JAL-629 Change behaviour of --open GLOB to increment defaultLinkedId to allow --allfr...

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 402024b..f33202d 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -81,11 +81,11 @@ public class Commands
     headless = h;
     boolean theseArgsWereParsed = false;
 
-    if (argParser != null && argParser.linkedIds() != null)
+    if (argParser != null && argParser.getLinkedIds() != null)
     {
-      for (String id : argParser.linkedIds())
+      for (String id : argParser.getLinkedIds())
       {
-        ArgValuesMap avm = argParser.linkedArgs(id);
+        ArgValuesMap avm = argParser.getLinkedArgs(id);
         theseArgsWereParsed = true;
         if (id == null)
         {
@@ -138,7 +138,7 @@ public class Commands
   protected boolean processLinked(String id)
   {
     boolean theseArgsWereParsed = false;
-    ArgValuesMap avm = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.getLinkedArgs(id);
     if (avm == null)
       return true;
 
@@ -571,7 +571,7 @@ public class Commands
 
   protected boolean processImages(String id)
   {
-    ArgValuesMap avm = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.getLinkedArgs(id);
     AlignFrame af = afMap.get(id);
 
     if (af == null)