JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt.OUTPUT to Opt.OUTPUTFILE for...

[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 8bac623..c502eec 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -28,7 +28,11 @@ public enum Arg
                   + ChannelProperties.getProperty("app_name"),
           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.",
+          "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),
+  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),
   JABAWS(Type.CONFIG, "Set a different URL to connect to a JABAWS server.",
           Opt.STRING, Opt.BOOTSTRAP),
@@ -140,7 +144,7 @@ public enum Arg
           "Output an image of the open alignment window. Format is specified by the subval modifier, a following --type argument or guessed from the file extension. Valid formats/extensions are:\n"
                   + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
-          Opt.REQUIREINPUT, Opt.OUTPUT, Opt.PRIMARY),
+          Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
   TYPE(Type.IMAGE,
           "Set the image format for the preceding --image. Valid values are:\n"
                   + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
@@ -160,7 +164,7 @@ public enum Arg
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   STRUCTUREIMAGE(Type.STRUCTUREIMAGE,
           "Export an image of a 3D structure opened in JMOL", Opt.STRING,
-          Opt.LINKED, Opt.MULTI),
+          Opt.LINKED, Opt.MULTI, Opt.OUTPUTFILE),
   STRUCTUREIMAGETYPE(Type.STRUCTUREIMAGE,
           "Set the structure image format for the preceding --structureimage. Valid values are:\n"
                   + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
@@ -188,7 +192,7 @@ public enum Arg
                   + "clustal (aln),\n" + "phylip (phy),\n"
                   + "jalview (jvp, jar).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
-          Opt.REQUIREINPUT, Opt.OUTPUT, Opt.PRIMARY),
+          Opt.REQUIREINPUT, Opt.OUTPUTFILE, 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"
@@ -325,8 +329,9 @@ public enum Arg
     INPUT, // This Arg counts as an input for REQUIREINPUT
     REQUIREINPUT, // This Arg can only be applied via --all if there is an
                   // input (i.e. --open or --append)
-    OUTPUT, // This Arg provides an output filename. With Opt.ALLOWALL *.ext is
-            // shorthand for --all --output={basename}.ext
+    OUTPUTFILE, // This Arg provides an output filename. With Opt.ALLOWALL *.ext
+                // is
+    // shorthand for --all --output={basename}.ext
     STORED, // This Arg resets and creates a new set of "opened" linkedIds
     HELP, // This Arg is a --help type arg
     PRIMARY, // This Arg is the main Arg for its type
@@ -489,6 +494,11 @@ public enum Arg
     return true;
   }
 
+  protected Opt[] getOptions()
+  {
+    return argOptions;
+  }
+
   protected void setOptions(Opt... options)
   {
     this.argOptions = options;