From dcee5ae80f30dcc8246aabae16dd0962f4af4287 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 10 May 2023 13:54:52 +0100
Subject: [PATCH] JAL-629 Check Arg options for obtaining boolean or negative
 boolean arg from subvals

---
 src/jalview/bin/argparser/ArgParser.java |   51 ++++++++++++++++++++++++++----
 1 file changed, 44 insertions(+), 7 deletions(-)

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index d551b26..c7fb323 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -844,22 +844,59 @@ public class ArgParser
   public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
           SubVals sv, String key, String pref, boolean def)
   {
+    if ((key == null && a == null) || (sv == null && a == null))
+      return false;
+
+    boolean usingArgKey = false;
     if (key == null)
+    {
       key = a.getName();
+      usingArgKey = true;
+    }
+
     String nokey = ArgParser.NEGATESTRING + key;
-    if (sv != null && sv.has(key) && sv.get(key) != null)
-      return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
 
-    if (sv != null && sv.has(key) && sv.get(key) != null)
-      return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+    // look for key or nokey in subvals first (if using Arg check options)
+    if (sv != null)
+    {
+      // check for true boolean
+      if (sv.has(key) && sv.get(key) != null)
+      {
+        if (usingArgKey)
+        {
+          if (!(a.hasOption(Opt.BOOLEAN) || a.hasOption(Opt.UNARY)))
+          {
+            Console.debug(
+                    "Looking for boolean in subval from non-boolean/non-unary Arg "
+                            + a.getName());
+            return false;
+          }
+        }
+        return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+      }
 
-    // check for negative boolean (subval "no..." will be "true")
-    if (sv != null && sv.has(nokey) && sv.get(nokey) != null)
-      return !sv.get(nokey).toLowerCase(Locale.ROOT).equals("true");
+      // check for negative boolean (subval "no..." will be "true")
+      if (sv.has(nokey) && sv.get(nokey) != null)
+      {
+        if (usingArgKey)
+        {
+          if (!(a.hasOption(Opt.BOOLEAN)))
+          {
+            Console.debug(
+                    "Looking for negative boolean in subval from non-boolean Arg "
+                            + a.getName());
+            return false;
+          }
+        }
+        return !sv.get(nokey).toLowerCase(Locale.ROOT).equals("true");
+      }
+    }
 
+    // check argvalues
     if (avm != null && avm.containsArg(a))
       return avm.getBoolean(a);
 
+    // return preference or default
     return pref != null ? Cache.getDefault(pref, def) : def;
   }
 
-- 
1.7.10.2