As requested:
GraphPane
/**
* File: GraphPane.java
* Created: Apr 10, 2008, at 10:54:12 PM
*
* Description: See the comments before the class below.
*/
import java.awt.*;
import javax.swing.*;
import java.util.*;
import java.io.*;
/* This class extends teh JPanel class and is
* used primarily to contain the Graphical dot-plot
*/
class GraphPane extends JPanel {
/* These are the attributes required for this class.
* Their primary purpose is to fit the graph to the
* panel.
*/
int scaleWidth = 600;
int scaleHeight = 600;
final int PAD = 20;
Image scaledImage;
DotPlot dp;
String sequence_1 = "";
String sequence_2 = "";
int window;
int threshold;
/* This is the sole constructor for GraphPane. The
* class is populted from these initial parameters.
*
*/
public GraphPane(String sequence_1, String sequence_2, int window, int threshold)
{
this.window = window;
this.threshold = threshold;
this.sequence_1 = sequence_1;
this.sequence_2 = sequence_2;
}
// Paints the graph to a panel
public void paint(Graphics g)
{
DotPlot dp = new DotPlot();
dp = new DotPlot();
dp.readInGenome(this.sequence_1,this.sequence_2,this.window,this.threshold);
dp.setDimensions();
Panel panel = new Panel();
panel.setBackground(new Color(235,235,235));
add(panel);
g.setColor(Color.red);
dp.draw(panel);
scaledImage = dp.img.getScaledInstance(scaleWidth,scaleHeight,0);
g.drawImage(scaledImage,0,0,panel);
}
}
DotPlotUI
/**
* File: DotPlotUI.java
* Created: Apr 10, 2008, at 10:52:47 PM
*
* Description: See the comments before the class below.
*/
import java.awt.*;
import javax.swing.*;
import java.util.*;
import java.io.*;
import java.awt.event.*;
/* This is the main driver for the Dot-Plot program.
* Compilation: javac DotPlotUI.java
* Usage: java DotPlotUI
*
*/
public class DotPlotUI implements ActionListener
{
// the following are the components used to make
// up the application UI
GraphPane graphPane;
JTabbedPane tabbedPane;
TextField tfDirectory = new TextField();
TextField tfFile = new TextField();
TextField tfFilter = new TextField();
FileDialog fd;
JFrame f;
final JButton button1;
final JButton button2;
final JButton button3;
TextArea textArea1;
TextArea textArea2;
JLabel window_label;
JTextField window;
JLabel threshold_label;
JTextField threshold;
TextArea status;
JLabel status_label;
JPanel pre_plot;
/* The is the sole constructionfor the DotPlotUI
* In this constructor all the components are added
* sequentially/
*/
public DotPlotUI()
{
f = new JFrame("Dot-plot Comparative Sequence Analysis");
f.getContentPane().setLayout(null);
f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
GraphicsEnvironment env = GraphicsEnvironment.getLocalGraphicsEnvironment();
Rectangle bounds = env.getMaximumWindowBounds();
button1 = new JButton("Fasta File 1");
button2 = new JButton("Fasta File 2");
button3 = new JButton("Create Dot-plot");
textArea1 = new TextArea("Fasta File 1", 10,10,TextArea.SCROLLBARS_NONE);
textArea2 = new TextArea("Fasta File 2", 10,10,TextArea.SCROLLBARS_NONE);
status = new TextArea("", 10,bounds.width,TextArea.SCROLLBARS_VERTICAL_ONLY);
status.setEditable(false);
window_label = new JLabel("Windows Size");
window = new JTextField(10);
threshold_label = new JLabel("Threshold Size");
threshold = new JTextField(10);
status_label = new JLabel("Process Status/Error Info");
pre_plot = new JPanel();
pre_plot.setBackground(new Color(235,235,235));
f.getContentPane().add(textArea1);
f.getContentPane().add(button1);
f.getContentPane().add(textArea2);
f.getContentPane().add(button2);
f.getContentPane().add(window_label);
f.getContentPane().add(window);
f.getContentPane().add(threshold_label);
f.getContentPane().add(threshold);
f.getContentPane().add(button3);
f.getContentPane().add(status);
f.getContentPane().add(status_label);
f.getContentPane().add(pre_plot);
button1.addActionListener(this);
button2.addActionListener(this);
window.addActionListener(this);
threshold.addActionListener(this);
button3.addActionListener(this);
textArea1.setBounds(10,10,182,150);
Dimension size = button1.getPreferredSize();
button1.setBounds(10,170,size.width,size.height);
textArea2.setBounds(10,180+size.height,182,150);
size = button1.getPreferredSize();
button2.setBounds(10,340+size.height,size.width,size.height);
size = threshold_label.getPreferredSize();
window_label.setBounds(10,420+size.height,size.width,size.height );
window.setBounds(10+size.width+10,420+size.height,size.width,size.height );
threshold_label.setBounds(10,445+size.height,size.width,size.height );
threshold.setBounds(10+size.width+10,445+size.height,size.width,size.height );
size = button3.getPreferredSize();
button3.setBounds(10,485+size.height,size.width+5,size.height+5);
button3.setBackground(new Color(153,153,153));
size = status_label.getPreferredSize();
//status_label.setBounds((int)((bounds.width/2)-(size.width/2)),bounds.height-115,size);
status.setBounds(10,bounds.height-100,bounds.width-30,65);
status.setBackground(new Color(255,255,204));
status.setForeground(Color.red);
pre_plot.setBounds(300,10, 600, 600);
f.setSize((int)bounds.getWidth(),(int)bounds.getHeight());
f.setLocation(0,0);
f.setVisible(true);
}
/* This handles all action events to the Application UI.
