Image displayed by child window captured by parent window.
This is a rather peculiar problem.
My application starts with a JFrame which takes some file as an input and then open another window and plot the graph.What happens is whatever is drawn on the child window(graph) is captured by the parent window which looks quite odd.Could anyone help me out the how to solve this problem??
sure... here are the codes......
//parent window:
package igib.genebrowser;
import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import igib.genebrowser.menu.*;
import igib.genebrowser.plot.*;
public class GeneBrowserMain extends JFrame
public GeneBrowserMain()
super("GenomeBrowser-1.0");
Container cp = this.getContentPane();
cp.setLayout(new BorderLayout());
DrawFeature df = new DrawFeature();
cp.add(df, BorderLayout.CENTER);
public static void main(String args[])
Point p = new Point(400,300);
GeneBrowserMain gbm = new GeneBrowserMain();
GeneBrowserMenu menu = new GeneBrowserMenu();
gbm.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
gbm.setSize(300,200);
gbm.setLocation(p);
gbm.setJMenuBar(menu);
gbm.setResizable(false);
gbm.setVisible(true);
//GeneBrowserMenu file
package igib.genebrowser.menu;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import igib.genebrowser.plot.*;
import igib.genebrowser.menu.*;
import igib.genebrowser.*;
public class GeneBrowserMenu extends JMenuBar implements ActionListener
JMenu fileMenu;
JMenuItem open;
JMenuItem quit;
GeneBrowserMain gbm;
public GeneBrowserMenu()
this.gbm = gbm;
fileMenu = new JMenu("File");
this.add(fileMenu);
open = new JMenuItem("open");
fileMenu.add(open);
quit = new JMenuItem("quit");
fileMenu.add(quit);
open.addActionListener(this);
quit.addActionListener(this);
public void actionPerformed(ActionEvent e)
if(e.getSource() == open)
try
Point p = new Point(300,200);
FileOpenWindow f = new FileOpenWindow();
f.setSize(450,250);
f.setLocation(p);
f.setVisible(true);
catch(Exception ex)
if(e.getSource() == quit)
System.exit(1);
//FileOpenWindow which takes file as input and opens GBMainFrame and plot graphs
package igib.genebrowser.menu;
import javax.swing.*;
import javax.swing.border.*;
import java.awt.event.*;
import java.awt.*;
import javax.swing.colorchooser.*;
import javax.swing.tree.*;
import javax.swing.event.*;
import javax.swing.filechooser.*;
import java.io.FileWriter;
import java.io.BufferedReader.*;
import java.io.File;
import igib.genebrowser.util.*;
import igib.genebrowser.plot.*;
import igib.genebrowser.*;
//import java.io.*;
public class FileOpenWindow extends JFrame implements ActionListener, ItemListener
public JTabbedPane tPane ;
public File seqFile, repeatFile, snpFile, geneFile;
JLabel sequenceFile, repeatfile, snpfile, genefile, jb, winsize, shiftsize;
JButton browse1, browse2, ok1, ok2, browse3, browse4, browse5, browse6;
JTextField jtf1, jtf2, jtf3, jtf4, jtf5, jtf6;
File f;
PlotGraph pg;
GBMainFrame gb;
GeneBrowserMain gbm;
JComboBox shiftSize, winSize;
public FileOpenWindow()
super("Open File");
ImageIcon icon = new ImageIcon("images/middle.gif");
Container cp = this.getContentPane();
tPane = new JTabbedPane();
JPanel jp1 = addNCBI();
JPanel jp2 = addOther();
tPane.addTab("NCBI", icon, jp1);
tPane.setSelectedIndex(0);
tPane.addTab("Other", icon, jp2);
tPane.setSelectedIndex(0);
//tPane.add(jp1);
cp.add(tPane,BorderLayout.CENTER);
this.setResizable(false);
private JPanel addNCBI()
JPanel cp = new JPanel();
cp.setLayout(new GridLayout(8,5));
//***********************1st row*************************************************//
for(int i = 0; i < 5; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************1st row*************************************************//
//***********************2nd row*************************************************//
