/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.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.Vector;
import javax.swing.ImageIcon;
-import javax.swing.JOptionPane;
import uk.ac.ebi.www.Data;
import uk.ac.ebi.www.InputParams;
{
this.ap = ap;
this.al = al;
- output.setText(MessageManager
- .getString("label.wswublast_client_credits"));
+ output.setText(
+ MessageManager.getString("label.wswublast_client_credits"));
- Desktop.addInternalFrame(output, MessageManager
- .getString("label.blasting_for_unidentified_sequence"), 800,
- 300);
+ Desktop.addInternalFrame(output, MessageManager.getString(
+ "label.blasting_for_unidentified_sequence"), 800, 300);
for (int i = 0; i < ids.size(); i++)
{
{
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)
{
{
// 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(
- jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
- .getAccessionId()));
+ jalview.datamodel.DBRefSource.UNIPROT, "0",
+ entries[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)
output.setFrameIcon(imageIcon[imageIndex]);
output.setTitle(MessageManager.formatMessage(
"label.blasting_for_unidentified_sequence_jobs_running",
- new String[] { Integer.valueOf(jobsRunning).toString() }));
+ new String[]
+ { Integer.valueOf(jobsRunning).toString() }));
} catch (Exception ex)
{
}
this.sequence = sequence;
}
+ @Override
public void run()
{
StartJob();