* It poulates the Fasta File TextFields, and ultimatley
* produces the dot-plot.
*/
public void actionPerformed(ActionEvent evt)
{
// load the first fasta file
if ((evt.getActionCommand()).equals("Fasta File 1")) {
fd = new FileDialog(f, null, FileDialog.LOAD);
fd.setDirectory(".\\");
}
// load the second fasta file
else if ((evt.getActionCommand()).equals("Fasta File 2"))
{
fd = new FileDialog(f, null, FileDialog.LOAD);
fd.setDirectory(".\\");
}
// display the dot-plot of the previously loaded data
else if ((evt.getActionCommand()).equals("Create Dot-plot"))
{
graphPane = new GraphPane(textArea1.getText(),textArea2.getText(),getWindow(),getWindow());
f.getContentPane().add(graphPane);
graphPane.setBounds(300,10, 600, 600);
// display program status
status.append("Info: Dot-plot sequence analysis diagram created!");
}
// Populate textArea_1 with sequences
if ((evt.getActionCommand()).equals("Fasta File 1"))
{
fd.show();
String sequence = this.readFile(fd.getDirectory()+fd.getFile());
textArea1.replaceRange(sequence,0,textArea1.getText().length());
// display program status
status.append("Info: Fast File 1 sequence data loaded, " + sequence.length()
+ " characters in length.\n");
}
// Populate textArea_2 with sequences
else if((evt.getActionCommand()).equals("Fasta File 2"))
{
fd.show();
String sequence = this.readFile(fd.getDirectory()+fd.getFile());
textArea2.replaceRange(sequence,0,textArea2.getText().length());
// display program status
status.append("Info: Fast File 2 sequence data loaded, " + sequence.length()
+" characters in length.\n");
}
}
/* This method is used to collect the window size in the
* text-fields. If they are empty or erroneous a default value
* of 100 is chosen, and a warning message outputted.
*/
public int getWindow()
{
String win_val = window.getText();
if(win_val.equals("") || win_val == null)
{
status.append("Warning: No window size selected, using default window size of 10");
return 100;
}
win_val.trim();
boolean is_number = true;
for(int i=0; i<win_val.length(); i++)
{
if(Character.isDigit(win_val.charAt(i)) == false)
{
is_number = false;
break;
}
}
if(is_number == false)
{
status.append("Error: The chosen window size is not a number, using default windoow");
return 100;
}
else
{
status.append("Info: Window size set at: " + win_val + ".\n");
return Integer.parseInt(win_val);
}
}
/* This method is used to collect the threshold size in the
* text-fields. If they are empty or erroneous a default value
* of 100 is chosen, and a warning message outputted.
*/
public int getThreshold()
{
String thres_val = window.getText();
if(thres_val.equals("") || thres_val == null)
{
status.append("Warning: No threshold size selected, using default threshold size");
return 100;
}
thres_val.trim();
boolean is_number = true;
for(int i=0; i<thres_val.length(); i++)
{
if(Character.isDigit(thres_val.charAt(i)) == false)
{
is_number = false;
break;
}
}
if(is_number == false)
{
status.append("Error: The chosen threshold size is not a number, using default th?");
return 100;
}
else
{
status.append("Info: Threshold size set at: " + thres_val + ".\n");
return Integer.parseInt(thres_val);
}
}
/* This method reads the genomic sequences from the file
* passed in the argument. The file must be of FASTA formatting.
*/
public String readFile(String file)
{
BufferedReader inFile = null;
String sequence = "";
try{
inFile = new BufferedReader(new FileReader(file));
String str = null;
while((str = inFile.readLine()) != null)
{
if(!str.equals(""))
{
if(str.substring(0,1).equals(">"))
{
while((str = inFile.readLine()) != null && !str.equals(""))
sequence = sequence.concat(str);
}
}
}
}
catch (IOException e)
{
System.out.println("INPUT ERROR: Input file not recognized at DotPlotUI.readFile");
System.exit(1);
}
return sequence;
}
public static void main(String[] args)
{
new DotPlotUI();
}
}
DotPlot
/**
* File: DotPlot.java
* Created: Apr 10, 2008, at 10:51:43 PM
*
* Description: See the comments before the class below.
