From 244c7f3f09b99ee3ebbd22733177c6479d07b13d Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 30 Mar 2023 09:34:55 +0100
Subject: [PATCH] JAL-629 fix SubVals npe

---
 src/jalview/bin/argparser/ArgParser.java |    3 +--
 src/jalview/bin/argparser/SubVals.java   |    8 ++++++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 19cf276..e58bcb5 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -360,8 +360,7 @@ public class ArgParser
             for (String v : globVals)
             {
               v = makeSubstitutions(v);
-              SubVals vsv = new SubVals(globSubVals == null ? null
-                      : globSubVals.getSubValsMap(), v);
+              SubVals vsv = new SubVals(globSubVals, v);
               avs.addValue(vsv, v, argIndex++);
               argIndexIncremented = true;
             }
diff --git a/src/jalview/bin/argparser/SubVals.java b/src/jalview/bin/argparser/SubVals.java
index aea6df3..dd20ca6 100644
--- a/src/jalview/bin/argparser/SubVals.java
+++ b/src/jalview/bin/argparser/SubVals.java
@@ -27,9 +27,13 @@ public class SubVals
 
   private String content = null;
 
-  public SubVals(Map<String, String> sv, String c)
+  public SubVals(SubVals sv, String c)
   {
-    this.subVals = sv;
+    if (sv != null)
+    {
+      this.subVals = sv.getSubValsMap();
+      this.index = sv.getIndex();
+    }
     this.content = c;
   }
 
-- 
1.7.10.2