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(DNA 配列の) クロマトグラムの画像を作成しました。

各ベースコールに番号を付けるにはどうすればよいですか?

写真のピクセル長と塩基数を取得できます。これらを割ると、ベースコール間の平均距離が得られ、各ベースコールがどこに行くかの適切な概算が得られます。

写真の上部に数字 (1 - [塩基数]) を配置するにはどうすればよいですか?

GUI の図とプログラムの外観は次のとおりです。

https://drive.google.com/file/d/0B5nGPfKaY21KVFVsaE9XSHJmWG8/view?usp=sharing

ソースコードは次のとおりです。

[getChrom ボタンが押されると、renderTrace メソッドが実行され、トレースがレンダリングされます。]

public class TraceRender extends javax.swing.JFrame {
public TraceRender() {
    initComponents();
}

/**
 * This method is called from within the constructor to initialize the form.
 * WARNING: Do NOT modify this code. The content of this method is always
 * regenerated by the Form Editor.
 */
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">                          
private void initComponents() {

    fileChooser = new javax.swing.JFileChooser();
    textarea = new javax.swing.JTextField();
    getChrom = new javax.swing.JButton();
    ScrollPane = new javax.swing.JScrollPane();
    Label = new javax.swing.JLabel();
    text = new javax.swing.JTextField();
    Menu = new javax.swing.JMenuBar();
    File = new javax.swing.JMenu();
    Open = new javax.swing.JMenuItem();
    Exit = new javax.swing.JMenuItem();
    Edit = new javax.swing.JMenu();
    Documentation = new javax.swing.JMenu();
    Help = new javax.swing.JMenu();

    fileChooser.setDialogTitle("This is my open dialog");
    fileChooser.setFileFilter(new myCustomFilter());

    setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);

    textarea.setEditable(false);
    textarea.setText("ABSOLUTE PATH");

    getChrom.setText("Execute");
    getChrom.addActionListener(new java.awt.event.ActionListener() {
        public void actionPerformed(java.awt.event.ActionEvent evt) {
            getChromActionPerformed(evt);
        }
    });

    Label.setText("[AVI]-Error.noImageLoaded");
    ScrollPane.setViewportView(Label);

    text.setText("nothing");

    File.setText("FILE");

    Open.setText("Get File");
    Open.addActionListener(new java.awt.event.ActionListener() {
        public void actionPerformed(java.awt.event.ActionEvent evt) {
            OpenActionPerformed(evt);
        }
    });
    File.add(Open);

    Exit.setText("Close Program");
    Exit.addActionListener(new java.awt.event.ActionListener() {
        public void actionPerformed(java.awt.event.ActionEvent evt) {
            ExitActionPerformed(evt);
        }
    });
    File.add(Exit);

    Menu.add(File);

    Edit.setText("EDIT");
    Menu.add(Edit);

    Documentation.setText("DOCUMENTATION");
    Menu.add(Documentation);

    Help.setText("HELP");
    Menu.add(Help);

    setJMenuBar(Menu);

    javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
    getContentPane().setLayout(layout);
    layout.setHorizontalGroup(
        layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
        .addGroup(layout.createSequentialGroup()
            .addContainerGap()
            .addComponent(textarea, javax.swing.GroupLayout.PREFERRED_SIZE, 1005, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 79, Short.MAX_VALUE)
            .addComponent(getChrom, javax.swing.GroupLayout.PREFERRED_SIZE, 291, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addGap(49, 49, 49))
        .addComponent(ScrollPane, javax.swing.GroupLayout.Alignment.TRAILING)
        .addGroup(layout.createSequentialGroup()
            .addGap(33, 33, 33)
            .addComponent(text, javax.swing.GroupLayout.PREFERRED_SIZE, 630, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
    );
    layout.setVerticalGroup(
        layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
        .addGroup(layout.createSequentialGroup()
            .addContainerGap()
            .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                .addComponent(textarea, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addComponent(getChrom))
            .addGap(48, 48, 48)
            .addComponent(ScrollPane, javax.swing.GroupLayout.PREFERRED_SIZE, 265, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addGap(53, 53, 53)
            .addComponent(text, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addContainerGap(113, Short.MAX_VALUE))
    );

    pack();
}// </editor-fold>                        

private void OpenActionPerformed(java.awt.event.ActionEvent evt) {                                     
    // TODO add your handling code here:

    int returnVal = fileChooser.showOpenDialog(this);
    if (returnVal == JFileChooser.APPROVE_OPTION) {
        File file = fileChooser.getSelectedFile();
        textarea.setText(String.valueOf(file.getAbsolutePath()));
    } else {
        System.out.println("File access cancelled by user.");
    }

