From 115334feb610d50d8ce91daf7e754baacbeb511b Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 4 Apr 2023 18:28:16 +0100
Subject: [PATCH 1/1] JAL-629 Start of Usage statement

---
 src/jalview/bin/Jalview.java       |    8 ++-
 src/jalview/bin/argparser/Arg.java |  104 +++++++++++++++++++++++++++++++++---
 2 files changed, 103 insertions(+), 9 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index d0e76f2..951578a 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -449,8 +449,12 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      if (aparser.contains("help") || aparser.contains("h")
-              || argparser.getBool(Arg.HELP))
+      if (bootstrapArgs.contains(Arg.HELP))
+      {
+        System.out.println(Arg.usage());
+        Jalview.exit(null, 0);
+      }
+      if (aparser.contains("help") || aparser.contains("h"))
       {
         showUsage();
         Jalview.exit(null, 0);
diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 7eaac09..65a865b 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -1,6 +1,7 @@
 package jalview.bin.argparser;
 
 import java.util.Arrays;
+import java.util.EnumSet;
 import java.util.List;
 import java.util.Locale;
 import java.util.stream.Collectors;
@@ -24,9 +25,9 @@ public enum Arg
 
   static
   {
-    HELP.setOptions(Opt.UNARY);
+    HELP.setOptions("Display this help message", Opt.UNARY, Opt.BOOTSTRAP);
     CALCULATION.setOptions(true, Opt.BOOLEAN); // default "true" implies only
-    // expecting "--nocalculation"
+                                               // expecting "--nocalculation"
     MENUBAR.setOptions(true, Opt.BOOLEAN);
     STATUS.setOptions(true, Opt.BOOLEAN);
     SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
@@ -103,6 +104,8 @@ public enum Arg
 
   private boolean defaultBoolValue = false;
 
+  private String description = null;
+
   private Arg()
   {
     this(new String[0]);
@@ -121,8 +124,21 @@ public enum Arg
 
   public String argString()
   {
-    return new StringBuilder(ArgParser.DOUBLEDASH).append(getName())
-            .toString();
+    return argString(false);
+  }
+
+  public String negateArgString()
+  {
+    return argString(true);
+  }
+
+  private String argString(boolean negate)
+  {
+    StringBuilder sb = new StringBuilder(ArgParser.DOUBLEDASH);
+    if (negate && hasOption(Opt.BOOLEAN))
+      sb.append(ArgParser.NEGATESTRING);
+    sb.append(getName());
+    return sb.toString();
   }
 
   public String toLongString()
@@ -175,17 +191,91 @@ public enum Arg
 
   protected void setOptions(Opt... options)
   {
-    setOptions(false, options);
+    setOptions("", false, options);
+  }
+
+  protected void setOptions(String desc, Opt... options)
+  {
+    setOptions(desc, false, options);
   }
 
   protected void setOptions(boolean defaultBoolValue, Opt... options)
   {
+    setOptions("", defaultBoolValue, options);
+  }
+
+  protected void setOptions(String desc, boolean defaultBoolValue,
+          Opt... options)
+  {
+    this.description = desc;
     this.defaultBoolValue = defaultBoolValue;
-    argOptions = options;
+    this.argOptions = options;
   }
 
   protected boolean getDefaultBoolValue()
   {
     return defaultBoolValue;
   }
-}
+
+  private void setDescription(String d)
+  {
+    description = d;
+  }
+
+  protected String getDescription()
+  {
+    return description;
+  }
+
+  public static final String usage()
+  {
+    StringBuilder sb = new StringBuilder();
+
+    sb.append("Usage: jalview [args]");
+    sb.append(System.lineSeparator());
+
+    int maxArgLength = 0;
+    for (Arg a : EnumSet.allOf(Arg.class))
+    {
+      StringBuilder argSb = new StringBuilder();
+      argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
+              : a.argString());
+      if (a.hasOption(Opt.STRING))
+        argSb.append("=value");
+      if (argSb.length() > maxArgLength)
+        maxArgLength = argSb.length();
+    }
+
+    // might want to order these
+    for (Arg a : EnumSet.allOf(Arg.class))
+    {
+      StringBuilder argSb = new StringBuilder();
+      argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
+              : a.argString());
+      if (a.hasOption(Opt.STRING))
+        argSb.append("=value");
+      sb.append(String.format("%-" + maxArgLength + "s  - %s",
+              argSb.toString(), a.getDescription()));
+      if (a.hasOption(Opt.BOOLEAN))
+      {
+        sb.append(" (default ");
+        sb.append(a.getDefaultBoolValue() ? a.argString()
+                : a.negateArgString());
+        sb.append(')');
+      }
+      sb.append(System.lineSeparator());
+    }
+    return sb.toString();
+  }
+
+  public static String booleanArgString(Arg a)
+  {
+    StringBuilder sb = new StringBuilder(a.argString());
+    if (a.hasOption(Opt.BOOLEAN))
+    {
+      sb.append('/');
+      sb.append(a.negateArgString());
+    }
+    return sb.toString();
+  }
+}
\ No newline at end of file
-- 
1.7.10.2