JAL-629 More NG arguments: --features, --annotations, --sortbytree, --tree, --groovy...

[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 f8454df..f83f267 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -9,16 +9,17 @@ import java.util.stream.Collectors;
 
 public enum Arg
 {
-  HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
-  COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
-  SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP, TREE,
-  VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC, TITLE, PAEMATRIX,
-  WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE, TYPE, FORMAT,
-  OVERWRITE, RENDERER, QUIT, CLOSE, DEBUG("d"), TRACE, QUIET("q"), ARGFILE,
-  NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH,
-  SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS;
-
-  protected static enum Opt
+  HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, SHOWANNOTATIONS,
+  COLOUR("color"), FEATURES, ANNOTATIONS, GROOVY, GROUPS, HEADLESS, JABAWS,
+  DISPLAY, NEWS, SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE,
+  SETPROP, TREE, VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
+  TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
+  TYPE, FORMAT, OVERWRITE, RENDERER, QUIT, CLOSE, DEBUG("d"), TRACE,
+  QUIET("q"), ARGFILE, NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS,
+  NIL, SPLASH, SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS,
+  TESTOUTPUT;
+
+  public static enum Opt
   {
     BOOLEAN, // This Arg can be specified as --arg or --noarg to give true or
              // false. A default can be given with setOptions(bool, Opt....).
@@ -70,30 +71,33 @@ public enum Arg
     MENUBAR.setOptions(true, Opt.BOOLEAN);
     STATUS.setOptions(true, Opt.BOOLEAN);
     SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
-    ANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
+    SHOWANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
     COLOUR.setOptions(Opt.STRING, Opt.LINKED);
     FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
             Opt.ALLOWSUBSTITUTIONS);
+    ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+            Opt.ALLOWSUBSTITUTIONS);
+    TREE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+            Opt.ALLOWSUBSTITUTIONS);
     GROOVY.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
             Opt.ALLOWSUBSTITUTIONS);
     GROUPS.setOptions(Opt.STRING, Opt.LINKED);
     HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
-    JABAWS.setOptions(Opt.STRING);
+    TESTOUTPUT.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
+    JABAWS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
     DISPLAY.setOptions(true, Opt.BOOLEAN);
-    GUI.setOptions(true, Opt.BOOLEAN);
     NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
     SPLASH.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
-    // expects a string value
-    SORTBYTREE.setOptions(true, Opt.BOOLEAN);
-    USAGESTATS.setOptions(true, Opt.BOOLEAN);
+    SORTBYTREE.setOptions(true, Opt.LINKED, Opt.BOOLEAN);
+    QUESTIONNAIRE.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+    USAGESTATS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+    WEBSERVICEDISCOVERY.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
     APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
             Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
     OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
             Opt.MULTI, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
     PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
-    QUESTIONNAIRE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     SETPROP.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP);
-    TREE.setOptions(Opt.STRING);
 
     VDOC.setOptions(Opt.UNARY);
     VSESS.setOptions(Opt.UNARY);
@@ -135,7 +139,6 @@ public enum Arg
     NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
     SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
-    WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     ALL.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
 
   }