package Gui; import Controller.*; import Util.*; import jas.plot.PrintHelper; import Plot.*; import javax.swing.*; import java.awt.*; import java.awt.event.*; import javax.swing.event.*; import javax.swing.JTree; import java.io.*; import java.util.*; import javax.swing.table.*; public class MainFrame extends JFrame implements ActionListener { // the controller private StructureApp app; // Gui Components // the overall pane private JSplitPane splitPane; // Three sub panels private JScrollPane screenPane; // Output Area private JScrollPane listScrollPane; // Tree Panel private JDesktopPane rightPane; // Right Doc Panel // the output are contained by screenPane private TextArea console; // the internal frame set contained by rightPane private JInternalFrame dataframe; private JInternalFrame projframe; private JInternalFrame simframe; private JInternalFrame resultframe; private JInternalFrame rstplotframe; private JInternalFrame summaryframe; private JMenuBar rst_mbar; // menu bar for result frame updated automatically by StructureApp // The listener to the internal panel windows event private FrameSetListener framelistener = new FrameSetListener(); private RstPlotManager rm; // Menus // top-level menu bar private JMenuBar menuBar; // Tool Bar private JToolBar toolBar; // File Menu private JMenuItem load_rst_menu; private JMenuItem data_open_menu; private JMenuItem data_close_menu; private JMenuItem new_proj_menu; private JMenuItem open_proj_menu; private JMenuItem close_proj_menu; private JMenuItem save_proj_menu; private JMenuItem exit_menu; private JMenuItem print_menu; // Edit Menu private JMenuItem copy_menu; private JMenuItem cut_menu; private JMenuItem paste_menu; // Project Menu private JMenuItem proj_job_menu; private JMenuItem proj_joblog_menu; private JMenuItem proj_killjob_menu; private JMenuItem proj_pgen_menu; // Simulation Menu private JMenuItem sim_param_menu; private JMenuItem sim_run_menu; private JMenuItem sim_stop_menu; private JMenuItem sim_new_menu; private JMenuItem sim_del_menu; //Plotting Menu private JMenu plot_data_menu; private JMenuItem data_fst_menu; private JMenuItem data_alpha_menu; private JMenuItem data_like_menu; private JMenuItem data_r_menu; private JMenuItem data_lnpd_menu; private JMenuItem data_rec_menu; private JMenuItem triangle_menu; // View Menu private JMenuItem view_proj_menu; private JMenuItem view_sim_menu; private JMenuItem view_result_menu; private JMenuItem view_clear_menu; // Help Menu private JMenuItem help_topic_menu; private JMenuItem help_about_menu; // File Button private JButton open_proj_button; private JButton save_proj_button; private JButton new_proj_button; // Sim Button private JButton sim_run_button; private JButton sim_stop_button; private JButton sim_new_button; private JButton sim_del_button; // Help Button private JButton help_topic_button; // Start point of File Chooser private File fc_dir; /**********************************************************/ /************** MainFrame Class Methods *******************/ // Constructor public MainFrame(StructureApp app){ this.app = app; createMenuItem(); } private void createMenuItem(){ Dimension d = new Dimension(23,23); data_open_menu = new JMenuItem("Open Data File ..."); load_rst_menu = new JMenuItem("Load structure results ..."); data_close_menu = new JMenuItem("Close File"); new_proj_menu = new JMenuItem("New Project ..."); open_proj_menu = new JMenuItem("Open Project ..."); close_proj_menu = new JMenuItem("Close Project"); save_proj_menu = new JMenuItem("Save Project"); exit_menu = new JMenuItem("Exit"); print_menu = new JMenuItem("Print ..."); open_proj_button = new JButton(new ImageIcon("images/New_Job.gif")); open_proj_button.setPreferredSize(d); open_proj_button.setToolTipText("Open Project"); save_proj_button = new JButton(new ImageIcon("images/Save_All.gif")); save_proj_button.setPreferredSize(d); save_proj_button.setToolTipText("Save Project"); new_proj_button = new JButton(new ImageIcon("images/New_Program_Wizard.gif")); new_proj_button.setToolTipText("New Project"); new_proj_button.setPreferredSize(d); copy_menu = new JMenuItem("Copy"); cut_menu = new JMenuItem("Cut"); paste_menu = new JMenuItem("Paste"); proj_job_menu = new JMenuItem("Start a Job"); proj_joblog_menu = new JMenuItem("View Job Log"); proj_killjob_menu = new JMenuItem("Kill Running Job"); proj_pgen_menu = new JMenuItem("Generate parameter files..."); sim_param_menu = new JMenuItem("Modify current set ..."); sim_run_menu = new JMenuItem("Run"); sim_stop_menu = new JMenuItem("Stop"); sim_new_menu = new JMenuItem("New ... "); sim_del_menu = new JMenuItem("Remove Parameter Set ... "); sim_new_button = new JButton(new ImageIcon("images/new2.gif")); sim_new_button.setPreferredSize(d); sim_new_button.setToolTipText("New Parameter Set"); sim_del_button = new JButton(new ImageIcon("images/delete.gif")); sim_del_button.setPreferredSize(d); sim_del_button.setToolTipText("Remove Parameter Set"); sim_run_button = new JButton(new ImageIcon("images/Run.gif")); sim_run_button.setPreferredSize(d); sim_run_button.setToolTipText("Run"); sim_stop_button = new JButton(new ImageIcon("images/Stop.gif")); sim_stop_button.setPreferredSize(d); sim_stop_button.setToolTipText("Stop"); plot_data_menu = new JMenu("Run-time"); data_fst_menu = new JMenuItem("Fst"); data_alpha_menu = new JMenuItem("Alpha"); data_r_menu = new JMenuItem("r (LOCPRIOR model)"); data_like_menu = new JMenuItem("Likelihood"); data_lnpd_menu = new JMenuItem("Ln P(D) "); data_rec_menu = new JMenuItem("Recombination Rate"); triangle_menu = new JMenuItem("Triangle Plot"); view_proj_menu = new JMenuItem("Project Info"); view_sim_menu = new JMenuItem("Active Parameter Set Info"); view_result_menu = new JMenuItem("Simulation Summary"); view_clear_menu = new JMenuItem("Clear Output Console"); help_topic_menu = new JMenuItem("Help Document"); help_about_menu = new JMenuItem("About Structure"); help_topic_button = new JButton(new ImageIcon("images/Home.gif")); help_topic_button.setPreferredSize(d); help_topic_button.setToolTipText("About Structure"); }; public JSplitPane createPane(int screenWidth, int screenHeight) { // prepare the component panes listScrollPane = new JScrollPane(); listScrollPane.getViewport().add(app.getProjTree()); rightPane = new JDesktopPane(); // create console area console = new TextArea(5,5); console.setBackground(Color.black); console.setForeground(Color.white); console.setEditable(false); screenPane = new JScrollPane(console); //Create a split pane with the two scroll panes in it JSplitPane upPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, listScrollPane, rightPane); upPane.setOneTouchExpandable(true); upPane.setDividerLocation(screenWidth/4); //Provide minimum sizes for the two components in the split pane Dimension minimumSize = new Dimension(screenWidth/8, screenHeight/6); listScrollPane.setMinimumSize(minimumSize); rightPane.setMinimumSize(minimumSize); screenPane.setMinimumSize(minimumSize); //Provide a preferred size for the split pane upPane.setPreferredSize(new Dimension(6*screenWidth/7, 5*screenHeight/7)); screenPane.setMaximumSize(minimumSize); splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, upPane, screenPane); splitPane.setOneTouchExpandable(true); splitPane.setDividerLocation(4*screenHeight/7); return