/*
- * 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.
*
*/
package jalview.ws.jws1;
+import java.util.Locale;
import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
+import jalview.bin.Console;
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 javax.swing.JOptionPane;
import ext.vamsas.Jpred;
import ext.vamsas.JpredServiceLocator;
* @param viewonly
* TODO
*/
- public JPredClient(ext.vamsas.ServiceHandle sh, String title,
- boolean msa, AlignmentView alview, AlignFrame parentFrame,
- boolean viewonly)
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa,
+ AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
{
super();
wsInfo = setWebService(sh);
Jpred server = locateWebService();
if (server == null)
{
- Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+ Console.warn("Couldn't find a Jpred webservice to invoke!");
return;
}
SeqCigar[] msf = null;
aln[i] = msf[i].getSeq('-');
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
- true);
+ Map<String, SequenceInfo> SequenceInfo =
+ jalview.analysis.SeqsetUtils.uniquify(aln, true);
if (viewonly)
{
// Remove hidden regions from sequence objects.
{
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 "
+ (viewonly ? "visible " : "") + "sequence " + seq.getName()
+ " from " + title;
String seqname = seq.getName();
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
.SeqCharacterHash(seq);
if (viewonly)
{
private String getPredictionName(String webServiceName)
{
- if (webServiceName.toLowerCase().indexOf(
- "secondary structure prediction") > -1)
+ if (webServiceName.toLowerCase(Locale.ROOT)
+ .indexOf("secondary structure prediction") > -1)
{
return webServiceName;
}
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
+ ") on sequence :\n>" + seq.getName() + "\n"
- + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\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]);
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
- true);
+ Map<String, SequenceInfo> SequenceInfo =
+ jalview.analysis.SeqsetUtils.uniquify(aln, true);
Jpred server = locateWebService();
if (server == null)
}
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()
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
+ String altitle = "JPred prediction for sequence " + seq.getName()
+ " from " + title;
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
.SeqCharacterHash(seq);
Jpred server = locateWebService();
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\".";
WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
- WebServiceReference, true);
+ WebServiceReference, Desktop.FRAME_MAKE_VISIBLE);
return wsInfo;
}
} 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.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)
{
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);
+ new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa, af,
+ true);
}
else
{