for(int i = 0; i < 5; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************2nd row*************************************************//
//***********************3rd row*************************************************//
jb = new JLabel(" Sequence");
cp.add(jb);
sequenceFile = new JLabel(" File :");
cp.add(sequenceFile);
browse1 = new JButton("browse");
cp.add(browse1);
jtf1 = new JTextField(" ");
cp.add(jtf1);
jb = new JLabel(" ");
cp.add(jb);
//***********************3rd row*************************************************//
//***********************4th row*************************************************//
jb = new JLabel(" Repeat");
cp.add(jb);
repeatfile = new JLabel(" File :");
cp.add(repeatfile);
browse2 = new JButton("browse");
cp.add(browse2);
jtf2 = new JTextField(" ");
cp.add(jtf2);
jb = new JLabel(" ");
cp.add(jb);
//***********************4th row*************************************************//
//***********************5th row*************************************************//
for(int i = 0; i < 5; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************5th row*************************************************//
//***********************1st row*************************************************//
winsize = new JLabel("Window Size: ");
cp.add(winsize);
winSize = new JComboBox();
winSize.addItem("100");
winSize.addItem("500");
winSize.addItem("1000");
winSize.addItem("5000");
cp.add(winSize);
jb = new JLabel(" ");
cp.add(jb);
shiftsize = new JLabel("Shift Size: ");
cp.add(shiftsize);
shiftSize = new JComboBox();
shiftSize.addItem("25");
shiftSize.addItem("50");
shiftSize.addItem("100");
shiftSize.addItem("500");
cp.add(shiftSize);
//***********************1st row*************************************************//
//***********************5th row*************************************************//
for(int i = 0; i < 5; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************5th row*************************************************//
//***********************6th row*************************************************//
for(int i = 0; i < 2; i++)
jb = new JLabel(" ");
cp.add(jb);
ok1 = new JButton("OK");
cp.add(ok1);
for(int i = 0; i < 2; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************6th row*************************************************//
browse1.addActionListener(this);
browse2.addActionListener(this);
ok1.addActionListener(this);
shiftSize.addItemListener(this);
winSize.addItemListener(this);
return cp;
private JPanel addOther()
JPanel cp = new JPanel();
cp.setLayout(new GridLayout(9,5));
//***********************1st row*************************************************//
for(int i = 0; i < 5; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************1st row*************************************************//
//***********************2nd row*************************************************//
jb = new JLabel(" ");
cp.add(jb);
sequenceFile = new JLabel("sequenceFile :");
cp.add(sequenceFile);
browse3 = new JButton("browse");
cp.add(browse3);
jtf3 = new JTextField(" ");
cp.add(jtf3);
jb = new JLabel(" ");
cp.add(jb);
//***********************2nd row*************************************************//
//***********************3rd row*************************************************//
jb = new JLabel(" ");
cp.add(jb);
repeatfile = new JLabel("RepeatFile :");
cp.add(repeatfile);
browse4 = new JButton("browse");
cp.add(browse4);
jtf4 = new JTextField(" ");
cp.add(jtf4);
jb = new JLabel(" ");
cp.add(jb);
//***********************3rd row*************************************************//
//***********************4th row*************************************************//
jb = new JLabel(" ");
cp.add(jb);
snpfile = new JLabel("SNP File :");
cp.add(snpfile);
browse5 = new JButton("browse");
cp.add(browse5);
jtf5 = new JTextField(" ");
cp.add(jtf5);
jb = new JLabel(" ");
