Merge branch 'develop' into feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_na...

[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 8003245..8bac623 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -128,14 +128,10 @@ public enum Arg
                   + "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n"
                   + "pymol.",
           Opt.STRING, Opt.LINKED, Opt.MULTI),
                   + "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n"
                   + "pymol.",
           Opt.STRING, Opt.LINKED, Opt.MULTI),

-  STRUCTUREIMAGE(Type.STRUCTURE,
-          "Export an image of a 3D structure opened in JMOL", Opt.STRING,
-          Opt.LINKED, Opt.MULTI),

   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
   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),
 
   SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
           Opt.ALLOWALL),
 

@@ -146,11 +142,11 @@ public enum Arg
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
           Opt.REQUIREINPUT, Opt.OUTPUT, Opt.PRIMARY),
   TYPE(Type.IMAGE,
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
           Opt.REQUIREINPUT, Opt.OUTPUT, Opt.PRIMARY),
   TYPE(Type.IMAGE,

-          "Set the image format for the preceding --image to name. Valid values for name are: svg,\n"
-                  + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
+          "Set the image format for the preceding --image. Valid values are:\n"
+                  + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",

           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   TEXTRENDERER(Type.IMAGE,
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   TEXTRENDERER(Type.IMAGE,

-          "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"
+          "Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:\n"

                   + "text,\n" + "lineart.",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   SCALE(Type.IMAGE,
                   + "text,\n" + "lineart.",
           Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
   SCALE(Type.IMAGE,

@@ -162,6 +158,27 @@ 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),
   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.STRUCTUREIMAGE,
+          "Export an image of a 3D structure opened in JMOL", Opt.STRING,
+          Opt.LINKED, Opt.MULTI),
+  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.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.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.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.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),
+

   OUTPUT(Type.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"
   OUTPUT(Type.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"

@@ -224,6 +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),
   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,
 
   // secret options
   TESTOUTPUT(Type.CONFIG,

@@ -323,6 +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"),
     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
     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

@@ -522,9 +546,9 @@ public enum Arg
   {
     StringBuilder sb = new StringBuilder();
 
   {
     StringBuilder sb = new StringBuilder();
 

-    sb.append("usage: jalview [" + Arg.HEADLESS.argString() + "] ["
+    sb.append("usage: jalview [" + Arg.HEADLESS.argString() + "] [["

             + Arg.OPEN.argString() + "/" + Arg.APPEND.argString()
             + Arg.OPEN.argString() + "/" + Arg.APPEND.argString()

-            + " file(s)] [args]");
+            + "] file(s)] [args]");

     sb.append(System.lineSeparator());
     sb.append(System.lineSeparator());
 
     sb.append(System.lineSeparator());
     sb.append(System.lineSeparator());
 

@@ -567,6 +591,7 @@ public enum Arg
       }
 
       Iterator<Arg> argsI = args.iterator();
       }
 
       Iterator<Arg> argsI = args.iterator();

+      Type typeSection = null;

       while (argsI.hasNext())
       {
         Arg a = argsI.next();
       while (argsI.hasNext())
       {
         Arg a = argsI.next();

@@ -577,10 +602,27 @@ public enum Arg
           continue;
         }
 
           continue;
         }
 

+        if (a.getType() != typeSection)
+        {
+          typeSection = a.getType();
+          String typeDescription = a.getType().description();
+          if (typeDescription != null && typeDescription.length() > 0)
+          {
+            // typeDescription = typeDescription.substring(0,
+            // 1).toUpperCase(Locale.ROOT) + typeDescription.substring(1);
+            typeDescription = typeDescription.toUpperCase(Locale.ROOT);
+            sb.append(typeDescription);
+            sb.append(System.lineSeparator());
+            sb.append(System.lineSeparator());
+          }
+        }
+

         appendArgUsage(sb, a, maxArgLength);
 
         if (argsI.hasNext())
         appendArgUsage(sb, a, maxArgLength);
 
         if (argsI.hasNext())

+        {

           sb.append(System.lineSeparator());
           sb.append(System.lineSeparator());

+        }

       }
     }
     return sb.toString();
       }
     }
     return sb.toString();