X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FArgParser.java;h=907b1fa5911717be31bbbb3b635940371a9df787;hb=388622051f3d669942d9df63557c7a1401d7ff6d;hp=b32baf58ef17d731cfe636b30279c22a3b77f568;hpb=943d92989c49c5381fbb8b2dc848587536d04524;p=jalview.git

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index b32baf5..907b1fa 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -48,7 +48,7 @@ public class ArgParser
 
   protected static final String DOUBLEDASH = "--";
 
-  protected static final char EQUALS = '=';
+  public static final char EQUALS = '=';
 
   protected static final String NEGATESTRING = "no";
 
@@ -336,12 +336,34 @@ public class ArgParser
         Arg a = argMap.get(argName);
         // check for boolean prepended by "no" e.g. --nowrap
         boolean negated = false;
-        if (a == null && argName.startsWith(NEGATESTRING) && argMap
-                .containsKey(argName.substring(NEGATESTRING.length())))
+        if (a == null)
         {
-          argName = argName.substring(NEGATESTRING.length());
-          a = argMap.get(argName);
-          negated = true;
+          if (argName.startsWith(NEGATESTRING) && argMap
+                  .containsKey(argName.substring(NEGATESTRING.length())))
+          {
+            argName = argName.substring(NEGATESTRING.length());
+            a = argMap.get(argName);
+            negated = true;
+          }
+          else
+          {
+            // after all other args, look for Opt.PREFIXKEV args if still not
+            // found
+            for (Arg potentialArg : EnumSet.allOf(Arg.class))
+            {
+              if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+                      && argName.startsWith(potentialArg.getName())
+                      && equalPos > -1)
+              {
+                val = argName.substring(potentialArg.getName().length())
+                        + EQUALS + val;
+                argName = argName.substring(0,
+                        potentialArg.getName().length());
+                a = potentialArg;
+                break;
+              }
+            }
+          }
         }
 
         // check for config errors