JAL-629 fixes to typed args

[jalview.git] / src / jalview / bin / argparser / BootstrapArgs.java

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index 1c54355..faa4a43 100644 (file)
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -7,6 +7,7 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -64,46 +65,50 @@ public class BootstrapArgs
         String val = null;
         Type type = null;
         // remove "--"
-        arg = arg.substring(ArgParser.DOUBLEDASH.length());
+        argName = arg.substring(ArgParser.DOUBLEDASH.length());
 
         // look for equals e.g. --arg=value
-        int equalPos = arg.indexOf(ArgParser.EQUALS);
-        if (equalPos > -1
-                && ArgParser.argMap.containsKey(arg.substring(0, equalPos)))
+        int equalPos = argName.indexOf(ArgParser.EQUALS);
+        if (equalPos > -1)
         {
-          argName = arg.substring(0, equalPos);
-          val = arg.substring(equalPos + 1);
+          val = argName.substring(equalPos + 1);
+          argName = argName.substring(0, equalPos);
         }
+
         // check for boolean prepended by "no"
-        else if (arg.startsWith(ArgParser.NEGATESTRING)
+        if (argName.startsWith(ArgParser.NEGATESTRING)
                 && ArgParser.argMap.containsKey(
-                        arg.substring(ArgParser.NEGATESTRING.length())))
+                        argName.substring(ArgParser.NEGATESTRING.length())))
         {
-          argName = arg.substring(ArgParser.NEGATESTRING.length());
           val = "false";
+          argName = argName.substring(ArgParser.NEGATESTRING.length());
         }
-        else if (ArgParser.argMap.containsKey(arg))
-        {
-          argName = arg;
-          val = "true";
-        }
-        else
+
+        // look for type modification e.g. --help-opening
+        int dashPos = argName.indexOf(ArgParser.SINGLEDASH);
+        if (dashPos > -1)
         {
-          // look for type modification e.g. --help-opening
-          int dashPos = arg.indexOf(ArgParser.SINGLEDASH);
-          if (dashPos > -1)
+          String potentialArgName = argName.substring(0, dashPos);
+          Arg potentialArg = ArgParser.argMap.get(potentialArgName);
+          if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE))
           {
-            String potentialArgName = arg.substring(0, dashPos);
-            Arg potentialArg = ArgParser.argMap.get(potentialArgName);
-            if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE))
+            String typeName = argName.substring(dashPos + 1);
+            try
             {
-              argName = arg.substring(0, dashPos);
-              String typeName = arg.substring(dashPos + 1);
-              type = Type.valueOf(typeName);
+              type = Type.valueOf(typeName.toUpperCase(Locale.ROOT));
+            } catch (IllegalArgumentException e)
+            {
+              type = Type.INVALID;
             }
+            argName = argName.substring(0, dashPos);
           }
         }
 
+        if (ArgParser.argMap.containsKey(argName) && val == null)
+        {
+          val = "true";
+        }
+
         Arg a = ArgParser.argMap.get(argName);
 
         if (a == null || !a.hasOption(Opt.BOOTSTRAP))