JAL-629 Fix --tempfac. Hide non-working --notempfac. Add --scale, --width, --height...

[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 95b6b43..6fcc011 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -16,6 +16,9 @@ public enum Arg
 
   // Initialising arguments (BOOTSTRAP)
   HELP("Display this help statement", Opt.UNARY, Opt.BOOTSTRAP),
+  VERSION("Display the version of "
+          + ChannelProperties.getProperty("app_name"), Opt.UNARY,
+          Opt.BOOTSTRAP),
   HEADLESS(
           "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.",
           Opt.UNARY, Opt.BOOTSTRAP),
@@ -99,7 +102,8 @@ public enum Arg
           Opt.STRING, Opt.LINKED, Opt.MULTI),
   NOTEMPFAC(
           "Do not show the temperature factor annotation for the preceding --structure.",
-          Opt.UNARY, Opt.LINKED),
+          Opt.UNARY, Opt.LINKED, Opt.SECRET), // keep this secret until it
+                                              // works!
   SHOWSSANNOTATIONS(null, Opt.BOOLEAN, Opt.LINKED),
 
   // Outputting files
@@ -114,6 +118,12 @@ public enum Arg
           "Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values for name are:\n"
                   + "text,\n" + "lineart.",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+  SCALE("Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
+          Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+  WIDTH("Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
+          Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+  HEIGHT("Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).",
+          Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   OUTPUT("Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
           + "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n"
           + "stockholm (sto, stk),\n" + "pir (pir),\n" + "blc (blc),\n"
@@ -459,6 +469,11 @@ public enum Arg
         options.add("allows substitutions");
       }
 
+      if (a.hasOption(Opt.ALLOWALL))
+      {
+        options.add("can be applied to all linked arguments");
+      }
+
       if (a.hasOption(Opt.PRIVATE))
       {
         options.add("for internal use only");