From 5bbd8870c4840d4092e69a1fb772f453dab9245d Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Sat, 25 Mar 2023 21:32:08 +0000
Subject: [PATCH] JAL-629 open initial non-Arg arguments as files in separate
 alignment frames

---
 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 82b1b92..c6580a7 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -98,24 +98,45 @@ public class ArgParser
 
   public ArgParser(String[] args)
   {
-    // make a mutable new ArrayList so that shell globbing parser works
+    // Make a mutable new ArrayList so that shell globbing parser works.
+    // (When shell file globbing is used, there are a sequence of non-Arg
+    // arguments (which are the expanded globbed filenames) that need to be
+    // consumed by the --open/--argfile/etc Arg which is most easily done by
+    // removing these filenames from the list one at a time. This can't be done
+    // with an ArrayList made with only Arrays.asList(String[] args). )
     this(new ArrayList<>(Arrays.asList(args)));
   }
 
   public ArgParser(List<String> args)
   {
-    init(args);
+    parse(args);
   }
 
-  private void init(List<String> args)
+  private void parse(List<String> args)
   {
-    // Enumeration<String> argE = Collections.enumeration(args);
     int argIndex = 0;
-    // while (argE.hasMoreElements())
+    boolean initialFilenameArgs = true;
     for (int i = 0; i < args.size(); i++)
     {
-      // String arg = argE.nextElement();
       String arg = args.get(i);
+
+      // If the first arguments do not start with "--" or "-" or is "open" and
+      // is a filename that exists it is probably a file/list of files to open
+      // so we fake an Arg.OPEN argument and when adding files only add the
+      // single arg[i] and increment the defaultLinkedIdCounter so that each of
+      // these files is opened separately.
+      if (initialFilenameArgs && !arg.startsWith(DOUBLEDASH)
+              && !arg.startsWith("-") && new File(arg).exists())
+      {
+        arg = DOUBLEDASH + Arg.OPEN.getName();
+        Console.debug("Adding argument '" + args.get(i)
+                + "' as a file to be opened");
+      }
+      else
+      {
+        initialFilenameArgs = false;
+      }
+
       String argName = null;
       String val = null;
       List<String> vals = null; // for Opt.GLOB only
@@ -200,7 +221,18 @@ public class ArgParser
           // will be used later. SubVals can be used.
           if (a.hasOption(Opt.GLOB))
           {
-            vals.addAll(getShellGlobbedFilenameValues(a, args, i + 1));
+            // if this is the first argument with a file list at the start of
+            // the args we add filenames from index i instead of i+1
+            // and assume they should be opened separately
+            if (initialFilenameArgs)
+            {
+              val = args.get(i);
+              defaultLinkedIdCounter++;
+            }
+            else
+            {
+              vals = getShellGlobbedFilenameValues(a, args, i + 1);
+            }
           }
           else
           {
@@ -292,6 +324,8 @@ public class ArgParser
         {
           avs = new ArgValues(a);
         }
+
+        boolean argIndexIncremented = false;
         // store appropriate value
         if (a.hasOption(Opt.STRING))
         {
@@ -300,6 +334,7 @@ public class ArgParser
             for (String v : vals)
             {
               avs.addValue(makeSubstitutions(v), argIndex++);
+              argIndexIncremented = true;
             }
           }
           else
@@ -317,6 +352,8 @@ public class ArgParser
           avs.setBoolean(true, argIndex);
         }
         avs.incrementCount();
+        if (!argIndexIncremented)
+          argIndex++;
 
         // store in appropriate place
         if (a.hasOption(Opt.LINKED))
-- 
1.7.10.2