consensusoptions.java

emboss的linux版本的源代码

/***************************************************************
*
* This program 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 2
* of the License, or (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
*
*  @author: Copyright (C) Tim Carver
*
***************************************************************/

package org.emboss.jemboss.editor;

import javax.swing.*;
import java.awt.Dimension;
import java.awt.Cursor;
import java.awt.event.*;
import org.emboss.jemboss.gui.form.TextFieldFloat;
import org.emboss.jemboss.gui.form.TextFieldInt;
import org.emboss.jemboss.gui.form.LabelTextBox;


/**
*
* Defines the options to be used in calculating a consensus
*
*/
public class ConsensusOptions extends JFrame
{

  /** plurality */
  private TextFieldFloat pluralFloat;
  /** identity */
  private TextFieldInt idInt;
  /** set the case */
  private TextFieldFloat caseFloat;
  /** graphic sequence collection */
  private GraphicSequenceCollection gsc;
  /** scoring matrix */
  private Matrix mat;
  private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
  private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
  private JScrollPane jspSequence; // Sequence scrollpane

  public ConsensusOptions(JScrollPane jspSequence)
  {
    super("Consensus Options");

    Box bdown = Box.createVerticalBox();
    bdown.add(Box.createVerticalStrut(4));

    Box bacross = Box.createHorizontalBox();
    pluralFloat = new TextFieldFloat();
//    pluralFloat.setText("1.0");
    Dimension d = new Dimension(65,30);
    pluralFloat.setPreferredSize(d);
    pluralFloat.setMaximumSize(d);
    bacross.add(pluralFloat);
    LabelTextBox pluralLabel = new LabelTextBox(
                "Minimum positive match score value for there to be a consensus",
                "Set a cut-off for the number of\n"+
                "positive matches below which\n"+
                "there is no consensus.");
    bacross.add(pluralLabel);
    bacross.add(Box.createHorizontalGlue());
    bdown.add(bacross);

    bacross = Box.createHorizontalBox();
    idInt = new TextFieldInt();
    idInt.setText("0");
    idInt.setPreferredSize(d);
    idInt.setMaximumSize(d);
    bacross.add(idInt);
    LabelTextBox  caselLabel = new LabelTextBox(
                "Minimum number of identities for there to be a consensus",
                "The required number of identities\n"+
                "at a site for it to give a consensus\n"+
                "at that position. Therefore, if this\n"+
                "is set to the number of sequences in\n"+
                "the alignment only columns of identities\n"+
                "contribute to the consensus.");
    bacross.add(caselLabel);
    bacross.add(Box.createHorizontalGlue());
    bdown.add(bacross);


    bacross = Box.createHorizontalBox();
    caseFloat = new TextFieldFloat();
//    caseFloat.setText("0.0");
    caseFloat.setPreferredSize(d);
    caseFloat.setMaximumSize(d);
    bacross.add(caseFloat);
    LabelTextBox  idLabel = new LabelTextBox(
          "Threshold positive match score for setting the consensus to upper-case",
          "Sets the threshold for the positive\n"+
          "matches above which the consensus is\n"+
          "in upper-case and below which the\n"+
          "consensus is in lower-case.");
    bacross.add(idLabel);
    bacross.add(Box.createHorizontalGlue());
    bdown.add(bacross);
 
     
    bacross = Box.createHorizontalBox();
    JButton calculate = new JButton("Calculate Consensus");
    calculate.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        setCursor(cbusy);
        gsc.deleteSequence("Consensus");
        Consensus conseq = new Consensus(mat,
                    gsc.getSequenceCollection(),
                    getPlurality(),
                    getCase(),
                    getIdentity());

        int fontSize = gsc.getFontSize();
        gsc.addSequence(conseq.getConsensusSequence(),true,5,fontSize);

        Dimension dpane = gsc.getPanelSize();
        gsc.setPreferredSize(dpane);
        gsc.setNamePanelWidth(gsc.getNameWidth());
//      jspSequence.setViewportView(gsc);
        setCursor(cdone);
      }
    });
    bacross.add(calculate);
    bacross.add(Box.createHorizontalGlue());
    bdown.add(bacross);


// set up a menu bar
    JMenuBar menuBar = new JMenuBar();

// File menu
    JMenu fileMenu = new JMenu("File");
    fileMenu.setMnemonic(KeyEvent.VK_F);

// exit
    fileMenu.add(new JSeparator());
    JMenuItem fileMenuExit = new JMenuItem("Close");
    fileMenuExit.setAccelerator(KeyStroke.getKeyStroke(
              KeyEvent.VK_E, ActionEvent.CTRL_MASK));

    fileMenuExit.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        setVisible(false);
      }
    });
    fileMenu.add(fileMenuExit);
    menuBar.add(fileMenu);
    setJMenuBar(menuBar);
 
    getContentPane().add(bdown);
    pack();
  }


  /**
  *
  * Get the minimum positive match score for a 
  * site to be included in the consensus.
  *
  */ 
  public float getPlurality()
  {
    return Float.parseFloat(pluralFloat.getText());
  }


  /**
  *
  * Get the minimum positive matches for a 
  * site to be made upper case in the consensus.
  *
  */
  public float getCase()
  {
    return Float.parseFloat(caseFloat.getText());
  }


  /**
  *
  * Get the minimum identical matches for a 
  * site to be included in the consensus.
  *
  */
  public int getIdentity()
  {
    return Integer.parseInt(idInt.getText());
  }


  /**
  *
  * Set the minimum positive matches for a
  * site to be made upper case in the consensus.
  * The float is rounded to 2 decimal places.
  *
  */
  protected void setCase(float caseValue)
  {
    caseValue = (Math.round(caseValue*100.f));
    caseFloat.setText(Float.toString(caseValue/100.f));
  }


  /**
  *
  * Set the graphic sequence collection
  *
  */
  protected void setGraphicSequenceCollection(GraphicSequenceCollection gsc)
  {
    this.gsc = gsc;
  }


  /**
  *
  * Set the matrix to use
  *
  */
  protected void setMatrix(Matrix mat)
  {
    this.mat = mat;
  }

   
  /**
  *
  * Set the minimum positive match score for a
  * site to be included in the consensus.
  * The float is rounded to 2 decimal places.
  *
  */
  protected void setPlurality(float plurality)
  {
    plurality = (Math.round(plurality*100.f));
    pluralFloat.setText(Float.toString(plurality/100.f));
  }

}