JAL-2089 patch broken merge to master for Release 2.10.0b1

[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 be18b51..34b8a72 100644 (file)
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -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;
@@ -35,16 +44,6 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-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;
-
 public class JabaParamStore implements ParamDatastoreI
 {
 
@@ -167,7 +166,9 @@ public class JabaParamStore implements ParamDatastoreI
       }
       if (narg == null)
       {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       else
       {
@@ -202,7 +203,9 @@ public class JabaParamStore implements ParamDatastoreI
               .getOption() : null;
       if (narg == null)
       {
-          throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       else
       {
@@ -240,7 +243,9 @@ public class JabaParamStore implements ParamDatastoreI
     }
     if (servicePresets.containsKey(name))
     {
-      throw new Error(MessageManager.getString("error.implementation_error_attempt_to_delete_service_preset"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_attempt_to_delete_service_preset"));
     }
   }
 
@@ -249,8 +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)
     {
@@ -266,13 +270,16 @@ public class JabaParamStore implements ParamDatastoreI
             : getPreset(presetName));
     if (jps == null)
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_locate_oldname_presetname", new String[]{oldName,presetName}));
+      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);
@@ -316,7 +323,9 @@ public class JabaParamStore implements ParamDatastoreI
   {
     if (!involves(urls))
     {
-      throw new IOException(MessageManager.getString("error.implementation_error_cannot_find_service_url_in_given_set"));
+      throw new IOException(
+              MessageManager
+                      .getString("error.implementation_error_cannot_find_service_url_in_given_set"));
 
     }
     JabaWsParamSet wsp = new JabaWsParamSet();
@@ -341,11 +350,17 @@ public class JabaParamStore implements ParamDatastoreI
   {
     if (!involves(pset.getApplicableUrls()))
     {
-      throw new IOException(MessageManager.formatMessage("error.implementation_error_cannot_find_service_url_in_given_set_param_store", new String[]{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(MessageManager.getString("error.implementation_error_jabaws_param_set_only_handled_by"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_jabaws_param_set_only_handled_by"));
     }
 
     StringBuffer rslt = new StringBuffer();