-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
-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;
-
-import com.sun.org.apache.bcel.internal.generic.ISHL;
-
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
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 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 RestClient(RestServiceDescription service2, AlignFrame alignFrame)
{
+ this(service2, alignFrame, false);
+ }
+
+ boolean headless = false;
+
+ public RestClient(RestServiceDescription service2, AlignFrame alignFrame,
+ boolean nogui)
+ {
service = service2;
af = alignFrame;
av = alignFrame.getViewport();
+ headless = nogui;
constructJob();
}
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = service.details.Action + " using "
- + 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)
if (!headless)
{
wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
- + WebServiceReference);
+ + WebServiceReference, true);
wsInfo.setRenderAsHtml(true);
}
final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(service.details.Action+" using "+service.details.Name);
+ submit.setToolTipText(MessageManager.formatMessage(
+ "label.rest_client_submit", new String[] {
+ service.details.Action, service.details.Name }));
submit.addActionListener(new ActionListener()
{
*/
protected boolean isAlignmentModified()
{
- if (undoredo == null)
+ if (undoredo == null || av == null || av.getAlignment() == null)
{
+ // always return modified if we don't have access to live GUI elements
+ // anymore.
return true;
}
if (av.isUndoRedoHashModified(undoredo))
{
-
+ // alignment has been modified in some way.
+ return true;
}
+ // TODO: look deeper into modification of selection state, etc that may
+ // affect RestJobThread.realiseResults(boolean merge);
return false;
}
*/
jalview.io.packed.JalviewDataset jds;
+ /**
+ * informative name for results
+ */
+ public String viewTitle;
+
protected void constructJob()
{
service.setInvolvesFlags();
-
// record all aspects of alignment view so we can merge back or recreate
// later
undoredo = av.getUndoRedoHash();
*/
boolean selExists = (av.getSelectionGroup() != null)
&& (av.getSelectionGroup().getSize() > 1);
- // TODO: revise to full focus+context+dataset input data staging model
+ // TODO: JAL-715: refactor to alignViewport methods and revise to full
+ // focus+context+dataset input data staging model
if (selExists)
{
if (service.partitiondata)
{
- if (av.getAlignment().getGroups()!=null && av.getAlignment().getGroups().size() > 0)
+ if (av.getAlignment().getGroups() != null
+ && av.getAlignment().getGroups().size() > 0)
{
// intersect groups with selected region
- _input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(),
- av.getSelectionGroup(),
- av.hasHiddenColumns(),
- true,
- true);
+ _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() });
}
else
{
// use selected region to partition alignment
- _input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(),
- av.getSelectionGroup(),
- av.hasHiddenColumns(),
- false,
- true);
+ _input = new AlignmentView(av.getAlignment(),
+ av.getColumnSelection(), av.getSelectionGroup(),
+ av.hasHiddenColumns(), false, true);
}
- // TODO: verify that some kind of partition can be constructed from input
+ viewTitle = MessageManager.formatMessage(
+ "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);
+ _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() });
}
- } else {
+ }
+ else
+ {
// standard alignment view without selection present
- _input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(),
- null,
- av.hasHiddenColumns(),
- false,
+ _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();
}
-
+
RestJobThread jobsthread = new RestJobThread(this);
-
+
if (jobsthread.isValid())
{
- setWebserviceInfo(false);
- wsInfo.setthisService(this);
- jobsthread.setWebServiceInfo(wsInfo);
+ setWebserviceInfo(headless);
+ if (!headless)
+ {
+ wsInfo.setthisService(this);
+ jobsthread.setWebServiceInfo(wsInfo);
+ }
jobsthread.start();
}
else
{
// TODO: try to tell the user why the job couldn't be started.
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Unable to start web service analysis",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ 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);
}
}
public static RestClient makeShmmrRestClient()
{
- String action = "Analyse", description = "Sequence Harmony and Multi-Relief", name = "SHMR";
+ 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);
-
+ // 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("ali_file", aliinput);
+ 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 = " ";
action,
description,
name,
- "http://www.ibi.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
+ "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);
public AlignmentPanel recoverAlignPanelForView()
{
- AlignmentPanel[] aps = Desktop.getAlignmentPanels(av.getSequenceSetId());
- for (AlignmentPanel alp:aps)
+ AlignmentPanel[] aps = Desktop
+ .getAlignmentPanels(av.getSequenceSetId());
+ for (AlignmentPanel alp : aps)
{
if (alp.av == av)
{
return true;
}
+ protected static Vector<String> services = null;
+
+ public static final String RSBS_SERVICES = "RSBS_SERVICES";
+
+ public static RestClient[] getRestClients()
+ {
+ if (services == null)
+ {
+ services = new Vector<String>();
+ try
+ {
+ for (RestServiceDescription descr : RestServiceDescription
+ .parseDescriptions(jalview.bin.Cache.getDefault(
+ RSBS_SERVICES,
+ makeShmmrRestClient().service.toString())))
+ {
+ services.add(descr.toString());
+ }
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Serious - RSBS descriptions in user preferences are corrupt!");
+ ex.printStackTrace();
+ }
+
+ }
+ RestClient[] lst = new RestClient[services.size()];
+ int i = 0;
+ for (String svc : services)
+ {
+ lst[i++] = new RestClient(new RestServiceDescription(svc));
+ }
+ return lst;
+ }
+
+ public String getAction()
+ {
+ return service.details.Action;
+ }
+
+ public RestServiceDescription getRestDescription()
+ {
+ return service;
+ }
+
+ public static Vector<String> getRsbsDescriptions()
+ {
+ Vector<String> rsbsDescrs = new Vector<String>();
+ for (RestClient rsbs : getRestClients())
+ {
+ rsbsDescrs.add(rsbs.getRestDescription().toString());
+ }
+ return rsbsDescrs;
+ }
+
+ public static void setRsbsServices(Vector<String> rsbsUrls)
+ {
+ if (rsbsUrls != null)
+ {
+ // TODO: consider validating services ?
+ services = new Vector<String>(rsbsUrls);
+ StringBuffer sprop = new StringBuffer();
+ for (String s : services)
+ {
+ sprop.append(s);
+ }
+ Cache.setProperty(RSBS_SERVICES, sprop.toString());
+ }
+ else
+ {
+ Cache.removeProperty(RSBS_SERVICES);
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff