JAL-629 Added --structureimage code and formatting args/subvals. Added tests for...

[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 2354cdd..8bac623 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -131,8 +131,7 @@ public enum Arg
   NOTEMPFAC(Type.STRUCTURE,
           "Do not show the temperature factor annotation for the preceding --structure.",
           Opt.UNARY, Opt.LINKED, Opt.ALLOWALL, Opt.SECRET), // keep this secret
-                                                            // until it
-  // works!
+                                                            // until it works!
   SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
           Opt.ALLOWALL),
 
@@ -159,25 +158,24 @@ public enum Arg
   HEIGHT(Type.IMAGE,
           "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),
-  STRUCTUREIMAGE(Type.IMAGE,
+  STRUCTUREIMAGE(Type.STRUCTUREIMAGE,
           "Export an image of a 3D structure opened in JMOL", Opt.STRING,
           Opt.LINKED, Opt.MULTI),
-
-  STRUCTUREIMAGETYPE(Type.IMAGE,
+  STRUCTUREIMAGETYPE(Type.STRUCTUREIMAGE,
           "Set the structure image format for the preceding --structureimage. Valid values are:\n"
                   + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
-  STRUCTUREIMAGETEXTRENDERER(Type.IMAGE,
-          "Sets whether text in a vector structure image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:\n"
+  STRUCTUREIMAGETEXTRENDERER(Type.STRUCTUREIMAGE,
+          "Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:\n"
                   + "text,\n" + "lineart.",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
-  STRUCTUREIMAGESCALE(Type.IMAGE,
+  STRUCTUREIMAGESCALE(Type.STRUCTUREIMAGE,
           "Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
-  STRUCTUREIMAGEWIDTH(Type.IMAGE,
+  STRUCTUREIMAGEWIDTH(Type.STRUCTUREIMAGE,
           "Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
-  STRUCTUREIMAGEHEIGHT(Type.IMAGE,
+  STRUCTUREIMAGEHEIGHT(Type.STRUCTUREIMAGE,
           "Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
 
@@ -243,6 +241,12 @@ public enum Arg
   QUIT(Type.FLOW,
           "After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
           Opt.UNARY),
+  NOQUIT(Type.FLOW,
+          "Secret arg to not quit after --headless mode for tests",
+          Opt.UNARY, Opt.SECRET),
+  ALLSTRUCTURES(Type.FLOW,
+          "Apply the following 3D structure formatting arguments to all structures within the open alignment.",
+          Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
 
   // secret options
   TESTOUTPUT(Type.CONFIG,
@@ -342,6 +346,7 @@ public enum Arg
     PROCESS("arguments used to process an alignment once opened"),
     OUTPUT("arguments used to save data from a processed alignment"),
     IMAGE("arguments used to export an image of an alignment"),
+    STRUCTUREIMAGE("arguments used to export an image of an structure"),
     FLOW("arguments that control processing of the other arguments"), //
     ALL("all arguments"), // mostly just a place-holder for --help-all
     NONE, // mostly a place-holder for --help