src/jalview/bin/argparser/ArgValuesMap.java
@@ -209,7 +209,16 @@ public class ArgValuesMap
    */
   public String getBasename()
   {
-    return getDirOrBasename(false);
+    return getDirBasenameOrExtension(false, false);
+  }
+
+  /*
+   * This method returns the basename of the first --append or --open value. 
+   * Used primarily for substitutions in output filenames.
+   */
+  public String getExtension()
+  {
+    return getDirBasenameOrExtension(false, true);
   }
 
   /*
@@ -218,10 +227,11 @@ public class ArgValuesMap
    */
   public String getDirname()
   {
-    return getDirOrBasename(true);
+    return getDirBasenameOrExtension(true, false);
   }
 
-  public String getDirOrBasename(boolean dirname)
+  public String getDirBasenameOrExtension(boolean dirname,
+          boolean extension)
   {
     String filename = null;
     String appendVal = getValue(Arg.APPEND);
@@ -234,7 +244,11 @@ public class ArgValuesMap
       return null;
 
     File file = new File(filename);
-    return dirname ? FileUtils.getDirname(file)
+    if (dirname)
+    {
+      return FileUtils.getDirname(file);
+    }
+    return extension ? FileUtils.getExtension(file)
             : FileUtils.getBasename(file);
   }
 
diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index 4d35cd2..e62a7d6 100644
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -130,26 +130,39 @@ public class FileUtils
   }
 
   /*
-   * This method returns the basename of the first --append or --open value. 
-   * Used primarily for substitutions in output filenames.
+   * This method returns the basename of File file
    */
   public static String getBasename(File file)
   {
+    return getBasenameOrExtension(file, false);
+  }
+
+  /*
+   * This method returns the extension of File file.
+   */
+  public static String getExtension(File file)
+  {
+    return getBasenameOrExtension(file, true);
+  }
+
+  public static String getBasenameOrExtension(File file, boolean extension)
+  {
     if (file == null)
       return null;
 
-    String basename = null;
+    String value = null;
     String filename = file.getName();
     int lastDot = filename.lastIndexOf('.');
     if (lastDot > 0) // don't truncate if starts with '.'
     {
-      basename = filename.substring(0, lastDot);
+      value = extension ? filename.substring(lastDot + 1)
+              : filename.substring(0, lastDot);
     }
     else
     {
-      basename = filename;
+      value = extension ? "" : filename;
     }
-    return basename;
+    return value;
   }
 
   /*
-- 
1.7.10.2