JAL-629 added eps and imagemap. Added --output and --format with test. Adjusted...

[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 a5c344d..f8454df 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -13,10 +13,10 @@ public enum Arg
   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, RENDERER,
-  QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, NEW, NPP("n++"),
-  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE,
-  WEBSERVICEDISCOVERY, ALL;
+  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
   {
@@ -115,10 +115,14 @@ public enum Arg
     IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
             Opt.ALLOWALL, Opt.REQUIREINPUT);
     TYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
+    FORMAT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
     RENDERER.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
     QUIT.setOptions(Opt.UNARY);
+    OVERWRITE.setOptions(Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL);
+    BACKUPS.setOptions(true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL);
     CLOSE.setOptions(Opt.UNARY, Opt.LINKED, Opt.ALLOWALL);
     DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
+    TRACE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
     ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
             Opt.ALLOWSUBSTITUTIONS);
@@ -126,7 +130,8 @@ public enum Arg
             Opt.INCREMENTDEFAULTCOUNTER);
     NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
     SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
-    INITSUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION);
+    INITSUBSTITUTIONS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP,
+            Opt.NOACTION); // defaulting substitutions to true
     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);