JAL-1379 a JPred v3.0.1 client via JABA 2.1

[jalview.git] / src / jalview / ws / jws2 / jabaws2 / Jws2InstanceFactory.java

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
index 3923bba..bcc7735 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
@@ -1,10 +1,30 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.jabaws2;
 
 import java.util.HashMap;
 
 import compbio.data.msa.JABAService;
-
 import jalview.ws.jws2.AAConClient;
+import jalview.ws.jws2.JPred301Client;
 import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
@@ -12,6 +32,12 @@ public class Jws2InstanceFactory
 {
   private static HashMap<String, AlignAnalysisUIText> aaConGUI;
 
+  private static String category_rewrite(String cat_name)
+  {
+    return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction"
+            : cat_name;
+  }
+
   private static void init()
   {
     if (aaConGUI == null)
@@ -21,6 +47,8 @@ public class Jws2InstanceFactory
               AAConClient.getAlignAnalysisUITest());
       aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
               RNAalifoldClient.getAlignAnalysisUITest());
+      aaConGUI.put(compbio.ws.client.Services.JpredWS.toString(),
+              JPred301Client.getAlignAnalysisUITest());
     }
   }
 
@@ -40,9 +68,9 @@ public class Jws2InstanceFactory
           JABAService service)
   {
     init();
-    Jws2Instance svc = new Jws2Instance(jwsservers, serviceType, name,
-            description, service);
-    
+    Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
+            category_rewrite(name), description, service);
+
     svc.aaui = aaConGUI.get(serviceType.toString());
     return svc;
   }