JAL-629 Fixed appending URLs

[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..9b5907f 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -10,13 +10,13 @@ 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,
-  QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
-  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
+  COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
+  SORTBYTREE, USAGESTATS, APPEND, OPEN, 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, NEWFRAME, NPP("n++"),
+  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE,
+  WEBSERVICEDISCOVERY;
 
   protected static enum Opt
   {
@@ -32,7 +32,7 @@ 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 +41,6 @@ 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);
@@ -50,9 +48,9 @@ public enum Arg
     // expects a string value
     SORTBYTREE.setOptions(true, Opt.BOOLEAN);
     USAGESTATS.setOptions(true, Opt.BOOLEAN);
-    OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+    APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
             Opt.ALLOWSUBSTITUTIONS);
-    OPENNEW.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+    OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
             Opt.ALLOWSUBSTITUTIONS);
     PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
     QUESTIONNAIRE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
@@ -65,18 +63,16 @@ 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);
@@ -85,13 +81,14 @@ public enum Arg
     QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
     ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
             Opt.ALLOWSUBSTITUTIONS);
-    INCREMENT.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
+    NEWFRAME.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);
+    WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     // Opt.BOOTSTRAP args are parsed (not linked with no SubVals so using a
     // simplified parser, see jalview.bin.argparser.BootstrapArgs)
     // before a full parse of arguments and so can be accessible at an earlier