/*
- * 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
+ * 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.io;
-import java.util.*;
-
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import uk.ac.ebi.www.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.ImageIcon;
+
+import uk.ac.ebi.www.Data;
+import uk.ac.ebi.www.InputParams;
+import uk.ac.ebi.www.WSFile;
+import uk.ac.ebi.www.WSWUBlast;
+import uk.ac.ebi.www.WSWUBlastService;
+import uk.ac.ebi.www.WSWUBlastServiceLocator;
/**
* DOCUMENT ME!
{
this.ap = ap;
this.al = al;
- output.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
- + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
- + "\n\nRunning WSWUBlast at EBI."
- + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
- + "\nSOAP-based services provided by the European Bioinformatics Institute."
- + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+ output.setText(
+ MessageManager.getString("label.wswublast_client_credits"));
- Desktop.addInternalFrame(output,
- "BLASTing for unidentified sequences ", 800, 300);
+ Desktop.addInternalFrame(output, MessageManager.getString(
+ "label.blasting_for_unidentified_sequence"), 800, 300);
for (int i = 0; i < ids.size(); i++)
{
Sequence sequence = (Sequence) ids.get(i);
- System.out.println(sequence.getName());
+ jalview.bin.Console.outPrintln(sequence.getName());
BlastThread thread = new BlastThread(sequence);
thread.start();
{
identitiesFound = true;
- int value = Integer.parseInt(data.substring(
- data.indexOf("(") + 1, data.indexOf("%")));
+ int value = Integer.parseInt(data
+ .substring(data.indexOf("(") + 1, data.indexOf("%")));
if (value >= maxFound)
{
maxFound = value;
buffer.append(" " + id2 + " " + value + "%; ");
- suggestedIds.addElement(new Object[]
- { seq, id2 });
+ suggestedIds.addElement(new Object[] { seq, id2 });
}
}
}
{
// This must be outside the run() body as java 1.5
// will not return any value from the OptionPane to the expired thread.
- int reply = JOptionPane.showConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showConfirmDialog(Desktop.desktop,
"Automatically update suggested ids?",
- "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
+ "Auto replace sequence ids", JvOptionPane.YES_NO_OPTION);
- if (reply == JOptionPane.YES_OPTION)
+ if (reply == JvOptionPane.YES_OPTION)
{
Enumeration keys = suggestedIds.elements();
while (keys.hasMoreElements())
}
}
- DBRefEntry[] entries = oldseq.getDBRef();
- if (entries != null)
+ List<DBRefEntry> entries = oldseq.getDBRefs();
+ // BH 2019.01.25 check for 0-length was missing here
+ if (entries != null && entries.size() > 0)
{
oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
- jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
- .getAccessionId()));
+ jalview.datamodel.DBRefSource.UNIPROT, "0",
+ entries.get(0).getAccessionId()));
}
}
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, false);
}
for (int i = 0; i < 9; i++)
{
- java.net.URL url = getClass().getResource(
- "/images/dna" + (i + 1) + ".gif");
+ java.net.URL url = getClass()
+ .getResource("/images/dna" + (i + 1) + ".gif");
if (url != null)
{
}
}
+ @Override
public void run()
{
while (jobsRunning > 0)
imageIndex++;
imageIndex %= 9;
output.setFrameIcon(imageIcon[imageIndex]);
- output.setTitle("BLASTing for unidentified sequences - "
- + jobsRunning + " jobs running.");
+ output.setTitle(MessageManager.formatMessage(
+ "label.blasting_for_unidentified_sequence_jobs_running",
+ new String[]
+ { Integer.valueOf(jobsRunning).toString() }));
} catch (Exception ex)
{
}
BlastThread(Sequence sequence)
{
- System.out.println("blasting for: " + sequence.getName());
+ jalview.bin.Console.outPrintln("blasting for: " + sequence.getName());
this.sequence = sequence;
}
+ @Override
public void run()
{
StartJob();
else
{
Thread.sleep(10000);
- System.out.println("WSWuBlastClient: I'm alive "
+ jalview.bin.Console.outPrintln("WSWuBlastClient: I'm alive "
+ sequence.getName() + " " + jobid); // log.debug
}
} catch (Exception ex)
{
jobComplete = true;
jobsRunning--;
- System.err.println("WSWUBlastClient error:\n" + exp.toString());
+ jalview.bin.Console
+ .errPrintln("WSWUBlastClient error:\n" + exp.toString());
exp.printStackTrace();
}
}
git://source.jalview.org / jalview.git / blobdiff