Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / ws / jws2 / JabaParamStore.java

diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index 65f939a..929c5e2 100644 (file)
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,16 @@
  */
 package jalview.ws.jws2;
 
+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.util.ArrayList;
 import java.util.Arrays;
@@ -27,7 +37,6 @@ 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;
@@ -35,19 +44,10 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-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;
-
 public class JabaParamStore implements ParamDatastoreI
 {
 
-  Hashtable<String, JabaWsParamSet> editedParams = new Hashtable<String, JabaWsParamSet>();
+  Hashtable<String, JabaWsParamSet> editedParams = new Hashtable<>();
 
   private Jws2Instance service;
 
@@ -84,8 +84,8 @@ public class JabaParamStore implements ParamDatastoreI
           }
           else
           {
-            System.err
-                    .println("Warning: Ignoring parameter set instance of type "
+            System.err.println(
+                    "Warning: Ignoring parameter set instance of type "
                             + paramset.getClass()
                             + " : Bound but not applicable for service at "
                             + service.getUri());
@@ -98,10 +98,10 @@ public class JabaParamStore implements ParamDatastoreI
   @Override
   public List<WsParamSetI> getPresets()
   {
-    List<WsParamSetI> prefs = new ArrayList();
+    List<WsParamSetI> prefs = new ArrayList<>();
     if (servicePresets == null)
     {
-      servicePresets = new Hashtable<String, JabaPreset>();
+      servicePresets = new Hashtable<>();
       PresetManager prman;
       if ((prman = service.getPresets()) != null)
       {
@@ -148,8 +148,8 @@ public class JabaParamStore implements ParamDatastoreI
   public static List<ArgumentI> getJwsArgsfromJaba(List jabargs,
           boolean sortByOpt)
   {
-    List<ArgumentI> rgs = new ArrayList<ArgumentI>();
-    List<String> rgnames = new ArrayList<String>();
+    List<ArgumentI> rgs = new ArrayList<>();
+    List<String> rgnames = new ArrayList<>();
     for (Object rg : jabargs)
     {
       ArgumentI narg = null;
@@ -166,9 +166,10 @@ public class JabaParamStore implements ParamDatastoreI
       }
       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
       {
@@ -199,13 +200,15 @@ public class JabaParamStore implements ParamDatastoreI
     List rgs = new ArrayList();
     for (ArgumentI rg : jwsargs)
     {
-      Argument narg = (rg instanceof JabaOption) ? ((JabaOption) rg)
-              .getOption() : null;
+      Argument narg = (rg instanceof JabaOption)
+              ? ((JabaOption) rg).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
       {
@@ -224,8 +227,8 @@ public class JabaParamStore implements ParamDatastoreI
   @Override
   public boolean presetExists(String name)
   {
-    return (editedParams.containsKey(name) || servicePresets
-            .containsKey(name));
+    return (editedParams.containsKey(name)
+            || servicePresets.containsKey(name));
   }
 
   @Override
@@ -243,8 +246,8 @@ public class JabaParamStore implements ParamDatastoreI
     }
     if (servicePresets.containsKey(name))
     {
-      throw new Error(
-              "Implementation error: Attempt to delete a service preset!");
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_attempt_to_delete_service_preset"));
     }
   }
 
@@ -253,8 +256,7 @@ 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)
     {
@@ -266,19 +268,20 @@ public class JabaParamStore implements ParamDatastoreI
   public void updatePreset(String oldName, String presetName, String text,
           List<ArgumentI> jobParams)
   {
-    JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) ? getPreset(oldName)
+    JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null)
+            ? getPreset(oldName)
             : 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);
@@ -306,7 +309,7 @@ public class JabaParamStore implements ParamDatastoreI
     boolean found = false;
     for (String url : urls)
     {
-      if (service.getServiceTypeURI().equals(url)
+      if (service.getNameURI().equals(url)
               || service.getUri().equalsIgnoreCase(url))
       {
         found = true;
@@ -322,8 +325,8 @@ public class JabaParamStore implements ParamDatastoreI
   {
     if (!involves(urls))
     {
-      throw new IOException(
-              "Implementation error: Cannot find service url in the given url set!");
+      throw new IOException(MessageManager.getString(
+              "error.implementation_error_cannot_find_service_url_in_given_set"));
 
     }
     JabaWsParamSet wsp = new JabaWsParamSet();
@@ -331,14 +334,14 @@ public class JabaParamStore implements ParamDatastoreI
     wsp.setDescription(descr);
     wsp.setApplicableUrls(urls.clone());
 
-    List<String> lines = new ArrayList<String>();
+    List<String> lines = new ArrayList<>();
     StringTokenizer st = new StringTokenizer(parameterfile, "\n");
     while (st.hasMoreTokens())
     {
       lines.add(st.nextToken());
     }
-    wsp.setjabaArguments(ParameterUtils.processParameters(lines,
-            serviceOptions, " "));
+    wsp.setjabaArguments(
+            ParameterUtils.processParameters(lines, serviceOptions, " "));
     return wsp;
   }
 
@@ -348,15 +351,15 @@ 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() + ") !");
-
+      throw new IOException(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");
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_jabaws_param_set_only_handled_by"));
     }
 
     StringBuffer rslt = new StringBuffer();