JAL-629 Added --opened arg which is like limiting --all to only the previously -...

[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 ba981fb..46de01b 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -54,20 +54,23 @@ public enum Arg
   // Opening an alignment
   OPEN("Opens one or more alignment files or URLs in new alignment windows.",
           Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, Opt.MULTI,
-          Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT),
+          Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.STORED),
   APPEND("Appends one or more alignment files or URLs to the open alignment window (or opens a new alignment if none already open).",
           Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
           Opt.ALLOWSUBSTITUTIONS, Opt.INPUT),
   TITLE("Specifies the title for the open alignment window as string.",
           Opt.STRING, Opt.LINKED),
-  COLOUR("Applies the colour scheme to the open alignment window. Valid values are:\n"
-          + "clustal,\n" + "blosum62,\n" + "pc-identity,\n" + "zappo,\n"
-          + "taylor,\n" + "gecos-flower,\n" + "gecos-blossom,\n"
-          + "gecos-sunset,\n" + "gecos-ocean,\n" + "hydrophobic,\n"
-          + "helix-propensity,\n" + "strand-propensity,\n"
-          + "turn-propensity,\n" + "buried-index,\n" + "nucleotide,\n"
-          + "nucleotide-ambiguity,\n" + "purine-pyrimidine,\n"
-          + "rna-helices,\n" + "t-coffee-scores,\n" + "sequence-id.",
+  COLOUR("color", // being a bit soft on the Americans!
+          "Applies the colour scheme to the open alignment window. Valid values are:\n"
+                  + "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
+                  + "zappo,\n" + "taylor,\n" + "gecos-flower,\n"
+                  + "gecos-blossom,\n" + "gecos-sunset,\n"
+                  + "gecos-ocean,\n" + "hydrophobic,\n"
+                  + "helix-propensity,\n" + "strand-propensity,\n"
+                  + "turn-propensity,\n" + "buried-index,\n"
+                  + "nucleotide,\n" + "nucleotide-ambiguity,\n"
+                  + "purine-pyrimidine,\n" + "rna-helices,\n"
+                  + "t-coffee-scores,\n" + "sequence-id.",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   FEATURES("Add a feature file or URL to the open alignment.", Opt.STRING,
           Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
@@ -173,6 +176,8 @@ public enum Arg
           Opt.UNARY, Opt.MULTI, Opt.NOACTION),
   ALL("Apply the following output arguments to all sets of linked arguments.",
           Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+  OPENED("Apply the following output arguments to all of the last --open'ed set of linked arguments.",
+          Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
   QUIT("After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
           Opt.UNARY),
 
@@ -256,6 +261,7 @@ public enum Arg
                   // input (i.e. --open or --append)
     OUTPUT, // This Arg provides an output filename. With Opt.ALLOWALL *.ext is
             // shorthand for --all --output={basename}.ext
+    STORED, // This Arg resets and creates a new set of "opened" linkedIds
   }
 
   private final String[] argNames;