JAL-629 helper function for getting sensible structure (or other arg value)

diff --git a/src/jalview/bin/ArgParser.java b/src/jalview/bin/ArgParser.java
index 2290182..3dc7921 100644 (file)
--- a/src/jalview/bin/ArgParser.java
+++ b/src/jalview/bin/ArgParser.java
@@ -121,8 +121,6 @@ public class ArgParser
 
     private boolean defaultBoolValue = false;
 
-    private int argIndex = -1;
-
     public String toLongString()
     {
       StringBuilder sb = new StringBuilder();
@@ -205,16 +203,6 @@ public class ArgParser
     {
       return defaultBoolValue;
     }
-
-    private void setArgIndex(int i)
-    {
-      this.argIndex = i;
-    }
-
-    protected int getArgIndex()
-    {
-      return this.argIndex;
-    }
   }
 
   public static class ArgValues
@@ -869,6 +857,25 @@ public class ArgParser
       ArgValues av = getArgValues(a);
       return av == null ? false : av.getBoolean();
     }
+
+    protected ArgValue getClosestPreviousArgValueOfArg(ArgValue thisAv,
+            Arg a)
+    {
+      ArgValue closestAv = null;
+      int thisArgIndex = thisAv.getArgIndex();
+      ArgValues compareAvs = this.getArgValues(a);
+      int closestPreviousIndex = -1;
+      for (ArgValue av : compareAvs.getArgValueList())
+      {
+        int argIndex = av.getArgIndex();
+        if (argIndex < thisArgIndex && argIndex > closestPreviousIndex)
+        {
+          closestPreviousIndex = argIndex;
+          closestAv = av;
+        }
+      }
+      return closestAv;
+    }
   }
 
   private static final Collection<String> bootstrapArgs = new ArrayList(