splitPane; } // public function that creates the menu bar public JMenuBar createMenuBar(){ menuBar = new JMenuBar(); toolBar = new JToolBar(); //Build the first menu. JMenu fileMenu = new JMenu("File"); JMenu editMenu = new JMenu("Edit"); JMenu projMenu = new JMenu("Project"); JMenu simMenu = new JMenu("Parameter Set"); JMenu viewMenu = new JMenu("View"); JMenu helpMenu = new JMenu("Help"); JMenu plotMenu = new JMenu("Plotting"); load_rst_menu.setActionCommand("loadrst"); load_rst_menu.addActionListener(this); data_open_menu.setActionCommand("datafile"); data_open_menu.addActionListener(this); data_close_menu.setActionCommand("closefile"); data_close_menu.addActionListener(this); new_proj_menu.setActionCommand("newproject"); new_proj_menu.addActionListener(this); new_proj_button.setActionCommand("newproject"); new_proj_button.addActionListener(this); open_proj_menu.setActionCommand("openproj"); open_proj_menu.addActionListener(this); open_proj_button.setActionCommand("openproj"); open_proj_button.addActionListener(this); close_proj_menu.setActionCommand("closeproj"); close_proj_menu.addActionListener(this); save_proj_menu.setActionCommand("saveproj"); save_proj_menu.addActionListener(this); save_proj_button.setActionCommand("saveproj"); save_proj_button.addActionListener(this); print_menu.setActionCommand("print"); print_menu.addActionListener(this); exit_menu.setActionCommand("exit"); exit_menu.addActionListener(this); proj_job_menu.setActionCommand("startjob"); proj_job_menu.addActionListener(this); proj_joblog_menu.setActionCommand("joblog"); proj_joblog_menu.addActionListener(this); proj_killjob_menu.setActionCommand("killjob"); proj_killjob_menu.addActionListener(this); proj_pgen_menu.setActionCommand("genparam"); proj_pgen_menu.addActionListener(this); sim_new_menu.setActionCommand("simnew"); sim_new_menu.addActionListener(this); sim_new_button.setActionCommand("simnew"); sim_new_button.addActionListener(this); sim_del_menu.setActionCommand("simdel"); sim_del_menu.addActionListener(this); sim_del_button.setActionCommand("simdel"); sim_del_button.addActionListener(this); sim_param_menu.setActionCommand("simsetting"); sim_param_menu.addActionListener(this); sim_run_menu.setActionCommand("simrun"); sim_run_menu.addActionListener(this); sim_run_button.setActionCommand("simrun"); sim_run_button.addActionListener(this); sim_stop_menu.setActionCommand("simstop"); sim_stop_menu.addActionListener(this); sim_stop_button.setActionCommand("simstop"); sim_stop_button.addActionListener(this); view_proj_menu.setActionCommand("viewproj"); view_proj_menu.addActionListener(this); view_sim_menu.setActionCommand("viewsim"); view_sim_menu.addActionListener(this); view_result_menu.setActionCommand("viewsummary"); view_result_menu.addActionListener(this); data_fst_menu.setActionCommand("viewfst"); data_fst_menu.addActionListener(this); data_alpha_menu.setActionCommand("viewalpha"); data_alpha_menu.addActionListener(this); data_r_menu.setActionCommand("viewr"); data_r_menu.addActionListener(this); data_like_menu.setActionCommand("viewlike"); data_like_menu.addActionListener(this); data_lnpd_menu.setActionCommand("viewlnpd"); data_lnpd_menu.addActionListener(this); data_rec_menu.setActionCommand("viewrec"); data_rec_menu.addActionListener(this); triangle_menu.setActionCommand("triangle"); triangle_menu.addActionListener(this); view_clear_menu.setActionCommand("clearconsole"); view_clear_menu.addActionListener(this); help_topic_menu.setActionCommand("helpdoc"); help_topic_menu.addActionListener(this); help_about_menu.setActionCommand("about"); help_about_menu.addActionListener(this); help_topic_button.setActionCommand("about"); help_topic_button.addActionListener(this); // build