X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2Fdm%2FAAConSettings.java;h=fa5687434f065dea3d27cd7fa0c02fb39156acda;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=d3ba1a7cda94c17c7d6a29f6596b22602eec0734;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index d3ba1a7..fa56874 100644
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -1,35 +1,35 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.ws.api.ServiceWithParameters;
import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
import jalview.ws.jws2.ParameterUtils;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
+import java.util.List;
+
+import compbio.metadata.Option;
+
/**
* preferences for running AACon service
*
@@ -38,74 +38,13 @@ import jalview.ws.params.WsParamSetI;
*/
public class AAConSettings extends jalview.ws.params.AutoCalcSetting
{
- Jws2Instance service;
-
- public AAConSettings(boolean autoUpdate, Jws2Instance service,
+ public AAConSettings(boolean autoUpdate, ServiceWithParameters service2,
WsParamSetI preset, List jobArgset)
{
- super(preset, jobArgset, autoUpdate);
- this.service = service;
- }
-
- public Jws2Instance getService()
- {
- return service;
- }
-
- public void setService(Jws2Instance service)
- {
- this.service = service;
- if (preset != null)
- {
- // migrate preset to new service
- for (String url : preset.getApplicableUrls())
- {
- if (url.equals(service.getUri()))
- {
- return;
- }
- }
- WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
- if (pr instanceof JabaPreset && preset instanceof JabaPreset)
- {
- // easy - Presets are identical (we assume)
- preset = pr;
- return;
- }
- List oldargs = new ArrayList(), newargs = new ArrayList();
- oldargs.addAll(preset.getArguments());
- // need to compare parameters
- for (ArgumentI newparg : pr.getArguments())
- {
- if (!oldargs.remove(newparg))
- {
- newargs.add(newparg);
- }
- }
- if (oldargs.size() == 0 && newargs.size() == 0)
- {
- // exact match.
- preset = pr;
- return;
- }
- // Try even harder to migrate arguments.
- throw new Error("Parameter migration not implemented yet");
- }
- }
-
- public List getJobArgset()
- {
- 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);
+ super(service2, preset, jobArgset, autoUpdate);
}
+ @Override
public String getWsParamFile()
{
List