uk.ac.babraham.SeqMonk.Filters.GeneSetFilter.GeneSetScatterPlotPanel.java Source code

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Here is the source code for uk.ac.babraham.SeqMonk.Filters.GeneSetFilter.GeneSetScatterPlotPanel.java

Source

/**
 * Copyright 2014-15 Laura Biggins
 *
 *    This file is part of SeqMonk.
 *
 *    SeqMonk 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.
 *
 *    SeqMonk 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 SeqMonk; if not, write to the Free Software
 *    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */
package uk.ac.babraham.SeqMonk.Filters.GeneSetFilter;

import java.awt.Color;
import java.awt.Graphics;

import org.apache.commons.math3.stat.regression.SimpleRegression;

import uk.ac.babraham.SeqMonk.DataTypes.DataStore;
import uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList;
import uk.ac.babraham.SeqMonk.Displays.ScatterPlot.ScatterPlotPanel;

public class GeneSetScatterPlotPanel extends ScatterPlotPanel {

    private static final int X_AXIS_SPACE = 50;
    private static final int Y_AXIS_SPACE = 30;
    private float[][] customRegressionValues = null;
    //   private SimpleRegression simpleRegression;

    public GeneSetScatterPlotPanel(DataStore xStore, DataStore yStore, ProbeList probeList, ProbeList[] subLists,
            boolean commonScale, int dotSize, float[][] customRegressionValues, SimpleRegression simpleRegression) {

        super(xStore, yStore, probeList, subLists, commonScale, dotSize);
        // TODO Auto-generated constructor stub

        this.customRegressionValues = customRegressionValues;
        //      this.simpleRegression = simpleRegression;

    }

    public void paint(Graphics g) {
        super.paint(g);

        if (customRegressionValues != null & readyToDraw) {
            g.setColor(Color.magenta);
            for (int i = 0; i < customRegressionValues[0].length; i++) {

                // some of the points fall off the plotting area
                if ((getX(customRegressionValues[0][i]) > X_AXIS_SPACE)
                        && (getY(customRegressionValues[1][i]) < getHeight() - Y_AXIS_SPACE)) {
                    g.fillOval(getX(customRegressionValues[0][i]), getY(customRegressionValues[1][i]), 3, 3);

                }
            }
        }

        //System.err.println("x for 5.377 = " + getX(5.377) + ", y for 4.761 = " + getY(4.761));

        //if(calculateLinearRegression && (simpleRegression != null)){
        /*      if(simpleRegression != null){
                  
                 int x1;
                 int x2;
                 int y1;
                 int y2;
                     
                 // at intersect of x axis
                 y1 = getY((simpleRegression.getSlope() * (double)(getValueFromX(X_AXIS_SPACE))) + simpleRegression.getIntercept());
                     
                 if(y1 < (getHeight()-Y_AXIS_SPACE)){               
        x1 = X_AXIS_SPACE;
                 }
                     
                 // if y1 is off the screen
                 else{
        y1 = getHeight()-Y_AXIS_SPACE;
            
        x1 = getX(((double)(getValueFromY(y1) - simpleRegression.getIntercept()))/simpleRegression.getSlope());
                 }
                     
                 y2 = getY((simpleRegression.getSlope() * (double)(getValueFromX((getWidth()-10)))) + simpleRegression.getIntercept());  
                     
                 if(y2 <= 10){
        y2 = 10;
        x2 = getX(((double)(getValueFromY(y2) - simpleRegression.getIntercept()))/simpleRegression.getSlope());
                 }
                     
                 else{
        x2 = (getWidth()-10);
                 }
                     
                 g.setColor(Color.BLACK);
                 g.drawLine(x1,y1,x2,y2);
        */

        /*   System.err.println("y intercept = " + simpleRegression.getIntercept() + ", slope = " + simpleRegression.getSlope() + 
           ", x intercept = " + (-(simpleRegression.getIntercept()/simpleRegression.getSlope())));
        */
    }
}