cp.add(jb);
//***********************4th row*************************************************//
//***********************5th row*************************************************//
jb = new JLabel(" ");
cp.add(jb);
genefile = new JLabel("Gene File :");
cp.add(genefile);
browse6 = new JButton("browse");
cp.add(browse6);
jtf6 = new JTextField(" ");
cp.add(jtf6);
jb = new JLabel(" ");
cp.add(jb);
//***********************5th row*************************************************//
//***********************6th row*************************************************//
for(int i = 0; i < 5; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************6th row*************************************************//
//***********************1st row*************************************************//
winsize = new JLabel("Window Size: ");
cp.add(winsize);
winSize = new JComboBox();
winSize.addItem("100");
winSize.addItem("500");
winSize.addItem("1000");
winSize.addItem("5000");
cp.add(winSize);
jb = new JLabel(" ");
cp.add(jb);
shiftsize = new JLabel("Shift Size: ");
cp.add(shiftsize);
shiftSize = new JComboBox();
shiftSize.addItem("25");
shiftSize.addItem("50");
shiftSize.addItem("100");
shiftSize.addItem("500");
cp.add(shiftSize);
//***********************1st row*************************************************//
//***********************6th row*************************************************//
for(int i = 0; i < 5; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************6th row*************************************************//
//***********************7th row*************************************************//
for(int i = 0; i < 2; i++)
jb = new JLabel(" ");
cp.add(jb);
ok2 = new JButton("OK");
cp.add(ok2);
for(int i = 0; i < 2; i++)
jb = new JLabel(" ");
cp.add(jb);
//***********************7th row*************************************************//
browse3.addActionListener(this);
browse4.addActionListener(this);
browse5.addActionListener(this);
browse6.addActionListener(this);
ok2.addActionListener(this);
return cp;
public void actionPerformed(ActionEvent e)
if(e.getSource()==ok1)
String ncbi = "";
String repeat= "";
try
ncbi = jtf1.getText();
repeat = jtf2.getText();
System.out.println("NCBI" + ncbi + "www");
if( ncbi.equals(" ") && repeat.equals(" "))
System.out.println("NCBI333" + ncbi);
DisplayInfo di = new DisplayInfo("Sorry!, Please select some file", "");
di.setSize(450,100);
di.setLocation(600,600);
di.setVisible(true);
GBFileProp.snpFile = "";
GBFileProp.geneFile = "";
return;
catch(Exception ex)
GBFileProp.fileFormat="NCBI";
GBFileProp.fileName = ncbi;
GBFileProp.repeatFile = repeat;
ReadNCBI readFile1 = new ReadNCBI(ncbi);
ReadRepeatFile rrf = new ReadRepeatFile(repeat);
try
gb = new GBMainFrame();
gb.setSize(1200,750);
catch(Exception ex)
DisplayInfo di = new DisplayInfo("Sorry!, Wrong File", "Enter file in \".gbk\" format");
di.setSize(450,100);
di.setLocation(600,600);
di.setVisible(true);
setVisible(false);
setDefaultCloseOperation(DISPOSE_ON_CLOSE);
if(e.getSource()==ok2)
String sequence= "";
String repeat= "";
String snp= "";
String gene= "";
try
sequence = jtf3.getText();
repeat = jtf4.getText();
snp = jtf5.getText();
gene = jtf6.getText();
if( sequence.equals(" ") && repeat.equals(" ") && snp.equals(" ") && gene.equals(" "))
DisplayInfo di = new DisplayInfo("Sorry!, Please select some file", "");
di.setSize(450,100);
di.setLocation(600,600);
di.setVisible(true);
System.out.println("File " + GBFileProp.repeatFile);
return;
catch(Exception ex)
GBFileProp.fileFormat="Other";
GBFileProp.fileName = sequence;
GBFileProp.repeatFile = repeat;
GBFileProp.snpFile = snp;
GBFileProp.geneFile = gene;
ReadGeneFile a = new ReadGeneFile(gene);
ReadSNPFile rsp = new ReadSNPFile(snp);
GCReadFile grf = new GCReadFile(sequence);
ReadRepeatFile rrf = new ReadRepeatFile(repeat);
