X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FArgParser.java;h=1558065cdbef3c21c2a242baa208bcf1923ba774;hb=65ed1da9a1710a9ce132c7edfce54955dc1ddf99;hp=f08e678112d83ba1221b6f05f293ad1f1397c5ff;hpb=b9293410486a5a6f9bc505e66b04b912a559cdd5;p=jalview.git

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index f08e678..1558065c 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";
 
@@ -302,12 +302,34 @@ 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
@@ -464,7 +486,8 @@ public class ArgParser
               val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
                       + val.substring(MATCHALLLINKEDIDS.length());
             }
-            else if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWALL)
+            else if (a.hasOption(Opt.OUTPUTFILE)
+                    && a.hasOption(Opt.ALLOWALL)
                     && val.startsWith(MATCHOPENEDLINKEDIDS))
             {
               // --output=open*.ext is shorthand for --opened --output