}                                    

private void ExitActionPerformed(java.awt.event.ActionEvent evt) {                                     
    // TODO add your handling code here:
    System.exit(0);
}                                    

private void getChromActionPerformed(java.awt.event.ActionEvent evt) {                                         
    try {
        // TODO add your handling code here:
        renderTrace();
    } catch (IOException | UnsupportedChromatogramFormatException ex) {
        Logger.getLogger(TraceRender.class.getName()).log(Level.SEVERE, null, ex);
    }
}                                        

private void renderTrace() throws IOException, UnsupportedChromatogramFormatException {
    ABIFChromatogram abiChrom = new ABIFChromatogram();

    File abi = new File(textarea.getText());

    ABITrace abiTrace = new ABITrace(abi);
    ABIFParser abiParse = new ABIFParser(abi);
    ChromatogramFactory chromFactory = new ChromatogramFactory();

    Chromatogram chrom = ChromatogramFactory.create(abi);

    ChromatogramGraphic gfx = new ChromatogramGraphic(chrom);

    gfx.setHeight(240);
    gfx.setHorizontalScale(2.0f);
    // set some options that affect the output
    // turn off filled-in "callboxes"
    gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_A,
            Boolean.FALSE);
    gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_C,
            Boolean.FALSE);
    gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_G,
            Boolean.FALSE);
    gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_T,
            Boolean.FALSE);
    gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER,
            Boolean.TRUE);
    gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS,
            Boolean.TRUE);

    // this option controls whether each trace/callbox/etc is scaled/positioned
    // individually, or whether the scaling is done on all shapes at the level
    // of the graphics context
    // enabling this option is recommended for higher-quality output

    gfx.setOption(ChromatogramGraphic.Option.USE_PER_SHAPE_TRANSFORM,
            Boolean.TRUE);

    BufferedImage bi = new BufferedImage(
            gfx.getWidth(),
            gfx.getHeight(),
            BufferedImage.TYPE_INT_RGB);
    Graphics2D g2 = bi.createGraphics();
    g2.setBackground(Color.white);
    g2.clearRect(0, 0, bi.getWidth(), bi.getHeight());
    if (g2.getClip() == null) {
        g2.setClip(new Rectangle(0, 0, bi.getWidth(), bi.getHeight()));
    }
    g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    // the main event
    gfx.drawTo(g2);
    // work-around an OS X bug where sometimes the last Shape drawn
    // doesn't show up in the output
    g2.draw(new java.awt.Rectangle(-10, -10, 5, 5));

    text.setText(String.valueOf(gfx.getWidth()));
    ImageIcon ii = new ImageIcon(bi);
    Label.setIcon(ii);
    /*
    try {
        ImageIO.write(bi, "png", new File("gfx-image.png"));
    } catch (IOException ex) {
        ex.printStackTrace();
    }
    */


}

/**
 * @param args the command line arguments
 */
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(TraceRender.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(TraceRender.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(TraceRender.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(TraceRender.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    }
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        public void run() {
            new TraceRender().setVisible(true);
        }
    });
}

class myCustomFilter extends javax.swing.filechooser.FileFilter {

    @Override
    public boolean accept(File file) {
        // Allow only directories, or files with ".txt" extension
        return file.isDirectory() || file.getAbsolutePath().endsWith(".ab1");
    }

    @Override
    public String getDescription() {
        // This description will be displayed in the dialog,
        // hard-coded = ugly, should be done via I18N
        return "ABIF Files (*.ab1)";
    }
}


// Variables declaration - do not modify                     
private javax.swing.JMenu Documentation;
private javax.swing.JMenu Edit;
private javax.swing.JMenuItem Exit;
private javax.swing.JMenu File;
private javax.swing.JMenu Help;
private javax.swing.JLabel Label;
private javax.swing.JMenuBar Menu;
private javax.swing.JMenuItem Open;
private javax.swing.JScrollPane ScrollPane;
private javax.swing.JFileChooser fileChooser;
private javax.swing.JButton getChrom;
private javax.swing.JTextField text;
private javax.swing.JTextField textarea;
// End of variables declaration                   
}
4

1 に答える 1

1

私のテストでは、これはうまくいきました（getCallboxBounds()取る整数引数が表示される数値ではなくインデックスであると仮定します）：

g.setColor(Color.BLACK);
for (int i = 9; i < sequenceLength; i += 10) {
    String str = String.valueOf(i + 1);
    g.drawString(str,
            getCallboxBounds(i).getX()
                    + (getCallboxBounds(i).getWidth() - g.getFontMetrics().stringWidth(str)) / 2,
            g.getFontMetrics().getHeight());
}

すべての数値を表示したい場合 ( の数値だけでなく% 10 == 0)、次のように変更します。

for (int i = 9; i < sequenceLength; i += 10) {

に

for (int i = 0; i < sequenceLength; i++) {

それがあなたにとってもうまくいくことを願っています。

于 2016-02-15T00:55:12.507 に答える