try
gb = new GBMainFrame();
gb.setSize(1200,800);
catch(Exception ex)
DisplayInfo di = new DisplayInfo("Sorry!, Wrong File", "Enter file in corresponding format");
di.setSize(450,100);
di.setLocation(600,600);
di.setVisible(true);
setVisible(false);
setDefaultCloseOperation(DISPOSE_ON_CLOSE);
if(e.getSource()==browse1)
String w;
Fselect(1);
try
w=f.toString();
jtf1.setText(w);
catch(Exception ex)
if(e.getSource()==browse2)
String w;
Fselect(4);
try
w=f.toString();
jtf2.setText(w);
catch(Exception ex)
if(e.getSource()==browse3)
String w;
Fselect(3);
try
w=f.toString();
jtf3.setText(w);
catch(Exception ex)
if(e.getSource()==browse4)
String w;
Fselect(2);
try
w=f.toString();
jtf4.setText(w);
catch(Exception ex)
if(e.getSource()==browse5)
String w;
Fselect(4);
try
w=f.toString();
jtf5.setText(w);
catch(Exception ex)
if(e.getSource()==browse6)
String w;
Fselect(2);
try
w=f.toString();
jtf6.setText(w);
catch(Exception ex)
if(e.getActionCommand().equals("sequence_ncbi"))
final JFileChooser chooser = new JFileChooser();
FileFilter type1 = new ExtensionFilter ("Fasta File(.faa)", new String[] {".faa",".txt"});
chooser.addChoosableFileFilter (type1);
chooser.setFileFilter (type1);
int returnVal = chooser.showOpenDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION)
seqFile = chooser.getSelectedFile();
else if(e.getActionCommand().equals("sequence_other"))
final JFileChooser chooser = new JFileChooser();
FileFilter type1 = new ExtensionFilter ("Fasta File(.faa)", new String[] {".faa",".txt"});
chooser.addChoosableFileFilter (type1);
chooser.setFileFilter (type1);
int returnVal = chooser.showOpenDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION)
seqFile = chooser.getSelectedFile();
public void itemStateChanged (ItemEvent e)
GBFileProp.windowsize = (int)Integer.parseInt(winSize.getSelectedItem().toString());
GBFileProp.shiftsize = (int)Integer.parseInt(shiftSize.getSelectedItem().toString());
public void Fselect(int sel)
final JFileChooser chooser = new JFileChooser();
ImageIcon openIcon = new ImageIcon("images/open.gif");
FileFilter type1 = new ExtensionFilter ("NCBI File(.gbk)", new String[] {".gbk",".txt"});
FileFilter type2 = new ExtensionFilter ("ptt File(.ptt)", new String[] {".ptt",".txt"});
FileFilter type3 = new ExtensionFilter ("Fasta File(.faa)", new String[] {".faa",".txt"});
FileFilter type4 = new ExtensionFilter ("Text File(.txt)", new String[] {".txt",".txt"});
chooser.setCurrentDirectory (new File (System.getProperty ("user.dir")));
if(sel == 1)
chooser.addChoosableFileFilter (type1);
chooser.setFileFilter (type1);
if(sel == 2)
chooser.addChoosableFileFilter (type2);
chooser.setFileFilter (type2);
if(sel == 3)
chooser.addChoosableFileFilter (type3);
chooser.setFileFilter (type3);
if(sel == 4)
chooser.addChoosableFileFilter (type4);
chooser.setFileFilter (type4);
int returnVal = chooser.showOpenDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION)
f = chooser.getSelectedFile();
//System.out.println("path of open "+ f);
//GBMainFrame file
package igib.genebrowser;
import javax.swing.*;
import java.awt.event.*;
import java.awt.*;
import igib.genebrowser.menu.*;
import igib.genebrowser.plot.*;
import igib.genebrowser.util.*;
public class GBMainFrame extends JFrame
GBMainMenu gb;
PlotGraph pg;
JPanel jf = new JPanel();
JPanel jf1;
LineGraph lg, lg1;
JPanel jp1, jp2;
JLabel jl;
public GBMainFrame()
super("File: " + GBFileProp.fileName + " " + GBFileProp.repeatFile + " " + GBFileProp.snpFile + " " + GBFileProp.geneFile);
Container cp = this.getContentPane();
cp.setLayout(new BorderLayout());
cp.setSize(1024,600);
Color c1=new Color(255,100,100);
jf = new JPanel(new GridLayout(1,15));
cp.add(jf, BorderLayout.NORTH);
pg = new PlotGraph();
pg.setBackground(Color.white);
cp.add(pg, BorderLayout.CENTER);
GBFileProp.jsb.setUnitIncrement(5);
cp.add(GBFileProp.jsb, BorderLayout.SOUTH);
lg1 = new LineGraph();
lg1.setBackground(Color.white);
lg1.setSize(50, 1000);
cp.add(lg1, BorderLayout.EAST);
lg = new LineGraph();
lg.setBackground(Color.white);
cp.add(lg, BorderLayout.WEST);
gb = new GBMainMenu();
jf.add(gb);
setVisible(true);
repaint();
//PlotGraph File
package igib.genebrowser.plot;
import javax.swing.*;
import java.awt.event.*;
import java.awt.*;
import java.util.*;
import java.awt.image.*;
import java.io.*;
//import Acme.JPM.Encoders.*;
//import Acme.*;
import java.awt.print.*;
import java.awt.Component;
import java.awt.print.PrinterJob;
import igib.genebrowser.menu.*;
import igib.genebrowser.util.*;
import igib.genebrowser.*;
public class PlotGraph extends JPanel implements MouseListener,MouseMotionListener
int xcoordinate;
JScrollBar scrollBar;
int mouseX;
int mouseY;
String st1 = " ";
JScrollPane jsp;
int check;
int n;
double base;
int value;
String repeatSymbol = "!";
int position[] = new int[1500];
public PlotGraph(String st)
check = 0;
GBFileProp.check = false;
setVisible(true);
ToolTipManager.sharedInstance().setInitialDelay(0);
addMouseListener(this);
addMouseMotionListener(this);
public PlotGraph()
check = 0;
//System.out.println(GBFileProp.gcmax + "max y");
if(GBFileProp.genescore>5)
GBFileProp.filesize = GBFileProp.readGeneEnd[GBFileProp.genescore - 6];
//System.out.println(GBFileProp.seqscore + " GBFileProp.seqscore");
if(GBFileProp.filesize < GBFileProp.seqscore)
GBFileProp.filesize = GBFileProp.seqscore;
if(GBFileProp.snpscore>5)
if(GBFileProp.filesize < GBFileProp.readSNPPosition[GBFileProp.snpscore-6])
GBFileProp.filesize = GBFileProp.readSNPPosition[GBFileProp.snpscore-6];
if(GBFileProp.repeatscore>2)
if(GBFileProp.filesize < GBFileProp.endRepeatPosition[GBFileProp.repeatscore-2])
GBFileProp.filesize = GBFileProp.endRepeatPosition[GBFileProp.repeatscore-2];
GBFileProp.scrollsize = (int)GBFileProp.filesize/285;
GBFileProp.check = true;
setVisible(true);
addMouseListener(this);
addMouseMotionListener(this);
try
AdjustmentListener lst = new AdjustmentListener()
public void adjustmentValueChanged(AdjustmentEvent e)
int i = e.getValue();
value = i;
GBFileProp.defaultStartCoordinate = (int)(e.getValue()*10*base);
GBFileProp.defaultEndCoordinate = GBFileProp.defaultStartCoordinate + (int)(10000*base);
repaint();
GBFileProp.jsb.addAdjustmentListener(lst);
catch(Exception e)
System.out.println("error here" + e);
//******************** For Painting all the graph**********************************//
public void paintComponent(final Graphics g)
super.paintComponent(g);
Font f = new Font("Times-Roman", Font.PLAIN, 16);
g.setFont(f);
GBFileProp.scrollsize = (int)GBFileProp.filesize/285;
base = (double)(100.0/GBFileProp.zoomSize);
n = (int)(GBFileProp.filesize/base);
GBFileProp.jsb.setMaximum(n/10);
if(GBFileProp.checkSave)
GBFileProp.checkSave = false;
Image img = this.createImage(1200,800);
Graphics gph = img.getGraphics();
this.paint(gph);
try
OutputStream os = new FileOutputStream(GBFileProp.save);
GifEncoderTest ge = new GifEncoderTest(img,os);
ge.encode();
os.close();
catch(Exception e){}
if(GBFileProp.checkPrint)
try
GBFileProp.checkPrint = false;
RepaintManager.currentManager(this).setDoubleBufferingEnabled(false);
PrinterJob pj=PrinterJob.getPrinterJob();
pj.printDialog();
pj.print();
catch (Exception PrintException)
System.out.println("print error" + PrintException);
GBFileProp.checkPrint = false;
if(SetVisibleClass.isMerge)
GBFileProp.snpposition = 500;
GBFileProp.geneposition = 500;
GBFileProp.repeatposition = 500;
GBFileProp.userdefinedpoint = 500;
else
GBFileProp.snpposition = 450;
GBFileProp.geneposition = 400;
GBFileProp.repeatposition = 150;
GBFileProp.userdefinedpoint = 500;
if(GBFileProp.check)
try
if(SetVisibleClass.isSNP)
drawSNPPage(g);
catch(Exception e)
