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 30e71b6..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;
 
@@ -167,6 +167,7 @@ public class Commands
       for (ArgValue av : openAvList)
       {
         Arg a = av.getArg();
+        SubVals sv = av.getSubVals();
         String openFile = av.getValue();
         if (openFile == null)
           continue;
@@ -246,20 +247,24 @@ public class Commands
           af.setAnnotationsVisibility(showAnnotations, false, true);
 
           // wrap alignment?
-          if (avm.getBoolean(Arg.WRAP))
-          {
-            af.getCurrentView().setWrapAlignment(true);
-          }
+          boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+                  null, "WRAP_ALIGNMENT", false);
+          af.getCurrentView().setWrapAlignment(wrap);
 
           // colour aligment?
-          if (avm.containsArg(Arg.COLOUR))
+          String colour = ArgParser.getFromSubValArgOrPref(avm, Arg.COLOUR,
+                  sv, null, "DEFAULT_COLOUR_PROT", "");
+
+          if ("" != colour)
           {
-            af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+            af.changeColour_actionPerformed(colour);
           }
 
           // change alignment frame title
-          if (avm.containsArg(Arg.TITLE))
-            af.setTitle(avm.getValue(Arg.TITLE));
+          String title = ArgParser.getFromSubValArgOrPref(avm, Arg.TITLE,
+                  sv, null, null, null);
+          if (title != null)
+            af.setTitle(title);
 
           // show secondary structure annotations?
           boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
@@ -566,7 +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)