*/
import java.awt.*;
import javax.swing.*;
import java.util.*;
import java.io.*;
/* Class DotPlot works out the technical aspects of the graph
* by computing the thresholds, window size and where sequences match.
* It is also responsible for drawing the points of the Dot-plot.
*/
class DotPlot
{
// Required attibutes including the Image to be displayed,seq_1, seq_2
// window and threshold vlaues
Image img;
String seq1 = null;
String seq2 = null;
int windowSize = 0;
int threshold = 0;
Vector vecPoints = new Vector();
int index = 0;
int noOfCoors = 0;
int imageWidth = 1000;
int imageHeight = 1000;
int scale = 1000;
// Initialise the classes attributes
public void readInGenome(String seq1, String seq2, int windowSize, int threshold)
{
this.windowSize = windowSize;
this.threshold = threshold;
this.seq1 = seq1;
this.seq2 = seq2;
}
/* Sets up the dimensions for the to be
* displayed image depending on whether the sequence
* is longer, shoter or equla to the default image dimensions
*/
public void setDimensions()
{
if(seq1.length() == seq2.length())//Both seqs same length
{
if(seq1.length() > scale)//Both greater than scale
{
imageWidth = scale;
imageHeight = scale;
}
else//Both less than scale
{
imageWidth = seq1.length();
imageHeight = seq2.length();
}
}
else//Different sized seqs
{
if(seq1.length() < scale && seq2.length() < scale)//seq_1 = seq_2
{
imageWidth = seq1.length();
imageHeight = seq2.length();
}
else if(seq1.length() > seq2.length())//seq_1 > seq_2
{
imageWidth = scale;
float fHeight = (float) ( (float)seq2.length()/(float)seq1.length() ) * (float)10;
imageHeight = (int) fHeight;
}
else if(seq2.length() > seq1.length())//seq_2 > seq_1
{
imageHeight = scale;
float fWidth = (float) ( (float)seq1.length()/(float)seq2.length() ) * (float)10;
imageWidth = (int) fWidth;
}
}
}
/* Calculates if the sequential seegment starting
* at 'a' and ending at 'b' meeets the current
* threshold
*/
public boolean satisfiesThreshold(int a, int b)
{
int outCount = 0;
int matchCount = 0;
for(int d=1; d<=windowSize; d++)
{
if(inBounds(a-d,b-d))
{
if(isMatch(a-d,b-d))
matchCount++;
}
else
outCount++;
if(inBounds(a+d,b+d))
{
if(isMatch(a+d,b+d))
matchCount++;
}
else
outCount++;
}
if(matchCount >= threshold)
return true;
else
return false;
}
/* Check if the base indexes match
* True or False is returned.
*/
public boolean isMatch(int a, int b)
{
String base1 = seq1.substring(a,a+1);
String base2 = seq2.substring(b,b+1);
if(base1.equals(base2))
return true;
else return false;
}
/* This makes sure we don't run over bounds with our
* windowing.
* True or False is returned.
*/
public boolean inBounds(int a, int b)
{
if(a < 0 || b < 0 || a > seq1.length()-1 || b > seq2.length()-1)
return false;
else return true;
}
/* Uses java.Grphics to draw the points
* tothe screen using the fore-mentioned
* integers a and b
*/
public void drawPoint(int a, int b, Graphics g)
{
int xcoor = 0;
int ycoor = 0;
if(seq1.length() > imageWidth)
{
float xx = (float) ( (float)a/(float)seq1.length() * (float)imageWidth );
xcoor = (int) xx;
}
else
xcoor = a;
if(seq2.length() > imageHeight)
{
float yy = (float) ( (float)b/(float)seq2.length() * (float)imageHeight );
ycoor = (int)yy;
}
else
ycoor = b;
g.drawLine(xcoor,ycoor,xcoor,ycoor);
}
/* Uses java.Graphics to set the points
* for the Gragh. this is somewhat of a culmination
* of methods.
*/
public void setUpPoints(Graphics g)
{
String base1 = null;
String base2 = null;
for(int i=0; i<seq1.length(); i++)
{
for(int j=0; j<seq2.length(); j++)
{
base1 = seq1.substring(i,i+1);
base2 = seq2.substring(j,j+1);
if(base1.equals(base2))
{
if(satisfiesThreshold(i,j))
drawPoint(i,j,g);
}
}
}
}
public void draw(Component c)
{
img = c.createImage(imageWidth,imageHeight);
Graphics g = img.getGraphics();
g.setColor(new Color(38,0,133));
setUpPoints(g);
}
}
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