/*
- * 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.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import ext.vamsas.Jpred;
import ext.vamsas.JpredServiceLocator;
{
if (!msa && msf.length > 1)
{
- throw new Error(MessageManager.getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
}
String altitle = getPredictionName(WebServiceName) + " for "
SequenceI seq = msf[0];
- String altitle = "JNet prediction on " + seq.getName()
+ String altitle = "JPred prediction on " + seq.getName()
+ " using alignment from " + title;
wsInfo.setProgressText("Job details for MSA based prediction (" + title
wsInfo.setProgressText("Job details for prediction on sequence :\n>"
+ seq.getName() + "\n"
+ AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
- String altitle = "JNet prediction for sequence " + seq.getName()
+ String altitle = "JPred prediction for sequence " + seq.getName()
+ " from " + title;
Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
private WebserviceInfo setWebService()
{
WebServiceName = "JNetWS";
- WebServiceJobTitle = MessageManager.getString("label.jnet_secondary_structure_prediction");
+ 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\".";
} catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL}),
- MessageManager.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
- wsInfo.setProgressText(MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL})
- + "\n"
- + ex.getMessage());
+ JvOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ 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)
{
method.setToolTipText(sh.getEndpointURL());
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();