System.out.println("Error in snp plotting");
try
drawGenePage(g);
catch(Exception e)
System.out.println("Error in gene plotting");
try
if(SetVisibleClass.isGC)
drawGCPage(g);
catch(Exception e)
//System.out.println("Error in GC plotting");
try
drawUserDefinedPage(g);
catch(Exception e)
System.out.println("Error in User Defined plotting");
try
if(SetVisibleClass.isRepeat)
drawRepeatPage(g);
catch(Exception e)
System.out.println("Error in Repeat plotting");
//******************** For Painting all the graph**********************************//
//***************************** For Painting Gene**********************************//
public void drawGenePage(Graphics g1)
Graphics2D g = (Graphics2D)g1;
g1.setColor(Color.darkGray);
g.drawLine(0,650,(int)10000,650);
//g1.setColor(Color.b);
BasicStroke pen = new BasicStroke(3.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
g.setStroke(pen);
//****************************** X coordinate *************************************//
for(int i = 0; i < 10000; )
int xcor = (GBFileProp.defaultStartCoordinate + (int)(i*base));
String xCoordinate = "" + xcor;
g.drawLine((int)(i/10),645,(int)(i/10),655);
g.drawString(xCoordinate,(int)(i/10),665);
i = i + 1000; //+ (int)(1000/base);
//****************************** X coordinate *************************************//
if(SetVisibleClass.isGene)
g1.setColor(Color.darkGray);
g1.drawString("Gene:", 10, (GBFileProp.geneposition - 25));
g1.setColor(GBColorSymbol.cGene);
for (int i = 0; i < GBFileProp.genescore ; i++) // - 5 to b subtracted from genescore
int basestart = (int)((GBFileProp.readGeneStart[i] - (int)(GBFileProp.defaultStartCoordinate))/base); ///10;
int baseend = (int)((GBFileProp.readGeneEnd[i] - (int)(GBFileProp.defaultStartCoordinate))/base);
if(basestart >=0 && baseend <=(int)(10000))
checkGenePosition(i);
g.drawLine((int)((basestart/10)),GBFileProp.geneposition,(int)((baseend/10)),GBFileProp.geneposition);
arrow(true,true,i, g, basestart, baseend);
if(basestart >=0 && baseend > (int)(10000))
checkGenePosition(i);
g.drawLine(basestart/10,GBFileProp.geneposition,1000,GBFileProp.geneposition);
arrow(true,false,i, g, basestart, 10000);
if(basestart < 0 && baseend <= (int)(10000))
checkGenePosition(i);
g.drawLine(0,GBFileProp.geneposition,baseend/10,GBFileProp.geneposition);
arrow(false,true,i, g, 0, baseend);
if(basestart < 0 && baseend > (int)(10000))
checkGenePosition(i);
g.drawLine(0,GBFileProp.geneposition,1000,GBFileProp.geneposition);
//System.out.println("GeneSt: " + GBFileProp.readGeneStart[i] + " GeneEd: " + GBFileProp.readGeneEnd[i] + " No " + i + "GeneScore " + GBFileProp.genescore);
//*****************************End For Painting Gene**********************************//
//*****************************Start For Painting snp**********************************//
public void drawSNPPage(Graphics g1)
//System.out.println(GBFileProp.snpscore + "for snp");
Graphics2D g = (Graphics2D) g1;
BasicStroke pen = new BasicStroke();
g.setStroke(pen);
//g.setColor(Color.Red);
g.drawString("SNP", 20, GBFileProp.snpposition);
g.setColor(GBColorSymbol.cSnp);
for(int i = 0; i < GBFileProp.snpscore; i++)
int basePosition = (int)((GBFileProp.readSNPPosition[i] - GBFileProp.defaultStartCoordinate)/base);
//System.out.println(" position " + (basePosition/10));
//g.drawString("|",(basePosition/10),GBFileProp.snpposition);
g.drawString(GBColorSymbol.snpSymValues[GBColorSymbol.snpSym],(basePosition/10),GBFileProp.snpposition);
//Line SNP score
//System.out.println(GBFileProp.snplinescore);
for(int i = 0; i < GBFileProp.snplinescore-1; i++)
int basePosition = (int)((GBFileProp.readSNPStartPosition[i] - GBFileProp.defaultStartCoordinate)/base);
//g.drawString("|",(basePosition/10),GBFileProp.snpposition);
g.drawString(GBColorSymbol.snpSymValues[GBColorSymbol.snpSym],(basePosition/10),GBFileProp.snpposition);
