JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / jws2 / jabaws2 / Jws2Instance.java

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index a7ad43d..7715dff 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -1,7 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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 jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.util.MessageManager;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.MsaWSClient;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
@@ -22,20 +43,48 @@ public class Jws2Instance
   public String hosturl;
 
   public String serviceType;
+
   public String action;
+
   public JABAService service;
+
   public String description;
 
-  public Jws2Instance(String hosturl, String serviceType, String action, String description, 
-          JABAService service)
+  public String docUrl;
+
+  /**
+   * 
+   * @param hosturl
+   *          Service endpoint
+   * @param serviceType
+   *          Category for this service's analysis
+   * @param action
+   *          text describing their action that service performs (eg 'aligning',
+   *          'analysing')
+   * @param description
+   *          Description from JABAWS registry
+   * @param service
+   *          JABAWS registry ID for service
+   */
+  public Jws2Instance(String hosturl, String serviceType, String action,
+          String description, JABAService service)
   {
     super();
     this.hosturl = hosturl;
     this.serviceType = serviceType;
     this.service = service;
-    this.action=action;
+    this.action = action;
     this.description = description;
-    
+    int p = description.indexOf("MORE INFORMATION:");
+    if (p > -1)
+    {
+      docUrl = description.substring(description.indexOf("http", p)).trim();
+      if (docUrl.indexOf('\n') > -1)
+      {
+        docUrl = docUrl.substring(0, docUrl.indexOf("\n")).trim();
+      }
+
+    }
   }
 
   PresetManager presets = null;
@@ -89,7 +138,7 @@ public class Jws2Instance
    */
   public String getActionText()
   {
-    return action+" with " + serviceType;
+    return action + " with " + serviceType;
   }
 
   /**
@@ -108,7 +157,7 @@ public class Jws2Instance
     {
       return ((SequenceAnnotation) service).getRunnerOptions();
     }
-    throw new Error("Implementation Error: Runner Config not available for a JABAWS service of type "+serviceType+" ("+service.getClass()+")");
+    throw new Error(MessageManager.formatMessage("error.implementation_error_runner_config_not_available", new String[]{serviceType,service.getClass().toString()}));
   }
 
   @Override
@@ -140,6 +189,8 @@ public class Jws2Instance
                         : null));
       } catch (Exception ex)
       {
+        System.err.println("Unexpected exception creating JabaParamStore.");
+        ex.printStackTrace();
       }
 
     }
@@ -177,15 +228,23 @@ public class Jws2Instance
     if (service instanceof MsaWS<?>)
     {
       new MsaWSClient().attachWSMenuEntry(atpoint, this, alignFrame);
-    } else 
-    if (service instanceof SequenceAnnotation<?>){
-      new SequenceAnnotationWSClient().attachWSMenuEntry(atpoint, this, alignFrame);
+    }
+    else if (service instanceof SequenceAnnotation<?>)
+    {
+      new SequenceAnnotationWSClient().attachWSMenuEntry(atpoint, this,
+              alignFrame);
     }
   }
 
-  
   public String getServiceTypeURI()
   {
-    return "java:"+service.getClass().toString();
+    return "java:" + serviceType;
+  }
+
+  jalview.ws.uimodel.AlignAnalysisUIText aaui;
+
+  public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
+  {
+    return aaui;
   }
-}
\ No newline at end of file
+}