/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Hashtable;
import java.util.Map;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import ext.vamsas.Jpred;
import ext.vamsas.JpredServiceLocator;
import ext.vamsas.JpredSoapBindingStub;
import ext.vamsas.ServiceHandle;
public class JPredClient extends WS1Client
{
/**
* crate a new GUI JPred Job
*
* @param sh
* ServiceHandle
* @param title
* String
* @param msa
* boolean - true - submit alignment as a sequence profile
* @param alview
* AlignmentView
* @param viewonly
* TODO
*/
public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa,
AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
{
super();
wsInfo = setWebService(sh);
startJPredClient(title, msa, alview, parentFrame, viewonly);
}
/**
* startJPredClient TODO: refine submission to cope with local prediction of
* visible regions or multiple single sequence jobs TODO: sequence
* representative support - could submit alignment of representatives as msa.
* TODO: msa hidden region prediction - submit each chunk for prediction.
* concatenate results of each. TODO: single seq prediction - submit each
* contig of each sequence for prediction (but must cope with flanking regions
* and short seqs)
*
* @param title
* String
* @param msa
* boolean
* @param alview
* AlignmentView
* @param viewonly
* if true then the prediction will be made just on the concatenated
* visible regions
*/
private void startJPredClient(String title, boolean msa,
jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
boolean viewonly)
{
AlignmentView input = alview;
if (wsInfo == null)
{
wsInfo = setWebService();
}
Jpred server = locateWebService();
if (server == null)
{
Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
return;
}
SeqCigar[] msf = null;
SequenceI seq = null;
int[] delMap = null;
// original JNetClient behaviour - submit full length of sequence or profile
// and mask result.
msf = input.getSequences();
seq = msf[0].getSeq('-');
if (viewonly)
{
delMap = alview.getVisibleContigMapFor(seq.gapMap());
}
if (msa && msf.length > 1)
{
String altitle = getPredictionName(WebServiceName) + " on "
+ (viewonly ? "visible " : "") + seq.getName()
+ " using alignment from " + title;
SequenceI aln[] = new SequenceI[msf.length];
for (int i = 0, j = msf.length; i < j; i++)
{
aln[i] = msf[i].getSeq('-');
}
Map SequenceInfo =
jalview.analysis.SeqsetUtils.uniquify(aln, true);
if (viewonly)
{
// Remove hidden regions from sequence objects.
String seqs[] = alview.getSequenceStrings('-');
for (int i = 0, j = msf.length; i < j; i++)
{
aln[i].setSequence(seqs[i]);
}
seq.setSequence(seqs[0]);
}
wsInfo.setProgressText("Job details for "
+ (viewonly ? "visible " : "") + "MSA based prediction ("
+ title + ") on sequence :\n>" + seq.getName() + "\n"
+ AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ "\n");
JPredThread jthread = new JPredThread(wsInfo, altitle, server,
SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
wsInfo.setthisService(jthread);
jthread.start();
}
else
{
if (!msa && msf.length > 1)
{
throw new Error(MessageManager.getString(
"error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
}
String altitle = getPredictionName(WebServiceName) + " for "
+ (viewonly ? "visible " : "") + "sequence " + seq.getName()
+ " from " + title;
String seqname = seq.getName();
SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
.SeqCharacterHash(seq);
if (viewonly)
{
// Remove hidden regions from input sequence
String seqs[] = alview.getSequenceStrings('-');
seq.setSequence(seqs[0]);
}
wsInfo.setProgressText("Job details for prediction on "
+ (viewonly ? "visible " : "") + "sequence :\n>" + seqname
+ "\n"
+ AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ "\n");
JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
SequenceInfo, seq, delMap, alview, parentFrame);
wsInfo.setthisService(jthread);
jthread.start();
}
}
private String getPredictionName(String webServiceName)
{
if (webServiceName.toLowerCase()
.indexOf("secondary structure prediction") > -1)
{
return webServiceName;
}
