X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabaParamStore.java;h=285777ae2df6be0bd99f9d07b3a7c71ee149b014;hb=8f1d9040aa9ddac452311d6bb232f7f28f7e83e7;hp=204e0df31457fda57eb0b05e7c91019394383402;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git

diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index 204e0df..285777a 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 +170,25 @@ 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);
+    ArgumentI tmp1;
+    int i=0;
+    while (rgssort.length-i>i)
+    {
+      tmp1=rgssort[rgssort.length-i-1];
+      rgssort[rgssort.length-i-1] = rgssort[i];
+      rgssort[i++]=tmp1;
+    }
+    return Arrays.asList(rgssort);
   }
 
   public static List getJabafromJwsArgs(List<ArgumentI> jwsargs)