From 633d7e7ce933a825d2bad0d948ca570eac97bb3a Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 1 Dec 2014 16:43:02 +0000
Subject: [PATCH] JAL-1601 ignore the JABA Jpred client in Jalview 2.8.2
 release

---
 src/jalview/ws/jws2/JabaWsServerQuery.java         |    3 ++-
 .../ws/jws2/jabaws2/Jws2InstanceFactory.java       |   25 ++++++++++++++++----
 2 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/src/jalview/ws/jws2/JabaWsServerQuery.java b/src/jalview/ws/jws2/JabaWsServerQuery.java
index 832a2cb..b3aee55 100644
--- a/src/jalview/ws/jws2/JabaWsServerQuery.java
+++ b/src/jalview/ws/jws2/JabaWsServerQuery.java
@@ -180,7 +180,8 @@ public class JabaWsServerQuery implements Runnable
               jws2Discoverer.addInvalidServiceUrl(jwsserver);
             }
             ;
-            if (service != null)
+            if (service != null
+                    && !Jws2InstanceFactory.ignoreService(srv.toString()))
             {
               noservices = false;
               Jws2Instance svc = null;
diff --git a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
index bcc7735..696dba3 100644
--- a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
@@ -20,18 +20,21 @@
  */
 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;
 
+import java.util.HashMap;
+import java.util.HashSet;
+
+import compbio.data.msa.JABAService;
+
 public class Jws2InstanceFactory
 {
   private static HashMap<String, AlignAnalysisUIText> aaConGUI;
 
+  private static HashSet<String> ignoreGUI;
   private static String category_rewrite(String cat_name)
   {
     return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction"
@@ -47,12 +50,27 @@ public class Jws2InstanceFactory
               AAConClient.getAlignAnalysisUITest());
       aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
               RNAalifoldClient.getAlignAnalysisUITest());
+      // disable the JPred301 client in jalview ...
+      ignoreGUI = new HashSet<String>();
+      ignoreGUI.add(compbio.ws.client.Services.JpredWS.toString());
       aaConGUI.put(compbio.ws.client.Services.JpredWS.toString(),
               JPred301Client.getAlignAnalysisUITest());
     }
   }
 
   /**
+   * exclusion list to avoid creating GUI elements for services we don't fully
+   * support
+   * 
+   * @param serviceType
+   * @return
+   */
+  public static boolean ignoreService(String serviceType)
+  {
+    init();
+    return (ignoreGUI.contains(serviceType.toString()));
+  }
+  /**
    * construct a service instance and configure it with any additional
    * properties needed so Jalview can access it correctly
    * 
@@ -70,7 +88,6 @@ public class Jws2InstanceFactory
     init();
     Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
             category_rewrite(name), description, service);
-
     svc.aaui = aaConGUI.get(serviceType.toString());
     return svc;
   }
-- 
1.7.10.2