Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into improvement...

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

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 2f25978..7882d7b 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -29,8 +29,8 @@ public enum Arg
           Opt.UNARY, Opt.BOOTSTRAP),
   HEADLESS(Type.CONFIG,
           "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. "
-                  + "Headless mode is assumed if an output file is to be generated, this can be overridden with --noheadless or --gui.",
-          Opt.BOOLEAN, Opt.BOOTSTRAP),
+                  + "Headless mode is assumed if an output file is to be generated, this can be overridden with --gui.",
+          Opt.UNARY, Opt.BOOTSTRAP),
   GUI(Type.CONFIG,
           "Do not run Jalview in headless mode.  This overrides the assumption of headless mode when an output file is to be generated.",
           Opt.UNARY, Opt.BOOTSTRAP),
@@ -93,11 +93,10 @@ public enum Arg
                   + "turn-propensity,\n" + "buried-index,\n"
                   + "nucleotide,\n" + "nucleotide-ambiguity,\n"
                   + "purine-pyrimidine,\n" + "rna-helices,\n"
-                  + "t-coffee-scores,\n" + "sequence-id.\n"
-                  +"\n"
+                  + "t-coffee-scores,\n" + "sequence-id.\n" + "\n"
                   + "Names of user defined colourschemes will also work,\n"
-                 +"and jalview colourscheme specifications like\n"
-                  +"--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
+                  + "and jalview colourscheme specifications like\n"
+                  + "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.",
           Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
@@ -200,7 +199,7 @@ public enum Arg
                   + "clustal (aln),\n" + "phylip (phy),\n"
                   + "jalview (jvp, jar).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
-          Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
+          Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.STDOUT, Opt.PRIMARY),
   FORMAT(Type.OUTPUT,
           "Sets the format for the preceding --output file. Valid formats are:\n"
                   + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n"
@@ -384,6 +383,11 @@ public enum Arg
      */
     OUTPUTFILE("output file --headless will be assumed unless --gui used"),
     /*
+     * A STDOUT Arg can take an output filename that can be '-' to mean print to STDOUT.
+     */
+    STDOUT("allows the output filename '" + ArgParser.STDOUTFILENAME
+            + "' to mean output to STDOUT"),
+    /*
      * A STORED Arg resets and creates a new set of "opened" linkedIds
      */
     STORED(null),