From 3737b35aa75cf9ba9203a244de45008fb0794bc4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 18 Jun 2013 21:38:16 +0100
Subject: [PATCH] JAL-1320 sort options and parameters according to their name

---
 src/jalview/ws/jws2/JabaParamStore.java |   34 +++++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index 204e0df..ec504dd 100644
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -19,10 +19,12 @@ package jalview.ws.jws2;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import org.jmol.util.ArrayUtil;
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
 import compbio.metadata.Parameter;
@@ -137,12 +139,28 @@ public class JabaParamStore implements ParamDatastoreI
 
   public static List<ArgumentI> getJwsArgsfromJaba(List jabargs)
   {
+    return getJwsArgsfromJaba(jabargs, true);
+  }
+
+  public static List<ArgumentI> getJwsArgsfromJaba(List jabargs,
+          boolean sortByOpt)
+  {
     List<ArgumentI> rgs = new ArrayList<ArgumentI>();
+    List<String> rgnames = new ArrayList<String>();
     for (Object rg : jabargs)
     {
-      ArgumentI narg = (rg instanceof Parameter) ? new JabaParameter(
-              (Parameter) rg) : (rg instanceof Option) ? new JabaOption(
-              (Option) rg) : null;
+      ArgumentI narg = null;
+      String nargstring = null;
+      if (rg instanceof Parameter)
+      {
+        narg = new JabaParameter((Parameter) rg);
+        nargstring = narg.getName(); // just sort by name for this
+      }
+      else if (rg instanceof Option)
+      {
+        narg = new JabaOption((Option) rg);
+        nargstring = (String) ((Option) rg).getOptionNames().get(0);
+      }
       if (narg == null)
       {
         throw new Error(
@@ -152,9 +170,17 @@ public class JabaParamStore implements ParamDatastoreI
       else
       {
         rgs.add(narg);
+        rgnames.add(nargstring);
       }
     }
-    return rgs;
+    if (!sortByOpt)
+    {
+      return rgs;
+    }
+    ArgumentI[] rgssort = rgs.toArray(new ArgumentI[rgs.size()]);
+    String[] rgssorton = rgnames.toArray(new String[rgs.size()]);
+    jalview.util.QuickSort.sort(rgssorton, rgssort);
+    return Arrays.asList(rgssort);
   }
 
   public static List getJabafromJwsArgs(List<ArgumentI> jwsargs)
-- 
1.7.10.2