org.csml.tommo.sugar.modules.heatmap.MappingQualityDialog.java Source code

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Here is the source code for org.csml.tommo.sugar.modules.heatmap.MappingQualityDialog.java

Source

/**
 *    Copyright Masao Nagasaki
 *    Nagasaki Lab
 *    Laboratory of Biomedical Information Analysis,
 *    Department of Integrative Genomics,
 *    Tohoku Medical Megabank Organization, Tohoku University 
 *    @since 2013
 *
 *    This file is part of SUGAR (Subtile-based GUI-Assisted Refiner).
 *    SUGAR is an extension of FastQC (copyright 2010-12 Simon Andrews)
 *
 *    FastQC 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.
 *
 *    FastQC 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 FastQC; if not, write to the Free Software
 *    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */
package org.csml.tommo.sugar.modules.heatmap;

import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.util.List;

import javax.swing.JDialog;
import javax.swing.JLabel;
import javax.swing.JPanel;

import org.csml.tommo.sugar.SugarApplication;
import org.csml.tommo.sugar.heatmap.MappingQualityMatrix;
import org.csml.tommo.sugar.heatmap.MappingQualityMatrixChart;
import org.csml.tommo.sugar.modules.MappingQuality;
import org.csml.tommo.sugar.sequence.TileCoordinates;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.renderer.PaintScale;

public class MappingQualityDialog extends JDialog {

    /**
     * 
     */
    private static final long serialVersionUID = 7755493135986780444L;

    protected JPanel centerPanel;
    protected int row;
    protected int col;
    protected MappingQualityTable table;

    public MappingQualityDialog(int row, int col, MappingQualityTable table) {
        super(SugarApplication.getApplication());
        initData(row, col, table);

        List<TileCoordinates> tileCoordinateList = table.getTileCoordinateList(row, col);
        int colSpan = col == table.getColumnCount() - 1 ? 1 : 2;
        int rowSpan = tileCoordinateList.size() / colSpan;
        centerPanel = new JPanel(new GridLayout(rowSpan, colSpan));
        setLayout(new BorderLayout());
        rebuild();
        add(centerPanel, BorderLayout.CENTER);
        setLocation(400, 350);
        setSize(250 * colSpan, 250 * rowSpan);
    }

    protected void initData(int row, int col, MappingQualityTable table) {
        this.row = row;
        this.col = col;
        this.table = table;
    }

    protected void rebuild() {
        centerPanel.removeAll();
        List<TileCoordinates> tileCoordinateList = table.getTileCoordinateList(row, col);
        MappingQuality mappingQuality = table.getModel().getMappingQuality();
        PaintScale paintScale = MappingQualityCellRenderer.getAveragePaintScale();
        for (int i = 0; i < tileCoordinateList.size(); i++) {
            TileCoordinates tc = tileCoordinateList.get(i);
            MappingQualityMatrix matrix = mappingQuality.getMeanQualityMatrix(tc);

            if (matrix != null) {
                ChartPanel panel = MappingQualityMatrixChart.createChartPanel(matrix, paintScale);
                panel.setToolTipText("tile=" + tc.getTile());
                centerPanel.add(panel);
            } else {
                centerPanel.add(new JLabel("Missing data for tile=" + tc.getTile()));
            }
        }

        TileCoordinates first = tileCoordinateList.get(0);
        String windowTitle = "Average MAPQ for tile=" + first.getTile() + " and neighbors";
        setTitle(windowTitle);

        centerPanel.revalidate();
        centerPanel.repaint();
    }
}