JAL-629 Test and fix --annotation --ssannotation args. Added a viewerType arg/subval...

[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 e22cfc6..f712010 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -10,11 +10,10 @@ import java.util.stream.Collectors;
 public enum Arg
 {
   HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
-  COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, ANNOTATION,
-  ANNOTATION2, DISPLAY, GUI, NEWS, SORTBYTREE, USAGESTATS, OPEN, OPENNEW,
-  PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE,
-  SSANNOTATION, NOTEMPFAC, TEMPFAC, TEMPFAC_LABEL, TEMPFAC_DESC,
-  TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, IMAGE,
+  COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
+  SORTBYTREE, USAGESTATS, OPEN, OPENNEW, PROPS, QUESTIONNAIRE, SETPROP,
+  TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
+  TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
   QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
   SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
 
@@ -32,7 +31,7 @@ public enum Arg
     MENUBAR.setOptions(true, Opt.BOOLEAN);
     STATUS.setOptions(true, Opt.BOOLEAN);
     SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
-    ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED);
+    ANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
     COLOUR.setOptions(Opt.STRING, Opt.LINKED);
     FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
             Opt.ALLOWSUBSTITUTIONS);
@@ -41,8 +40,6 @@ public enum Arg
     GROUPS.setOptions(Opt.STRING, Opt.LINKED);
     HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
     JABAWS.setOptions(Opt.STRING);
-    ANNOTATION.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
-    ANNOTATION2.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
     DISPLAY.setOptions(true, Opt.BOOLEAN);
     GUI.setOptions(true, Opt.BOOLEAN);
     NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
@@ -65,18 +62,16 @@ public enum Arg
     OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
     OUTPUTTYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
 
-    SSANNOTATION.setOptions(Opt.BOOLEAN, Opt.LINKED);
+    SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
     NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
     TEMPFAC.setOptions(Opt.STRING, Opt.LINKED);
-    TEMPFAC_LABEL.setOptions(Opt.STRING, Opt.LINKED);
-    TEMPFAC_DESC.setOptions(Opt.STRING, Opt.LINKED);
-    TEMPFAC_SHADING.setOptions(Opt.BOOLEAN, Opt.LINKED);
     TITLE.setOptions(Opt.STRING, Opt.LINKED);
     PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
             Opt.ALLOWSUBSTITUTIONS);
     NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
     STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
             Opt.ALLOWSUBSTITUTIONS);
+    STRUCTUREVIEWER.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
     WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
     IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
     QUIT.setOptions(Opt.UNARY);