/*
- * 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.
*
*/
package jalview.io;
-import java.util.*;
+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 javax.swing.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
-import uk.ac.ebi.www.*;
+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!
{
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();
+ DBRefEntry[] entries = oldseq.getDBRefs();
if (entries != null)
{
oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
}
}
+ @Override
public void run()
{
while (jobsRunning > 0)
imageIndex++;
imageIndex %= 9;
output.setFrameIcon(imageIcon[imageIndex]);
- output.setTitle(MessageManager.formatMessage("label.blasting_for_unidentified_sequence_jobs_running", new String[]{jobsRunning}));
+ output.setTitle(MessageManager.formatMessage(
+ "label.blasting_for_unidentified_sequence_jobs_running",
+ new String[] { Integer.valueOf(jobsRunning).toString() }));
} catch (Exception ex)
{
}
this.sequence = sequence;
}
+ @Override
public void run()
{
StartJob();