JAL-629 More consistent printing of --arguments. Example nf-core argfile

[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 e658434..7eaac09 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -14,7 +14,7 @@ public enum Arg
   SSANNOTATION, NOTEMPFAC, TEMPFAC, TEMPFAC_LABEL, TEMPFAC_DESC,
   TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, IMAGE,
   QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
-  SUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
+  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
 
   protected static enum Opt
   {
@@ -26,7 +26,7 @@ public enum Arg
   {
     HELP.setOptions(Opt.UNARY);
     CALCULATION.setOptions(true, Opt.BOOLEAN); // default "true" implies only
-                                               // expecting "--nocalculation"
+    // expecting "--nocalculation"
     MENUBAR.setOptions(true, Opt.BOOLEAN);
     STATUS.setOptions(true, Opt.BOOLEAN);
     SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
@@ -86,6 +86,7 @@ public enum Arg
     INCREMENT.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
     NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
     SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
+    INITSUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION);
     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);
@@ -118,6 +119,12 @@ public enum Arg
       System.arraycopy(names, 0, this.argNames, 1, names.length);
   }
 
+  public String argString()
+  {
+    return new StringBuilder(ArgParser.DOUBLEDASH).append(getName())
+            .toString();
+  }
+
   public String toLongString()
   {
     StringBuilder sb = new StringBuilder();