/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
-import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Hashtable;
import java.util.Vector;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = MessageManager.formatMessage("label.webservice_job_title", new String[]{service.details.Action,service.details.Name});
+ WebServiceJobTitle = MessageManager.formatMessage(
+ "label.webservice_job_title", new String[] {
+ service.details.Action, service.details.Name });
WebServiceName = service.details.Name;
WebServiceReference = "No reference - go to url for more info";
if (service.details.description != null)
final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(MessageManager.formatMessage("label.rest_client_submit", new String[]{service.details.Action,service.details.Name}));
+ submit.setToolTipText(MessageManager.formatMessage(
+ "label.rest_client_submit", new String[] {
+ service.details.Action, service.details.Name }));
submit.addActionListener(new ActionListener()
{
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
- viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ viewTitle = MessageManager.formatMessage(
+ "label.select_visible_region_of",
+ new String[] {
+ (av.hasHiddenColumns() ? MessageManager
+ .getString("label.visible") : ""),
+ af.getTitle() });
}
else
{
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), false, true);
}
- viewTitle = MessageManager.formatMessage("label.select_unselect_visible_regions_from", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ viewTitle = MessageManager.formatMessage(
+ "label.select_unselect_visible_regions_from",
+ new String[] {
+ (av.hasHiddenColumns() ? MessageManager
+ .getString("label.visible") : ""),
+ af.getTitle() });
}
else
{
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), av.getSelectionGroup(),
av.hasHiddenColumns(), true, true);
- viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ viewTitle = MessageManager.formatMessage(
+ "label.select_visible_region_of",
+ new String[] {
+ (av.hasHiddenColumns() ? MessageManager
+ .getString("label.visible") : ""),
+ af.getTitle() });
}
}
else
_input = new AlignmentView(av.getAlignment(),
av.getColumnSelection(), null, av.hasHiddenColumns(), false,
true);
- viewTitle = "" + (av.hasHiddenColumns() ? (new StringBuffer(" ").append(MessageManager.getString("label.visible_region_of")).toString()) : "")
- + af.getTitle();
+ viewTitle = ""
+ + (av.hasHiddenColumns() ? (new StringBuffer(" ")
+ .append(MessageManager
+ .getString("label.visible_region_of"))
+ .toString()) : "") + af.getTitle();
}
RestJobThread jobsthread = new RestJobThread(this);
else
{
// TODO: try to tell the user why the job couldn't be started.
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
- : MessageManager.getString("label.job_couldnt_be_started_check_input")),
- MessageManager.getString("label.unable_start_web_service_analysis"),
- JOptionPane.WARNING_MESSAGE);
+ : MessageManager
+ .getString("label.job_couldnt_be_started_check_input")),
+ MessageManager
+ .getString("label.unable_start_web_service_analysis"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
- public static RestClient makeShmmrRestClient()
- {
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager.getString("label.multiharmony");
- 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);
-
- jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
- // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
- // so we always upload our files.
- aliinput.token = "ali_file";
- aliinput.writeAsFile = true;
- iparams.put(aliinput.token, aliinput);
- jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
- sgroups.setMinsize(2);
- sgroups.min = 2;// need at least two group defined to make a partition
- iparams.put("groups", sgroups);
- sgroups.token = "groups";
- sgroups.sep = " ";
- RestServiceDescription shmrService = new RestServiceDescription(
- action,
- description,
- name,
- "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);
- return new RestClient(shmrService);
- }
-
public AlignmentPanel recoverAlignPanelForView()
{
AlignmentPanel[] aps = Desktop
for (RestServiceDescription descr : RestServiceDescription
.parseDescriptions(jalview.bin.Cache.getDefault(
RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ ShmrRestClient.makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
return lst;
}
- public static void main(String args[])
- {
- try
- {
- RestClient[] clients = getRestClients();
- System.out.println("Got " + clients.length + " clients.");
- int i = 0;
- Vector<String> urls = new Vector<String>();
- for (RestClient cl : clients)
- {
- System.out.println("" + (++i) + ": " + cl.service.toString());
- urls.add(cl.service.toString());
- }
- setRsbsServices(urls);
- if (clients.length != getRestClients().length)
- {
- System.err
- .println("Failed. Differing numbers of clients when stringified and parsed again.");
- }
-
- } catch (Throwable x)
- {
- System.err.println("Failed. Unexpected exception.");
- x.printStackTrace();
- }
- }
-
public String getAction()
{
return service.details.Action;
git://source.jalview.org / jalview.git / blobdiff