X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabaParamStore.java;h=34b8a72da3568002ae63c873e513feda56d33423;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=bdea5be032376b109c4eb620ca2faf7ca1342532;hpb=c13784724ba3826e6cc3faeb85571cf30776592d;p=jalview.git

diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index bdea5be..34b8a72 100644
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -1,10 +1,38 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jws2;
 
-import java.io.BufferedReader;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.JabaOption;
+import jalview.ws.jws2.dm.JabaParameter;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
+
 import java.io.IOException;
-import java.io.Reader;
-import java.io.Writer;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.StringTokenizer;
@@ -16,15 +44,6 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
-import jalview.ws.jws2.dm.JabaOption;
-import jalview.ws.jws2.dm.JabaParameter;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParamManager;
-import jalview.ws.params.WsParamSetI;
-
 public class JabaParamStore implements ParamDatastoreI
 {
 
@@ -123,24 +142,56 @@ 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(
-                "Implementation Error: Cannot handle Jaba parameter object "
-                        + rg.getClass());
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       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)
@@ -152,9 +203,9 @@ public class JabaParamStore implements ParamDatastoreI
               .getOption() : null;
       if (narg == null)
       {
-        throw new Error(
-                "Implementation Error: Cannot handle Jaba parameter object "
-                        + rg.getClass());
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       else
       {
@@ -193,7 +244,8 @@ public class JabaParamStore implements ParamDatastoreI
     if (servicePresets.containsKey(name))
     {
       throw new Error(
-              "Implementation error: Attempt to delete a service preset!");
+              MessageManager
+                      .getString("error.implementation_error_attempt_to_delete_service_preset"));
     }
   }
 
@@ -202,8 +254,7 @@ public class JabaParamStore implements ParamDatastoreI
           List<ArgumentI> jobParams)
   {
     JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
-    jps.setApplicableUrls(new String[]
-    { service.getUri() });
+    jps.setApplicableUrls(new String[] { service.getUri() });
     editedParams.put(jps.getName(), jps);
     if (manager != null)
     {
@@ -219,15 +270,16 @@ public class JabaParamStore implements ParamDatastoreI
             : getPreset(presetName));
     if (jps == null)
     {
-      throw new Error("Implementation error: Can't locate either oldname ("
-              + oldName + ") or presetName (" + presetName
-              + "in the datastore!");
+      throw new Error(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_cannot_locate_oldname_presetname",
+                              new String[] { oldName, presetName }));
     }
     jps.setName(presetName);
     jps.setDescription(text);
     jps.setArguments(jobParams);
-    jps.setApplicableUrls(new String[]
-    { service.getUri() });
+    jps.setApplicableUrls(new String[] { service.getUri() });
     if (oldName != null && !oldName.equals(jps.getName()))
     {
       editedParams.remove(oldName);
@@ -255,7 +307,8 @@ public class JabaParamStore implements ParamDatastoreI
     boolean found = false;
     for (String url : urls)
     {
-      if (service.getUri().equalsIgnoreCase(url))
+      if (service.getServiceTypeURI().equals(url)
+              || service.getUri().equalsIgnoreCase(url))
       {
         found = true;
         break;
@@ -271,7 +324,8 @@ public class JabaParamStore implements ParamDatastoreI
     if (!involves(urls))
     {
       throw new IOException(
-              "Implementation error: Cannot find service url in the given url set!");
+              MessageManager
+                      .getString("error.implementation_error_cannot_find_service_url_in_given_set"));
 
     }
     JabaWsParamSet wsp = new JabaWsParamSet();
@@ -297,14 +351,16 @@ public class JabaParamStore implements ParamDatastoreI
     if (!involves(pset.getApplicableUrls()))
     {
       throw new IOException(
-              "Implementation error: Cannot find service url in the given url set for this service parameter store ("
-                      + service.getUri() + ") !");
-
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_cannot_find_service_url_in_given_set_param_store",
+                              new String[] { service.getUri() }));
     }
     if (!(pset instanceof JabaWsParamSet))
     {
       throw new Error(
-              "Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
+              MessageManager
+                      .getString("error.implementation_error_jabaws_param_set_only_handled_by"));
     }
 
     StringBuffer rslt = new StringBuffer();