JAL-629 STDOUT documentation. Opt.STDOUT narrower option. Fix for subvals and STDOU...

[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 6c97ebc..0088c60 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -44,9 +44,10 @@ public enum Arg
   QUESTIONNAIRE(Type.CONFIG,
           "Show (or don't show) the questionnaire if one is available.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),
   QUESTIONNAIRE(Type.CONFIG,
           "Show (or don't show) the questionnaire if one is available.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),

-  USAGESTATS(Type.CONFIG,
-          "Send (or don't send) initial launch usage stats.", true,
-          Opt.BOOLEAN, Opt.BOOTSTRAP),
+  NOUSAGESTATS(Type.CONFIG, "Don't send initial launch usage stats.",
+          Opt.UNARY, Opt.BOOTSTRAP),
+  NOSTARTUPFILE(Type.CONFIG, "Don't show the default startup file.",
+          Opt.UNARY, Opt.BOOTSTRAP),

   WEBSERVICEDISCOVERY(Type.CONFIG,
           "Attempt (or don't attempt) to connect to JABAWS web services.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),
   WEBSERVICEDISCOVERY(Type.CONFIG,
           "Attempt (or don't attempt) to connect to JABAWS web services.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),

@@ -65,6 +66,9 @@ public enum Arg
   INITSUBSTITUTIONS(Type.CONFIG,
           "Set ‑‑substitutions to be initially enabled (or initially disabled).",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),
   INITSUBSTITUTIONS(Type.CONFIG,
           "Set ‑‑substitutions to be initially enabled (or initially disabled).",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),

+  P(Type.CONFIG, "Set a Jalview preference value for this session.",
+          Opt.PREFIXKEV, Opt.PRESERVECASE, Opt.STRING, Opt.BOOTSTRAP,
+          Opt.MULTI, Opt.NOACTION, Opt.SECRET), // keep this secret for now.

 
   // Opening an alignment
   OPEN(Type.OPENING,
 
   // Opening an alignment
   OPEN(Type.OPENING,

@@ -80,7 +84,7 @@ public enum Arg
           "Specifies the title for the open alignment window as string.",
           Opt.STRING, Opt.LINKED),
   COLOUR(Type.OPENING, "color", // being a bit soft on the Americans!
           "Specifies the title for the open alignment window as string.",
           Opt.STRING, Opt.LINKED),
   COLOUR(Type.OPENING, "color", // being a bit soft on the Americans!

-          "Applies the colour scheme to the open alignment window. Valid values are:\n"
+          "Applies the colour scheme to the open alignment window. Valid values include:\n"

                   + "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
                   + "zappo,\n" + "taylor,\n" + "gecos-flower,\n"
                   + "gecos-blossom,\n" + "gecos-sunset,\n"
                   + "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
                   + "zappo,\n" + "taylor,\n" + "gecos-flower,\n"
                   + "gecos-blossom,\n" + "gecos-sunset,\n"

@@ -89,7 +93,10 @@ public enum Arg
                   + "turn-propensity,\n" + "buried-index,\n"
                   + "nucleotide,\n" + "nucleotide-ambiguity,\n"
                   + "purine-pyrimidine,\n" + "rna-helices,\n"
                   + "turn-propensity,\n" + "buried-index,\n"
                   + "nucleotide,\n" + "nucleotide-ambiguity,\n"
                   + "purine-pyrimidine,\n" + "rna-helices,\n"

-                  + "t-coffee-scores,\n" + "sequence-id.",
+                  + "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\"",

           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),
           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),

@@ -192,7 +199,7 @@ public enum Arg
                   + "clustal (aln),\n" + "phylip (phy),\n"
                   + "jalview (jvp, jar).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
                   + "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"
   FORMAT(Type.OUTPUT,
           "Sets the format for the preceding --output file. Valid formats are:\n"
                   + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n"

@@ -374,7 +381,12 @@ public enum Arg
      * An OUTPUTFILE Arg provides an output filename. With Opt.ALLOWALL *.ext is shorthand for
      * --all --output={basename}.ext
      */
      * An OUTPUTFILE Arg provides an output filename. With Opt.ALLOWALL *.ext is shorthand for
      * --all --output={basename}.ext
      */

-    OUTPUTFILE("value is an output file"),
+    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
      */
     /*
      * A STORED Arg resets and creates a new set of "opened" linkedIds
      */

@@ -399,6 +411,14 @@ public enum Arg
      * A LAST arg gets moved to appear last in the usage statement (within type)
      */
     LAST(null),
      * A LAST arg gets moved to appear last in the usage statement (within type)
      */
     LAST(null),

+    /*
+     * After other args are checked, the following args can prefix a KEY=VALUE argument
+     */
+    PREFIXKEV("prefixes key=value"),
+    /*
+     * do not lowercase the name when getting the arg name or arg string
+     */
+    PRESERVECASE(null),

     //
     ;
 
     //
     ;
 

@@ -486,15 +506,15 @@ public enum Arg
   private Arg(Type type, String alternativeName, String description,
           boolean defaultBoolean, Opt... options)
   {
   private Arg(Type type, String alternativeName, String description,
           boolean defaultBoolean, Opt... options)
   {

+    this.type = type;
+    this.description = description;
+    this.defaultBoolValue = defaultBoolean;
+    this.setOptions(options);

     this.argNames = alternativeName != null
             ? new String[]
             { this.getName(), alternativeName }
             : new String[]
             { this.getName() };
     this.argNames = alternativeName != null
             ? new String[]
             { this.getName(), alternativeName }
             : new String[]
             { this.getName() };

-    this.type = type;
-    this.description = description;
-    this.defaultBoolValue = defaultBoolean;
-    this.setOptions(options);

   }
 
   public String argString()
   }
 
   public String argString()

@@ -544,7 +564,9 @@ public enum Arg
 
   public String getName()
   {
 
   public String getName()
   {

-    return this.name().toLowerCase(Locale.ROOT).replace('_', '-');
+    String name = hasOption(Opt.PRESERVECASE) ? this.name()
+            : this.name().toLowerCase(Locale.ROOT);
+    return name.replace('_', '-');

   }
 
   @Override
   }
 
   @Override

@@ -794,7 +816,16 @@ public enum Arg
     argSb.append(
             a.hasOption(Opt.BOOLEAN) ? booleanArgString(a) : a.argString());
     if (a.hasOption(Opt.STRING))
     argSb.append(
             a.hasOption(Opt.BOOLEAN) ? booleanArgString(a) : a.argString());
     if (a.hasOption(Opt.STRING))

-      argSb.append("=value");
+    {
+      if (a.hasOption(Opt.PREFIXKEV))
+      {
+        argSb.append("key=value");
+      }
+      else
+      {
+        argSb.append("=value");
+      }
+    }

     return argSb.toString();
   }
 
     return argSb.toString();
   }