/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
*/
package jalview.ws.rest;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
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;
* @author JimP
*
*/
-public class RestClient extends WSClient implements WSClientI,
- WSMenuEntryProviderI
+public class RestClient extends WSClient
+implements WSClientI, WSMenuEntryProviderI, ApplicationSingletonI
{
+
+ @SuppressWarnings("unused")
+ private RestClient()
+ {
+ // accessed by ApplicationSingletonProvider
+ }
+
+
+private static RestClient getInstance()
+{
+return (RestClient) ApplicationSingletonProvider.getInstance(RestClient.class);
+}
+
+public static final String RSBS_SERVICES = "RSBS_SERVICES";
+
+
+ protected Vector<String> services = null;
+
+
RestServiceDescription service;
public RestClient(RestServiceDescription rsd)
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = MessageManager.formatMessage(
- "label.webservice_job_title", new String[] {
- service.details.Action, service.details.Name });
- WebServiceName = service.details.Name;
+ WebServiceJobTitle = MessageManager
+ .formatMessage("label.webservice_job_title", new String[]
+ { service.details.getAction(), service.details.getName() });
+ WebServiceName = service.details.getName();
WebServiceReference = "No reference - go to url for more info";
- if (service.details.description != null)
+ if (service.details.getDescription() != null)
{
- WebServiceReference = service.details.description;
+ WebServiceReference = service.details.getDescription();
}
if (!headless)
{
- wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
- + WebServiceReference, true);
+ wsInfo = new WebserviceInfo(WebServiceJobTitle,
+ WebServiceName + "\n" + WebServiceReference, Desktop.FRAME_MAKE_VISIBLE);
wsInfo.setRenderAsHtml(true);
}
public void attachWSMenuEntry(final JMenu wsmenu,
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 }));
+ JMenuItem submit = new JMenuItem(service.details.getName());
+ submit.setToolTipText(MessageManager
+ .formatMessage("label.rest_client_submit", new String[]
+ { service.details.getAction(), service.details.getName() }));
submit.addActionListener(new ActionListener()
{
{
// intersect groups with selected region
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true,
+ true);
viewTitle = MessageManager.formatMessage(
- "label.select_visible_region_of",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
else
{
// use selected region to partition alignment
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), false, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), false,
+ true);
}
viewTitle = MessageManager.formatMessage(
- "label.select_unselect_visible_regions_from",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_unselect_visible_regions_from", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
else
{
// just take selected region intersection
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true, true);
viewTitle = MessageManager.formatMessage(
- "label.select_visible_region_of",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
}
{
// standard alignment view without selection present
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), null, av.hasHiddenColumns(), false,
- true);
+ av.getAlignment().getHiddenColumns(), null,
+ av.hasHiddenColumns(), false, true);
viewTitle = ""
- + (av.hasHiddenColumns() ? (new StringBuffer(" ")
- .append(MessageManager
- .getString("label.visible_region_of"))
- .toString()) : "") + af.getTitle();
+ + (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
- .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);
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ (jobsthread.hasWarnings() ? jobsthread.getWarnings()
+ : 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
return true;
}
- protected static Vector<String> services = null;
-
- public static final String RSBS_SERVICES = "RSBS_SERVICES";
-
public static RestClient[] getRestClients()
{
+ return getInstance().getClients();
+ }
+
+ private RestClient[] getClients()
+ {
if (services == null)
{
- services = new Vector<String>();
+ services = new Vector<>();
try
{
for (RestServiceDescription descr : RestServiceDescription
.parseDescriptions(jalview.bin.Cache.getDefault(
RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ ShmrRestClient.makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
} catch (Exception ex)
{
- System.err
- .println("Serious - RSBS descriptions in user preferences are corrupt!");
+ System.err.println(
+ "Serious - RSBS descriptions in user preferences are corrupt!");
ex.printStackTrace();
}
public String getAction()
{
- return service.details.Action;
+ return service.details.getAction();
}
public RestServiceDescription getRestDescription()
public static Vector<String> getRsbsDescriptions()
{
- Vector<String> rsbsDescrs = new Vector<String>();
+ Vector<String> rsbsDescrs = new Vector<>();
for (RestClient rsbs : getRestClients())
{
rsbsDescrs.add(rsbs.getRestDescription().toString());
{
if (rsbsUrls != null)
{
+
// TODO: consider validating services ?
- services = new Vector<String>(rsbsUrls);
+ getInstance().services = new Vector<String>(rsbsUrls);
StringBuffer sprop = new StringBuffer();
- for (String s : services)
+ for (String s : getInstance().services)
{
sprop.append(s);
}
git://source.jalview.org / jalview.git / blobdiff