JAL-629 Much better way of dealing with list of filenames/URLs without an --open...

[jalview.git] / src / jalview / bin / argparser / ArgParser.java

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 9c66f32..3862375 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -211,12 +211,15 @@ public class ArgParser
   public ArgParser(String[] args, boolean initsubstitutions,
           BootstrapArgs bsa)
   {
-    // 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 --append/--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). )
+    /*
+     *  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 --append/--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) as
+     * that is not mutable. )
+     */
     this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
             bsa);
   }
@@ -262,27 +265,30 @@ public class ArgParser
           boolean allowPrivate)
   {
     this.substitutions = initsubstitutions;
-    boolean openEachInitialFilenames = true;
-    for (int i = 0; i < args.size(); i++)
-    {
-      String arg = args.get(i);
 
-      // If the first arguments do not start with "--" or "-" or is not "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 (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
-              && !arg.startsWith("-") && !arg.equals("open")
-              && (new File(arg).exists()
-                      || HttpUtils.startsWithHttpOrHttps(arg)))
-      {
-        arg = Arg.OPEN.argString();
-      }
-      else
+    /*
+     *  If the first argument does not start with "--" or "-" or is not "open",
+     *  and is a filename that exists or a URL, it is probably a file/list of
+     *  files to open so we insert an Arg.OPEN argument before it. This will
+     *  mean the list of files at the start of the arguments are all opened
+     *  separately.
+     */
+    if (args.size() > 0)
+    {
+      String arg0 = args.get(0);
+      if (arg0 != null
+              && (!arg0.startsWith(DOUBLEDASH) && !arg0.startsWith("-")
+                      && !arg0.equals("open") && (new File(arg0).exists()
+                              || HttpUtils.startsWithHttpOrHttps(arg0))))
       {
-        openEachInitialFilenames = false;
+        // insert "--open" at the start
+        args.add(0, Arg.OPEN.argString());
       }
+    }
+
+    for (int i = 0; i < args.size(); i++)
+    {
+      String arg = args.get(i);
 
       // look for double-dash, e.g. --arg
       if (arg.startsWith(DOUBLEDASH))
@@ -433,7 +439,7 @@ public class ArgParser
           {
             // There is no "=" so value is next arg or args (possibly shell
             // glob-expanded)
-            if ((openEachInitialFilenames ? i : i + 1) >= args.size())
+            if (i + 1 >= args.size())
             {
               // no value to take for arg, which wants a value
               Console.error("Argument '" + a.getName()
@@ -448,8 +454,7 @@ public class ArgParser
             {
               // 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
-              globVals = getShellGlobbedFilenameValues(a, args,
-                      openEachInitialFilenames ? i : i + 1);
+              globVals = getShellGlobbedFilenameValues(a, args, i + 1);
             }
             else
             {