From d7a4a1a91d850ed8c246c0e69edf1e2dd760b49c Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 4 Apr 2023 20:45:08 +0100
Subject: [PATCH] JAL-629 more info in usage statement

---
 src/jalview/bin/argparser/Arg.java |   63 +++++++++++++++++++++++++++---------
 1 file changed, 48 insertions(+), 15 deletions(-)

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 65a865b..e22cfc6 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -1,5 +1,6 @@
 package jalview.bin.argparser;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.EnumSet;
 import java.util.List;
@@ -227,6 +228,17 @@ public enum Arg
     return description;
   }
 
+  public static String booleanArgString(Arg a)
+  {
+    StringBuilder sb = new StringBuilder(a.argString());
+    if (a.hasOption(Opt.BOOLEAN))
+    {
+      sb.append('/');
+      sb.append(a.negateArgString());
+    }
+    return sb.toString();
+  }
+
   public static final String usage()
   {
     StringBuilder sb = new StringBuilder();
@@ -237,6 +249,8 @@ public enum Arg
     int maxArgLength = 0;
     for (Arg a : EnumSet.allOf(Arg.class))
     {
+      if (a.hasOption(Opt.PRIVATE))
+        continue;
       StringBuilder argSb = new StringBuilder();
       argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
               : a.argString());
@@ -246,9 +260,11 @@ public enum Arg
         maxArgLength = argSb.length();
     }
 
-    // might want to order these
+    // might want to sort these
     for (Arg a : EnumSet.allOf(Arg.class))
     {
+      if (a.hasOption(Opt.PRIVATE))
+        continue;
       StringBuilder argSb = new StringBuilder();
       argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
               : a.argString());
@@ -256,26 +272,43 @@ public enum Arg
         argSb.append("=value");
       sb.append(String.format("%-" + maxArgLength + "s  - %s",
               argSb.toString(), a.getDescription()));
+
+      List<String> options = new ArrayList<>();
+
       if (a.hasOption(Opt.BOOLEAN))
       {
-        sb.append(" (default ");
-        sb.append(a.getDefaultBoolValue() ? a.argString()
-                : a.negateArgString());
+        options.add("default " + (a.getDefaultBoolValue() ? a.argString()
+                : a.negateArgString()));
+      }
+
+      if (a.hasOption(Opt.MULTI))
+      {
+        options.add("multiple");
+      }
+
+      if (a.hasOption(Opt.LINKED))
+      {
+        options.add("can be linked");
+      }
+
+      if (a.hasOption(Opt.GLOB))
+      {
+        options.add("allows file globs");
+      }
+
+      if (a.hasOption(Opt.ALLOWSUBSTITUTIONS))
+      {
+        options.add("allows substitutions");
+      }
+
+      if (options.size() > 0)
+      {
+        sb.append(" (");
+        sb.append(String.join("; ", options));
         sb.append(')');
       }
       sb.append(System.lineSeparator());
     }
     return sb.toString();
   }
-
-  public static String booleanArgString(Arg a)
-  {
-    StringBuilder sb = new StringBuilder(a.argString());
-    if (a.hasOption(Opt.BOOLEAN))
-    {
-      sb.append('/');
-      sb.append(a.negateArgString());
-    }
-    return sb.toString();
-  }
 }
\ No newline at end of file
-- 
1.7.10.2