removed unnecessary parameters and changed alignment upload to use file upload parame...

[jalview.git] / src / jalview / ws / rest / RestClient.java

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index ee23790..95de391 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -1,3 +1,20 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ *******************************************************************************/
 /**
  * 
  */
@@ -15,6 +32,7 @@ import javax.swing.JOptionPane;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
@@ -286,23 +304,24 @@ public class RestClient extends WSClient implements WSClientI,
 
   public static RestClient makeShmmrRestClient()
   {
-    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (UNSTABLE!)", name = "Sequence Harmony";
+    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = "Multi-Harmony";
     Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
     jalview.ws.rest.params.JobConstant toolp;
     //toolp = new jalview.ws.rest.JobConstant("tool","jalview");
     //iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("blast","0");
-    iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("blast","0");
+    //iparams.put(toolp.token, toolp);
     
     jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
-    aliinput.token = "ali";//_file";
-    aliinput.writeAsFile=false;//true;
+    // SHMR server has a 65K limit for content pasted into the 'ali' parameter, so we always upload our files.
+    aliinput.token = "ali_file";//_file";
+    aliinput.writeAsFile=true;//true;
     //aliinput.token = "ali_file";
     //aliinput.writeAsFile=true;
     iparams.put(aliinput.token, aliinput);
@@ -316,7 +335,7 @@ public class RestClient extends WSClient implements WSClientI,
             action,
             description,
             name,
-            "http://www.ibi.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
+            "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
             "?tool=jalview", iparams, true, false, '-');
     // a priori knowledge of the data returned from the service
     shmrService.addResultDatatype(JvDataType.ANNOTATION);
@@ -343,13 +362,14 @@ public class RestClient extends WSClient implements WSClientI,
   }
 
   protected static Vector<String> services=null;
+  public static final String RSBS_SERVICES="RSBS_SERVICES";
   public static RestClient[] getRestClients()
   {
     if (services==null)
     {
       services = new Vector<String>();
       try {
-      for (RestServiceDescription descr: RestServiceDescription.parseDescriptions(jalview.bin.Cache.getDefault("RSBS_SERVICES",makeShmmrRestClient().service.toString()))) 
+      for (RestServiceDescription descr: RestServiceDescription.parseDescriptions(jalview.bin.Cache.getDefault(RSBS_SERVICES,makeShmmrRestClient().service.toString()))) 
       {
         services.add(descr.toString());
       }
@@ -412,8 +432,21 @@ public class RestClient extends WSClient implements WSClientI,
 
   public static void setRsbsServices(Vector<String> rsbsUrls)
   {
-    // TODO: consider validating services ?
-    services = new Vector<String>(rsbsUrls);    
+    if (rsbsUrls!=null)
+    {
+      // TODO: consider validating services ?
+      services = new Vector<String>(rsbsUrls);
+      StringBuffer sprop = new StringBuffer();
+      for (String s:services)
+      {
+        sprop.append(s);
+      }
+      Cache.setProperty(RSBS_SERVICES, sprop.toString());
+    } 
+    else
+    {
+      Cache.removeProperty(RSBS_SERVICES);
+    }
   }
 
 }