for(int i = 0; i < GBFileProp.snplinescore-1; i++)
int basestart = (int)((GBFileProp.readSNPStartPosition[i] - (int)(GBFileProp.defaultStartCoordinate))/base); ///10;
int baseend = (int)((GBFileProp.readSNPEndPosition[i] - (int)(GBFileProp.defaultEndCoordinate))/base);
System.out.println(basestart + " " + baseend);
if(basestart >=0 && baseend <=(int)(10000))
g.drawLine((int)((basestart/10)),GBFileProp.snpposition,(int)((baseend/10)),GBFileProp.snpposition);
if(basestart >=0 && baseend >(int)(10000))
g.drawLine((int)((basestart/10)),GBFileProp.snpposition,(int)((1000)),GBFileProp.snpposition);
if(basestart < 0 && baseend <=(int)(10000))
g.drawLine((int)((0)),GBFileProp.snpposition,(int)((baseend/10)),GBFileProp.snpposition);
if(basestart < 0 && baseend > (int)(10000))
g.drawLine((int)((0)),GBFileProp.snpposition,(int)((1000)),GBFileProp.snpposition);
//*****************************Start For Painting GCPlotting**********************************//
public void drawGCPage(Graphics g1)
Graphics2D g = (Graphics2D) g1;
g1.setColor(Color.darkGray);
g.drawString("GC Percentage", 20, 20);
BasicStroke pen = new BasicStroke();
g.setStroke(pen);
g1.setColor(Color.black);
//System.out.println(GBFileProp.seqscore + " score");
for(int i = 0; i < (int)((10000)*base); )
//System.out.println(GBFileProp.defaultEndCoordinate + " " i" " + GBFileProp.defaultStartCoordinate);
//System.out.println(GBFileProp.gcposition);
int firstPosition = (int)GBFileProp.GCPercentage[(int)((((int)(i) + GBFileProp.defaultStartCoordinate)/GBFileProp.shiftsize))] * (3*100)/GBFileProp.gcmax;
int secondPosition = (int)GBFileProp.GCPercentage[(int)((((int)((i+GBFileProp.shiftsize)) + GBFileProp.defaultStartCoordinate)/GBFileProp.shiftsize))] * (3*100)/(GBFileProp.gcmax);
g.drawLine((int)((i/10)/base), GBFileProp.gcposition - firstPosition, (int)(((i+GBFileProp.shiftsize)/10)/base), GBFileProp.gcposition - secondPosition);
i = i + GBFileProp.shiftsize;
for(int i = 0; i < GBFileProp.seqscore -1; i++)
int firstPosition = (int)Integer.parseInt(GBFileProp.GCPoint.elementAt(i).toString()) * 3;
int secondPosition = (int)Integer.parseInt(GBFileProp.GCPoint.elementAt(i+50).toString()) * 3;
//int secondPosition = (int)GBFileProp.GCPercentage[i+50] * 3;
//g.drawString("|",basePosition,300);
g.drawLine((int)(i/10), 300 - firstPosition, (int)(i+50)/10, 300 - secondPosition);
i = i + 49;
//*****************************End For Painting GCPlotting**********************************//
//*****************************Start For Painting Repeat File**********************************//
public void drawRepeatPage(Graphics g1)
int check = 0;
Graphics2D g = (Graphics2D) g1;
g.setColor(Color.darkGray);
g.drawString("Repeat", 10, 480);
for (int i = 0; i < GBFileProp.repeatscore ; i++)//- 1 to b subtracted from repeatscore
int basestart = (int)((GBFileProp.startRepeatPosition[i] - (int)(GBFileProp.defaultStartCoordinate))/base); ///10;
int baseend = (int)((GBFileProp.startRepeatPosition[i] - (int)(GBFileProp.defaultStartCoordinate))/base);
if(basestart > 0 && basestart < 10000)
try
if(GBFileProp.repeatFamily.equals("LINE"))
System.out.println(" Line" );
GBFileProp.repeatposition = 575;
repeatSymbol = GBColorSymbol.repeatSymValues[GBColorSymbol.lineSym];
if(GBFileProp.repeatName[i].length() >= 2)
if(GBFileProp.repeatName[i].substring(0,2).equals("L1"))
g.setColor(GBColorSymbol.cL1);
g.drawString(repeatSymbol, (int)(basestart/10), GBFileProp.repeatposition);
else if(GBFileProp.repeatName[i].substring(0,2).equals("L2"))
g.setColor(GBColorSymbol.cL2);
g.drawString(repeatSymbol, (int)(basestart/10), GBFileProp.repeatposition);
else if(GBFileProp.repeatName[i].substring(0,2).equals("L3"))
g.setColor(GBColorSymbol.cL3);
g.drawString(repeatSymbol, (int)(basestart/10), GBFileProp.repeatposition);
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