From 96b2b15303c2c7b075eb2dee5a84b6b04ef1a335 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Sat, 11 Mar 2023 12:45:18 +0000
Subject: [PATCH] JAL-629 --substitutions --nosubstitutions flags,
 --nil[{++n}] just in case needed

---
 src/jalview/bin/ArgParser.java |   25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/src/jalview/bin/ArgParser.java b/src/jalview/bin/ArgParser.java
index 9af5e4a..dfd3457 100644
--- a/src/jalview/bin/ArgParser.java
+++ b/src/jalview/bin/ArgParser.java
@@ -57,10 +57,14 @@ public class ArgParser
 
   private int idCounter = 0;
 
+  // flag to say whether {n} subtitutions in output filenames should be made.
+  // Turn on and off with --subs and --nosubs
+  private boolean substitutions = false;
+
   private static enum Opt
   {
     BOOLEAN, STRING, UNARY, MULTI, LINKED, NODUPLICATEVALUES, BOOTSTRAP,
-    GLOB
+    GLOB, NOACTION
   }
 
   public enum Arg
@@ -79,7 +83,7 @@ public class ArgParser
     VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATION, NOTEMPFAC, TEMPFAC,
     TEMPFAC_LABEL, TEMPFAC_DESC, TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP,
     NOSTRUCTURE, STRUCTURE, IMAGE, QUIT, CLOSE, DEBUG("d"), QUIET("q"),
-    ARGFILE, INCREMENT, NPP("n++");
+    ARGFILE, INCREMENT, NPP("n++"), SUBSTITUTIONS, NIL;
 
     static
     {
@@ -135,8 +139,10 @@ public class ArgParser
       DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
       QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
       ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB);
-      INCREMENT.setOptions(Opt.UNARY, Opt.MULTI);
-      NPP.setOptions(Opt.UNARY, Opt.MULTI);
+      INCREMENT.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
+      NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
+      SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
+      NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
       // BOOTSTRAP args are parsed before a full parse of arguments and
       // so are accessible at an earlier stage to (e.g.) set debug log level,
       // provide a props file (that might set log level), run headlessly, read
@@ -583,16 +589,19 @@ public class ArgParser
           }
         }
 
+        // make NOACTION adjustments
         // default and auto counter increments
         if (a == Arg.INCREMENT)
         {
           defaultLinkedIdCounter++;
-          continue;
         }
         else if (a == Arg.NPP)
         {
           idCounter++;
-          continue;
+        }
+        else if (a == Arg.SUBSTITUTIONS)
+        {
+          substitutions = !negated;
         }
 
         String autoCounterString = null;
@@ -634,6 +643,10 @@ public class ArgParser
         if (!linkedArgs.containsKey(linkedId))
           linkedArgs.put(linkedId, new ArgValuesMap());
 
+        // do not continue for NOACTION args
+        if (a.hasOption(Opt.NOACTION))
+          continue;
+
         ArgValuesMap avm = linkedArgs.get(linkedId);
 
         // not dealing with both NODUPLICATEVALUES and GLOB
-- 
1.7.10.2