else
{
return webServiceName + "secondary structure prediction";
}
}
public JPredClient(ext.vamsas.ServiceHandle sh, String title,
SequenceI seq, AlignFrame parentFrame)
{
super();
wsInfo = setWebService(sh);
startJPredClient(title, seq, parentFrame);
}
public JPredClient(ext.vamsas.ServiceHandle sh, String title,
SequenceI[] msa, AlignFrame parentFrame)
{
wsInfo = setWebService(sh);
startJPredClient(title, msa, parentFrame);
}
public JPredClient(String title, SequenceI[] msf)
{
startJPredClient(title, msf, null);
}
public JPredClient(String title, SequenceI seq)
{
startJPredClient(title, seq, null);
}
public JPredClient()
{
super();
// add a class reference to the list
}
private void startJPredClient(String title, SequenceI[] msf,
AlignFrame parentFrame)
{
if (wsInfo == null)
{
wsInfo = setWebService();
}
SequenceI seq = msf[0];
String altitle = "JPred prediction on " + seq.getName()
+ " using alignment from " + title;
wsInfo.setProgressText("Job details for MSA based prediction (" + title
+ ") on sequence :\n>" + seq.getName() + "\n"
+ AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ "\n");
SequenceI aln[] = new SequenceI[msf.length];
for (int i = 0, j = msf.length; i < j; i++)
{
aln[i] = new jalview.datamodel.Sequence(msf[i]);
}
Map SequenceInfo =
jalview.analysis.SeqsetUtils.uniquify(aln, true);
Jpred server = locateWebService();
if (server == null)
{
return;
}
JPredThread jthread = new JPredThread(wsInfo, altitle, server,
SequenceInfo, aln, null, null, parentFrame, WsURL);
wsInfo.setthisService(jthread);
jthread.start();
}
public void startJPredClient(String title, SequenceI seq,
AlignFrame parentFrame)
{
if (wsInfo == null)
{
wsInfo = setWebService();
}
wsInfo.setProgressText("Job details for prediction on sequence :\n>"
+ seq.getName() + "\n"
+ AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ "\n");
String altitle = "JPred prediction for sequence " + seq.getName()
+ " from " + title;
SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
.SeqCharacterHash(seq);
Jpred server = locateWebService();
if (server == null)
{
return;
}
JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
SequenceInfo, seq, null, null, parentFrame);
wsInfo.setthisService(jthread);
jthread.start();
}
private WebserviceInfo setWebService()
{
WebServiceName = "JNetWS";
WebServiceJobTitle = MessageManager
.getString("label.jnet_secondary_structure_prediction");
WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, "
+ "Proteins 40:502-511\".";
WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
WebServiceReference, Desktop.FRAME_MAKE_VISIBLE);
return wsInfo;
}
private ext.vamsas.Jpred locateWebService()
{
ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
ext.vamsas.Jpred server = null;
try
{
server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set
// from properties
((JpredSoapBindingStub) server).setTimeout(60000); // one minute stub
// ((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C,
// Boolean.TRUE);
} catch (Exception ex)
{
JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.secondary_structure_prediction_service_couldnt_be_located",
new String[]
{ WebServiceName, WsURL }),
MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
wsInfo.setProgressText(MessageManager.formatMessage(
"label.secondary_structure_prediction_service_couldnt_be_located",
new String[]
{ WebServiceName, WsURL }) + "\n" + ex.getMessage());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
return server;
}
@Override
public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
final AlignFrame af)
{
final JMenuItem method = new JMenuItem(sh.getName());
method.setToolTipText(sh.getEndpointURL());
method.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
if (msa.getSequences().length == 1)
{
// Single Sequence prediction
new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa, af,
true);
}
else
{
if (msa.getSequences().length > 1)
{
// Sequence profile based prediction
new jalview.ws.jws1.JPredClient(sh, af.getTitle(), true, msa,
af, true);
}
}
}
});
wsmenu.add(method);
}
}