From 915ef58a91b8aa971abc3ee6ec68fcf85c872d25 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 21 Apr 2014 21:21:36 +0100 Subject: [PATCH] JAL-1383 scrubbed envision GUI and documentation --- help/html/menus/alignmentMenu.html | 7 ------- help/html/menus/wsmenu.html | 7 ------- help/html/webServices/index.html | 14 -------------- resources/lang/Messages.properties | 1 - src/jalview/gui/AlignFrame.java | 6 ------ src/jalview/gui/Preferences.java | 3 --- src/jalview/jbgui/GWsPreferences.java | 11 ----------- src/jalview/util/GroupUrlLink.java | 1 + src/jalview/ws/EnfinEnvision2OneWay.java | 2 ++ 9 files changed, 3 insertions(+), 49 deletions(-) diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 1e1cfdc..f4ad784 100755 --- 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.
-
  • Envision2 Services
    Submits one or - more sequences, sequence IDs or database references to analysis - workflows provided by the EnVision2 web - application. This allows Jalview users to easily access the EnCore - network of databases and analysis services developed by members of - ENFIN.

    • 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 --- 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.
    -

  • Envision2 Services
    Submits one or - more sequences, sequence IDs or database references to analysis - workflows provided by the EnVision2 web - application. This allows Jalview users to easily access the EnCore - network of databases and analysis services developed by members of - ENFIN.

    • 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 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -49,8 +49,6 @@ structure prediction based at the University of Dundee.

  • Services for alignment analysis, such as Multi-Harmony. -
  • Services for submitting IDs and sequences to external - bioinformatics services such as Envision2 (see below).

    • Web Service Dialog Box @@ -81,17 +79,5 @@ the advent of JABAWS, however, it is possible for anyone to host Jalview web services.

    -

    - Envision2 Services - -

    -

    - 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 EnVision2 - web application. This allows Jalview users to easily access the - EnCore network of databases and analysis services developed by ENFIN (www.enfin.org). -

    diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 775df57..906db68 100644 --- 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 label.index_by_host = Index by host label.index_by_type = Index by type -label.enable_enfin_services = Enable Enfin Services label.enable_jabaws_services = Enable JABAWS Services label.display_warnings = Display warnings label.move_url_up = Move URL up diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index da34013..353a139 100644 --- 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 --- 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 --- 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 --- 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 --- 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 -- 1.7.10.2