/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 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.gui;
import java.util.*;
-
import java.awt.*;
import java.awt.event.*;
import java.awt.print.*;
+
import javax.swing.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
import jalview.viewmodel.PCAModel;
/**
JOptionPane
.showMessageDialog(
Desktop.desktop,
- "The sequences must be aligned before calculating PCA.\n"
- + "Try using the Pad function in the edit menu,\n"
- + "or one of the multiple sequence alignment web services.",
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.pca_sequences_not_aligned"),
+ MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
return;
}
worker.start();
}
+ @Override
+ protected void scoreMatrix_menuSelected()
+ {
+ scoreMatrixMenu.removeAll();
+ for (final String sm : ResidueProperties.scoreMatrices.keySet())
+ {
+ if (ResidueProperties.getScoreMatrix(sm) != null)
+ {
+ // create an entry for this score matrix for use in PCA
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
+ jm.setText(MessageManager
+ .getStringOrReturn("label.score_model", sm));
+ jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+ if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
+ .get(sm).isProtein())
+ || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
+ .get(sm).isDNA())
+ {
+ final PCAPanel us = this;
+ jm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (!pcaModel.getScore_matrix().equals((String) sm))
+ {
+ pcaModel.setScore_matrix((String) sm);
+ Thread worker = new Thread(us);
+ worker.start();
+ }
+ }
+ });
+ scoreMatrixMenu.add(jm);
+ }
+ }
+ }
+ }
+
public void bgcolour_actionPerformed(ActionEvent e)
{
- Color col = JColorChooser.showDialog(this, "Select Background Colour",
+ Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
rc.bgColour);
if (col != null)
{
long progId = System.currentTimeMillis();
IProgressIndicator progress = this;
- String message = "Recalculating PCA";
+ String message = MessageManager.getString("label.pca_recalculating");
if (getParent() == null)
{
progress = ap.alignFrame;
- message = "Calculating PCA";
+ message = MessageManager.getString("label.pca_calculating");
}
progress.setProgressBar(message, progId);
try
if (getParent() == null)
{
addKeyListener(rc);
- Desktop.addInternalFrame(this, "Principal component analysis", 475,
- 450);
+ Desktop.addInternalFrame(this, MessageManager
+ .getString("label.principal_component_analysis"), 475, 450);
}
}
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
+ pcaModel.setScore_matrix("DNA");
Thread worker = new Thread(this);
worker.start();
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
+ pcaModel.setScore_matrix("BLOSUM62");
Thread worker = new Thread(this);
worker.start();
}
try
{
cap.setText(pcaModel.getDetails());
- Desktop.addInternalFrame(cap, "PCA details", 500, 500);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pca_details"), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("opening PCA details", oom);
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.original_data_for_params", new String[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
}
/*
cap.setText(pcaModel.getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
cap.setText(pcaModel.getPointsasCsv(true,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
- 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.transformed_points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
git://source.jalview.org / jalview.git / blobdiff