/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
* 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.
+ * 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/>.
+ * 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.jws1;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+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.WebserviceInfo;
+import jalview.util.MessageManager;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.*;
+import java.util.Hashtable;
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
-import ext.vamsas.*;
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import ext.vamsas.Jpred;
+import ext.vamsas.JpredServiceLocator;
+import ext.vamsas.JpredSoapBindingStub;
+import ext.vamsas.ServiceHandle;
public class JPredClient extends WS1Client
{
* visible regions
*/
private void startJPredClient(String title, boolean msa,
- jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+ AlignmentView alview, AlignFrame parentFrame,
boolean viewonly)
{
AlignmentView input = alview;
aln[i] = msf[i].getSeq('-');
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
- true);
+ Hashtable SequenceInfo = SeqsetUtils.uniquify(aln, true);
if (viewonly)
{
// Remove hidden regions from sequence objects.
{
if (!msa && msf.length > 1)
{
- throw new Error(
- "Implementation Error! Multiple single sequence prediction jobs are not yet 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
- .SeqCharacterHash(seq);
+ Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
if (viewonly)
{
// Remove hidden regions from input sequence
aln[i] = new jalview.datamodel.Sequence(msf[i]);
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+ Hashtable SequenceInfo = SeqsetUtils.uniquify(aln,
true);
Jpred server = locateWebService();
String altitle = "JNet prediction for sequence " + seq.getName()
+ " from " + title;
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seq);
+ Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
Jpred server = locateWebService();
if (server == null)
private WebserviceInfo setWebService()
{
WebServiceName = "JNetWS";
- WebServiceJobTitle = "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);
+ WebServiceReference, true);
return wsInfo;
}
} catch (Exception ex)
{
JOptionPane.showMessageDialog(Desktop.desktop,
- "The Secondary Structure Prediction Service named "
- + WebServiceName + " at " + WsURL
- + " couldn't be located.", "Internal Jalview Error",
+ 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("Serious! " + WebServiceName
- + " Service location failed\nfor URL :" + WsURL + "\n"
+ 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);
git://source.jalview.org / jalview.git / blobdiff