JAL-629 Add --renderer arg/subval for vector output and fixed annotation renderer...

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

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 415e065..f1781fc 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -773,19 +773,24 @@ public class ArgParser
     FIRST, BEFORE, AFTER
   }
 
-  public static String getValueFromSubValOrArg(ArgValuesMap avm, Arg a,
-          SubVals sv)
+  // get from following Arg of type a or subval of same name (lowercase)
+  public static String getValueFromSubValOrArg(ArgValuesMap avm,
+          ArgValue av, Arg a, SubVals sv)
   {
-    return getFromSubValArgOrPref(avm, a, sv, null, null, null);
+    return getFromSubValArgOrPref(avm, av, a, sv, null, null, null);
   }
 
-  public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
-          SubVals sv, String key, String pref, String def)
+  // get from following Arg of type a or subval key or preference pref or
+  // default def
+  public static String getFromSubValArgOrPref(ArgValuesMap avm, ArgValue av,
+          Arg a, SubVals sv, String key, String pref, String def)
   {
-    return getFromSubValArgOrPref(avm, a, Position.FIRST, null, sv, key,
-            pref, def);
+    return getFromSubValArgOrPref(avm, a, Position.AFTER, av, sv, key, pref,
+            def);
   }
 
+  // get from following(AFTER), first occurence of (FIRST) or previous (BEFORE)
+  // Arg of type a or subval key or preference pref or default def
   public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
           Position pos, ArgValue av, SubVals sv, String key, String pref,
           String def)
@@ -796,7 +801,6 @@ public class ArgParser
       return sv.get(key);
     if (avm != null && avm.containsArg(a))
     {
-      String val = null;
       if (pos == Position.FIRST && avm.getValue(a) != null)
         return avm.getValue(a);
       else if (pos == Position.BEFORE