+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ *******************************************************************************/
/**
*
*/
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.Collection;
import java.util.Hashtable;
import java.util.Vector;
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;
*/
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)
av.hasHiddenColumns(),
true,
true);
+ viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle();
}
else
{
false,
true);
}
- // TODO: verify that some kind of partition can be constructed from input
+ viewTitle = "select and unselected "+(av.hasHiddenColumns() ? "visible" : "") + " regions from "+af.getTitle();
}
else
{
av.hasHiddenColumns(),
true,
true);
+ viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle();
}
} else {
// standard alignment view without selection present
av.hasHiddenColumns(),
false,
true);
+ viewTitle = ""+(av.hasHiddenColumns() ? "visible region of " : "") + af.getTitle();
}
RestJobThread jobsthread = new RestJobThread(this);
{
// 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);
+ (jobsthread.hasWarnings() ? jobsthread.getWarnings() : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."),
+ "Unable to 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 = "Multi-Harmony";
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.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();
- aliinput.token = "ali_file";
- aliinput.writeAsFile=true;
- iparams.put("ali_file", aliinput);
+ // SHMR server has a 65K limit for content pasted into the 'ali' parameter, so we always upload our files.
+ aliinput.token = "ali_file";//_file";
+ aliinput.writeAsFile=true;//true;
+ //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 = " ";
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);
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 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;
+ }
+
+ 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