X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2Fdm%2FAAConSettings.java;h=997913e837bf801cedafe3741191e37dceb9dc73;hb=dbf124d82413368d7aba34f8e3d8e7ad25167dea;hp=49c8aa91774cb07caff2f85cf36c32747cf0790e;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index 49c8aa9..997913e 100644
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -1,29 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
-import java.util.ArrayList;
-import java.util.List;
-
-import compbio.metadata.Argument;
-import compbio.metadata.Option;
-
+import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.jws2.ParameterUtils;
@@ -31,6 +29,12 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.metadata.Argument;
+import compbio.metadata.Option;
+
/**
* preferences for running AACon service
*
@@ -39,16 +43,16 @@ import jalview.ws.params.WsParamSetI;
*/
public class AAConSettings extends jalview.ws.params.AutoCalcSetting
{
- Jws2Instance service;
+ ServiceWithParameters service;
- public AAConSettings(boolean autoUpdate, Jws2Instance service,
+ public AAConSettings(boolean autoUpdate, ServiceWithParameters service2,
WsParamSetI preset, List jobArgset)
{
super(preset, jobArgset, autoUpdate);
- this.service = service;
+ this.service = service2;
}
- public Jws2Instance getService()
+ public ServiceWithParameters getService()
{
return service;
}
@@ -73,7 +77,8 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
preset = pr;
return;
}
- List oldargs = new ArrayList(), newargs = new ArrayList();
+ List oldargs = new ArrayList<>(),
+ newargs = new ArrayList<>();
oldargs.addAll(preset.getArguments());
// need to compare parameters
for (ArgumentI newparg : pr.getArguments())
@@ -90,23 +95,25 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting
return;
}
// Try even harder to migrate arguments.
- throw new Error("Parameter migration not implemented yet");
+ throw new Error(MessageManager
+ .getString("error.parameter_migration_not_implemented_yet"));
}
}
public List getJobArgset()
{
- return jobArgset == null ? null : JabaParamStore
- .getJabafromJwsArgs(jobArgset);
+ return jobArgset == null ? null
+ : JabaParamStore.getJabafromJwsArgs(jobArgset);
}
public void setJobArgset(List jobArgset)
{
// TODO: test if parameters valid for service
- this.jobArgset = jobArgset == null ? null : JabaParamStore
- .getJwsArgsfromJaba(jobArgset);
+ this.jobArgset = jobArgset == null ? null
+ : JabaParamStore.getJwsArgsfromJaba(jobArgset);
}
+ @Override
public String getWsParamFile()
{
List