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
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
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>
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>
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
JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
this);
}
-
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
- {
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, this);
- }
}
/*
*/
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;
return ret;
}
- void recentListSelectionChanged(String selection)
+ void recentListSelectionChanged(Object selection)
{
setSelectedFile(null);
-
- File file = new File(selection);
- if (getFileFilter() instanceof JalviewFileFilter)
+ if (selection != null)
{
- JalviewFileFilter jvf = (JalviewFileFilter) this.getFileFilter();
-
- if (!jvf.accept(file))
+ File file = new File((String) selection);
+ if (getFileFilter() instanceof JalviewFileFilter)
{
- setFileFilter(getChoosableFileFilters()[0]);
+ JalviewFileFilter jvf = (JalviewFileFilter) this.getFileFilter();
+
+ if (!jvf.accept(file))
+ {
+ setFileFilter(getChoosableFileFilters()[0]);
+ }
}
- }
- setSelectedFile(file);
+ setSelectedFile(file);
+ }
}
class RecentlyOpened extends JPanel
{
public void mousePressed(MouseEvent evt)
{
- recentListSelectionChanged(list.getSelectedValue().toString());
+ recentListSelectionChanged(list.getSelectedValue());
}
});
strandColour_actionPerformed(e);
}
});
- turnColour.setText(MessageManager.getString("Turn Propensity"));
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed(e);
}
});
- buriedColour.setText(MessageManager.getString("Buried Index"));
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
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"));
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));
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|,",
/**
* 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
git://source.jalview.org / jalview.git / commitdiff
