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 b32baf5..3862375 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -48,7 +48,9 @@ public class ArgParser
 
   protected static final String DOUBLEDASH = "--";
 
-  protected static final char EQUALS = '=';
+  public static final char EQUALS = '=';
+
+  public static final String STDOUTFILENAME = "-";
 
   protected static final String NEGATESTRING = "no";
 
@@ -209,12 +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);
   }
@@ -260,27 +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))
@@ -336,12 +344,34 @@ public class ArgParser
         Arg a = argMap.get(argName);
         // check for boolean prepended by "no" e.g. --nowrap
         boolean negated = false;
-        if (a == null && argName.startsWith(NEGATESTRING) && argMap
-                .containsKey(argName.substring(NEGATESTRING.length())))
+        if (a == null)
         {
-          argName = argName.substring(NEGATESTRING.length());
-          a = argMap.get(argName);
-          negated = true;
+          if (argName.startsWith(NEGATESTRING) && argMap
+                  .containsKey(argName.substring(NEGATESTRING.length())))
+          {
+            argName = argName.substring(NEGATESTRING.length());
+            a = argMap.get(argName);
+            negated = true;
+          }
+          else
+          {
+            // after all other args, look for Opt.PREFIXKEV args if still not
+            // found
+            for (Arg potentialArg : EnumSet.allOf(Arg.class))
+            {
+              if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+                      && argName.startsWith(potentialArg.getName())
+                      && equalPos > -1)
+              {
+                val = argName.substring(potentialArg.getName().length())
+                        + EQUALS + val;
+                argName = argName.substring(0,
+                        potentialArg.getName().length());
+                a = potentialArg;
+                break;
+              }
+            }
+          }
         }
 
         // check for config errors
@@ -409,7 +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()
@@ -424,8 +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
             {