JAL-1383 scrubbed envision GUI and documentation

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 1e1cfdc..f4ad784 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -524,13 +524,6 @@
                                                sequences against the EBI databases plus any active DAS sequence
                                                sources, or you can verify against a specific source from one of
                                                the sub-menus.</em><br></li>
-                               <li><strong>Envision2 Services</strong><br /><em> Submits one or
-                                       more sequences, sequence IDs or database references to analysis
-                                       workflows provided by the <a
-                                       href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
-                                               application</a>. This allows Jalview users to easily access the EnCore
-                                       network of databases and analysis services developed by members of
-                                       <a href="http://www.enfin.org">ENFIN</a></em>.</li>
                        </ul>
                        <p>Selecting items from the following submenus will start a
                                remote service on compute facilities at the University of Dundee, or

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index 86fa307..1997101 100755 (executable)
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -33,13 +33,6 @@
                                                sequences against the EBI databases plus any active DAS sequence
                                                sources, or you can verify against a specific source from one of
                                                the sub-menus.</em><br></li>
-                               <li><strong>Envision2 Services</strong><br /><em> Submits one or
-                                       more sequences, sequence IDs or database references to analysis
-                                       workflows provided by the <a
-                                       href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
-                                               application</a>. This allows Jalview users to easily access the EnCore
-                                       network of databases and analysis services developed by members of
-                                       <a href="http://www.enfin.org">ENFIN</a></em>.</li>
                        </ul>
                        <p>Selecting items from the following submenus will start a
                                remote service on compute facilities at the University of Dundee, or

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 9245ec3..c3d83fa 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -49,8 +49,6 @@
                                                structure prediction</a> based at the University of Dundee.</li>
                                <li>Services for alignment analysis, such as <a
                                        href="shmr.html">Multi-Harmony</a>.
-                               <li>Services for submitting IDs and sequences to external
-                                       bioinformatics services such as Envision2 (see <a href="#envision2">below</a>).</li>
                        </ul>
                        <p>
                                <strong>Web Service Dialog Box</strong>
@@ -81,17 +79,5 @@
                the advent of <a href="http://www.compbio.dundee.ac.uk/JABAWS">JABAWS</a>,
                however, it is possible for anyone to host Jalview web services.
        </p>
-       <p>
-               <strong><a name="envision2">Envision2 Services</a>
-               </strong>
-       </p>
-       <p>
-               Since version 2.5, Jalview has included a client to enable the user to
-               submit one or more sequences or sequence IDs to analysis workflows
-               provided by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
-                       web application</a>. This allows Jalview users to easily access the
-               EnCore network of databases and analysis services developed by ENFIN (<a
-                       href="http://www.enfin.org">www.enfin.org</a>).
-       </p>
 </body>
 </html>

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 775df57..906db68 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -685,7 +685,6 @@ label.case_sensitive = Case Sensitive
 label.lower_case_colour = Lower Case Colour\r
 label.index_by_host = Index by host\r
 label.index_by_type = Index by type\r
-label.enable_enfin_services = Enable Enfin Services\r
 label.enable_jabaws_services = Enable JABAWS Services\r
 label.display_warnings = Display warnings\r
 label.move_url_up = Move URL up\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index da34013..353a139 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4424,12 +4424,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
               this);
     }
-
-    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
-    {
-      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
-              webService, this);
-    }
   }
 
   /*

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 2a31518..20a136f 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -100,9 +100,6 @@ public class Preferences extends GPreferences
      */
 
     groupURLLinks = new Vector();
-    // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
-    // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
-
   }
 
   Vector nameLinks, urlLinks;

diff --git a/src/jalview/jbgui/GWsPreferences.java b/src/jalview/jbgui/GWsPreferences.java
index 889fcb7..3ad5bb1 100644 (file)
--- a/src/jalview/jbgui/GWsPreferences.java
+++ b/src/jalview/jbgui/GWsPreferences.java
@@ -178,16 +178,6 @@ public class GWsPreferences extends JPanel
         indexByType_actionPerformed(e);
       }
     });
-    enableEnfinServices
-            .setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    enableEnfinServices.setText(MessageManager.getString("label.enable_enfin_services"));
-    enableEnfinServices.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        enableEnfinServices_actionPerformed(e);
-      }
-    });
     enableJws2Services
             .setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     enableJws2Services.setText(MessageManager.getString("label.enable_jabaws_services"));
@@ -398,7 +388,6 @@ public class GWsPreferences extends JPanel
     wsMenuButtons.add(indexByHost);
     wsMenuButtons.add(indexByType);
     wsMenuButtons.add(enableJws2Services);
-    wsMenuButtons.add(enableEnfinServices);
     wsMenuButtons.add(displayWsWarning);
     wsMenuRefreshButs.setLayout(new FlowLayout());
     wsMenuRefreshButs.setPreferredSize(new Dimension(480, 30));

diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 243be63..7224681 100644 (file)
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -819,6 +819,7 @@ public class GroupUrlLink
 
   public static void main(String argv[])
   {
+    // note - JAL-1383 - these services are all dead
     String[] links = new String[]
     {
         "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",

diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 12d81ed..792f150 100644 (file)
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -56,7 +56,9 @@ import com.lowagie.text.html.HtmlEncoder;
 /**
  * Lightweight runnable to discover dynamic 'one way' group URL services
  * 
+ * as of Jalview 2.8.1 this class is mothballed and will be dropped in v3.
  * @author JimP
+ * @deprecated
  * 
  */
 public class EnfinEnvision2OneWay extends DefaultHandler implements