file menu fileMenu.add(data_open_menu); fileMenu.add(data_close_menu); fileMenu.addSeparator(); fileMenu.add(new_proj_menu); fileMenu.add(open_proj_menu); fileMenu.add(close_proj_menu); fileMenu.add(save_proj_menu); //fileMenu.addSeparator(); //fileMenu.add(print_menu); fileMenu.addSeparator(); fileMenu.add(load_rst_menu); fileMenu.addSeparator(); fileMenu.add(app.getHistoryMenu()); fileMenu.addSeparator(); fileMenu.add(exit_menu); // build edit menu editMenu.add(copy_menu); editMenu.add(cut_menu); editMenu.add(paste_menu); // buld sim menu simMenu.add(app.getSimMenu()); simMenu.addSeparator(); simMenu.add(sim_param_menu); simMenu.add(sim_new_menu); simMenu.add(sim_del_menu); simMenu.addSeparator(); simMenu.add(sim_run_menu); simMenu.add(sim_stop_menu); // build proj menu projMenu.add(proj_job_menu); projMenu.add(proj_joblog_menu); projMenu.add(proj_killjob_menu); projMenu.addSeparator(); projMenu.add(proj_pgen_menu); // build view menu viewMenu.add(view_proj_menu); viewMenu.add(view_sim_menu); viewMenu.add(view_result_menu); plot_data_menu.add(data_fst_menu); plot_data_menu.add(data_alpha_menu); plot_data_menu.add(data_rec_menu); plot_data_menu.add(data_r_menu); plot_data_menu.add(data_like_menu); plot_data_menu.add(data_lnpd_menu); plotMenu.add(plot_data_menu); //splotMenu.addSeparator(); //plotMenu.add(triangle_menu); viewMenu.add(view_clear_menu); // build help menu helpMenu.add(help_topic_menu); helpMenu.add(help_about_menu); // Finally compose the menuBar menuBar.add(fileMenu); // menuBar.add(editMenu); menuBar.add(projMenu); menuBar.add(simMenu); menuBar.add(plotMenu); menuBar.add(viewMenu); menuBar.add(helpMenu); toolBar.addSeparator(); toolBar.add(open_proj_button); toolBar.add(save_proj_button); toolBar.add(new_proj_button); toolBar.addSeparator(); toolBar.addSeparator(); toolBar.add(sim_new_button); toolBar.add(sim_del_button); toolBar.addSeparator(); toolBar.add(sim_run_button); toolBar.add(sim_stop_button); toolBar.addSeparator(); toolBar.addSeparator(); toolBar.add(help_topic_button); return menuBar; } /***********************************************************/ /*********** UI (mostly menus) Update Mehtods **************/ // this method update UIs according to the program state // state 0 : program started, no project loaded // state 1 : project loaded , no active sim selected // state 2 : Active simulation selected but not running // state 3 : Active simulation is running // state 4 : Active job is running public void updateUI(int state){ if(state == 0){ new_proj_menu.setEnabled(true); new_proj_button.setEnabled(true); open_proj_menu.setEnabled(true); open_proj_button.setEnabled(true); close_proj_menu.setEnabled(false); save_proj_menu.setEnabled(false); save_proj_button.setEnabled(false); proj_job_menu.setEnabled(false); proj_joblog_menu.setEnabled(false); proj_killjob_menu.setEnabled(false); proj_pgen_menu.setEnabled(false); app.getSimMenu().setEnabled(false); sim_param_menu.setEnabled(false); sim_run_menu.setEnabled(false); sim_run_button.setEnabled(false); sim_stop_menu.setEnabled(false); sim_stop_button.setEnabled(false); sim_new_menu.setEnabled(false); sim_new_button.setEnabled(false); sim_del_menu.setEnabled(false); sim_del_button.setEnabled(false); view_proj_menu.setEnabled(false); view_sim_menu.setEnabled(false); view_result_menu.setEnabled(false); view_clear_menu.setEnabled(false); plot_data_menu.setEnabled(false); triangle_menu.setEnabled(false); console.setText(""); if(dataframe != null ) dataframe.dispose(); if(projframe != null ){ projframe.dispose(); projframe = null; } if(simframe != null ) simframe.dispose(); if(resultframe != null){ resultframe.dispose(); rst_mbar = null; } if(rstplotframe != null) rstplotframe.dispose(); if(summaryframe != null) summaryframe.dispose(); return; } if(state == 1){ new_proj_menu.setEnabled(false); open_proj_menu.setEnabled(false); close_proj_menu.setEnabled(true); save_proj_menu.setEnabled(true); new_proj_button.setEnabled(false); open_proj_button.setEnabled(false); save_proj_button.setEnabled(true); proj_job_menu.setEnabled(true); proj_joblog_menu.setEnabled(false); proj_killjob_menu.setEnabled(false); proj_pgen_menu.setEnabled(true); app.getSimMenu().setEnabled(true); sim_param_menu.setEnabled(false); sim_run_menu.setEnabled(false); sim_stop_menu.setEnabled(false); sim_new_menu.setEnabled(true); sim_run_button.setEnabled(false); sim_stop_button.setEnabled(false); sim_new_button.setEnabled(true); sim_del_menu.setEnabled(true); sim_del_button.setEnabled(true); view_proj_menu.setEnabled(true); view_sim_menu.setEnabled(false); view_result_menu.setEnabled(true); view_clear_menu.setEnabled(true); plot_data_menu.setEnabled(false); triangle_menu.setEnabled(true); return; } if(state == 2){ new_proj_menu.setEnabled(false); open_proj_menu.setEnabled(false); close_proj_menu.setEnabled(true); save_proj_menu.setEnabled(true); new_proj_button.setEnabled(false); open_proj_button.setEnabled(false); save_proj_button.setEnabled(true); proj_job_menu.setEnabled(true); proj_joblog_menu.setEnabled(false); proj_killjob_menu.setEnabled(false); proj_pgen_menu.setEnabled(true); app.getSimMenu().setEnabled(true); sim_param_menu.setEnabled(true); sim_run_menu.setEnabled(true); sim_stop_menu.setEnabled(false); sim_new_menu.setEnabled(true); sim_run_button.setEnabled(true); sim_stop_button.setEnabled(false); sim_new_button.setEnabled(true); sim_del_menu.setEnabled(true); sim_del_button.setEnabled(true); view_proj_menu.setEnabled(true); view_sim_menu.setEnabled(true); view_result_menu.setEnabled(true); view_clear_menu.setEnabled(true); plot_data_menu.setEnabled(false); triangle_menu.setEnabled(true); return; } if(state == 3){ new_proj_menu.setEnabled(false); open_proj_menu.setEnabled(false); close_proj_menu.setEnabled(false); save_proj_menu.setEnabled(true); new_proj_button.setEnabled(false); open_proj_button.setEnabled(false); save_proj_button.setEnabled(true); proj_job_menu.setEnabled(false); proj_joblog_menu.setEnabled(false); proj_killjob_menu.setEnabled(false); proj_pgen_menu.setEnabled(true); app.getSimMenu().setEnabled(false); sim_param_menu.setEnabled(true); sim_run_menu.setEnabled(false); sim_stop_menu.setEnabled(true); sim_new_menu.setEnabled(true); sim_run_button.setEnabled(false); sim_stop_button.setEnabled(true); sim_new_button.setEnabled(true); sim_del_menu.setEnabled(true); sim_del_button.setEnabled(true); view_proj_menu.setEnabled(true); view_sim_menu.setEnabled(true); view_result_menu.setEnabled(true); view_clear_menu.setEnabled(false); plot_data_menu.setEnabled(true); triangle_menu.setEnabled(true); return; } if(state == 4){ new_proj_menu.setEnabled(false); open_proj_menu.setEnabled(false); close_proj_menu.setEnabled(false); save_proj_menu.setEnabled(true); new_proj_button.setEnabled(false); open_proj_button.setEnabled(false); save_proj_button.setEnabled(true); proj_job_menu.setEnabled(false); proj_joblog_menu.setEnabled(true); proj_killjob_menu.setEnabled(true); proj_pgen_menu.setEnabled(true); app.getSimMenu().setEnabled(false); sim_param_menu.setEnabled(false); sim_run_menu.setEnabled(false); sim_stop_menu.setEnabled(false); sim_new_menu.setEnabled(true); sim_run_button.setEnabled(false); sim_stop_button.setEnabled(false); sim_new_button.setEnabled(true); sim_del_menu.setEnabled(false); sim_del_button.setEnabled(false); view_proj_menu.setEnabled(true); view_sim_menu.setEnabled(true); view_result_menu.setEnabled(true); view_clear_menu.setEnabled(false); plot_data_menu.setEnabled(true); triangle_menu.setEnabled(true); return; } } public void setRstMenu(JMenuBar newbar){ rst_mbar = newbar; } /*****************************************************/ /*********** The Action Handler **************/ // The Action handler forward most of the data requst // action to the controller except the project-independent // data loading, and update the Guis - tree and simListMenu // will be notified by contoller and cooperate the update public void actionPerformed(ActionEvent e){ String action = e.getActionCommand(); // TODO: let app handle this, some // clean-up work is required if(action.compareTo("exit") == 0){ app.exit_structure();; } if(action.compareTo("newproject") == 0){ app.newProject(); return; } if(action.compareTo("closeproj") == 0){ app.closeProj(); } if(action.equals("closefile")){ JInternalFrame frame = rightPane.getSelectedFrame(); if(frame != dataframe && frame != projframe && frame != simframe && frame != resultframe && frame != rstplotframe && frame != summaryframe){ frame.dispose(); } return; } if(action.compareTo("saveproj") == 0){ app.saveProj(); } if(action.compareTo("openproj") == 0 ){ app.openProj(); return; } if(action.compareTo("simnew") == 0){ app.newSim(); return; } if(action.compareTo("simdel")==0){ app.removeSimObj(); return; } if(action.compareTo("simsetting") == 0){ app.simSetting(); return; } if(action.compareTo("simrun") == 0){ app.runProc(); return; } if(action.compareTo("simstop") == 0){ app.stopProc(); return; } if(action.compareTo("datafile") == 0){ loadData(); return; } if(action.equals("loadrst")){ app.loadOutsideRst(); } if(action.equals("startjob")){ app.startJob(); return; } if(action.equals("joblog")){ app.showJobLog(); return; } if(action.equals("killjob")){ app.killJob(); return; } if(action.equals("genparam")){ app.genParamFiles(); } /*********************************************************/ // plotting handler // /*********************************************************/ // run-time plotting handler if(action.compareTo("viewfst")==0){ app.plotDynamic("Fst"); return; } if(action.equals("viewalpha")){ app.plotDynamic("Alpha"); return; } if(action.equals("viewrec")){ app.plotDynamic("Rec"); return; } if(action.equals("viewlike")){ app.plotDynamic("Like"); return; } if(action.equals("viewlnpd")){ app.plotDynamic("LnPD"); return; } if(action.equals("viewr")){ app.plotDynamic("r"); return; } //off-time data plotting handler if(action.compareTo("sviewfst")==0){ app.plotStatic("Fst"); return; } if(action.equals("sviewalpha")){ app.plotStatic("Alpha"); return; } if(action.equals("sviewrec")){ app.plotStatic("Rec"); return; } if(action.equals("sviewr")){ app.plotStatic("r"); return; } if(action.equals("sviewlnpd")){ app.plotStatic("LnPD"); return; } if(action.equals("sviewlike")){ app.plotStatic("Like"); return; } // hist plotters if(action.equals("histfst")){ app.plotStatic("FstHist"); return; } if(action.equals("histalpha")){ app.plotStatic("AlphaHist"); return; } if(action.equals("histrec")){ app.plotStatic("RecHist"); return; } if(action.equals("histr")){ app.plotStatic("rHist"); return; } if(action.equals("histlike")){ app.plotStatic("LikHist"); return; } if(action.equals("histlnpd")){ app.plotStatic("LnpdHist"); return; } if(action.equals("triplot")){ app.triPlot(1); } if(action.equals("treeplot")){ app.treePlot(); } if(action.equals("treePlotLicense")){ app.treePlotLicense(); } //triangle plotter if(action.equals("triangle")){ app.triPlot(0); return; } /**************************************************/ /* content panel loaders */ /**************************************************/ if(action.compareTo("viewproj")==0){ app.loadDataFrame("proj",null); return; } if(action.equals("viewsim")){ app.loadDataFrame("sim",null); return; } if(action.equals("viewsummary")){ app.loadSummary(); return; } if(action.equals("clearconsole")){ console.setText(""); return; } if(action.equals("print")){ processPrinting(); return; } if(action.equals("barplot")){ app.loadBarPlot(); } if(action.equals("helpdoc")){ JOptionPane.showMessageDialog(this, "Help document (structure_doc.pdf) is availble in \"doc\" directory\n"+ "It is also available online in HTML format\n\n", "Structure Document", JOptionPane.INFORMATION_MESSAGE); return; } if(action.equals("about")){ JOptionPane.showMessageDialog(this, "Structure 2.3.2 (Sept 2009)\n", "About Structure 2.3.1", JOptionPane.INFORMATION_MESSAGE); return; } } /***********************************************************/ /******************* Uitility Method ***********************/ // Render Console to output process manager public TextArea getConsole(){ return console; } public JToolBar getToolBar(){ return toolBar; } /************************************************************/ /********** Loading Project-Independent Data ************/ public void loadData(){ final JFileChooser fc = new JFileChooser(); fc.setCurrentDirectory(fc_dir); int returnVal = fc.showOpenDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); fc_dir = file.getParentFile(); InputStream in; Lexer lexer; String filename = file.getAbsolutePath(); /******************************************/ /***** open input and output files... *****/ in = OpenInputFile(filename); if (in == null) return; /****************************************************/ /***** create Lexer and start reading tokens... *****/ lexer = new Lexer(in); // first parse get file info while(lexer.getNextString()!=null) ; int col = lexer.getTokenCol(); int row = lexer.getLine(); try { // to close files... in.close(); } catch (IOException e) { /* just ignore */ }//try-catch // reopen the file in = OpenInputFile(filename); if (in == null) return; lexer = new Lexer(in); // second parse , assign vals for the table String[][] data = new String[row][col]; InFile infile = null; try{ infile = new InFile(filename); }catch(Exception e){ JOptionPane.showMessageDialog(null, "Can not Read Data Source", "Error", JOptionPane.ERROR_MESSAGE); return; } String token = ""; String str = ""; int row_count = 0; Hashtable stat = new Hashtable(); // file counter while(true){ try{ str = infile.readLine(); }catch(Exception re){ } if(str == null ) break; StringTokenizer st = new StringTokenizer(str); if(!st.hasMoreTokens()) continue; int col_count = 0; int word_count = 0; while(st.hasMoreTokens()){ token = st.nextToken(); try { data[row_count][col_count++] = token; word_count++; }catch(ArrayIndexOutOfBoundsException e){ } } // write to stat hashtable Integer index = new Integer(word_count); if(stat.containsKey(index)){ Integer obj = (Integer)stat.get(index); int objVal = obj.intValue(); stat.put(index,new Integer(++objVal)); }else{ stat.put(new Integer(word_count), new Integer(1)); } row_count++; } String[] name = new String[col]; for(int i=0;i=colNum-lociCol){ TableColumn column = cm.getColumn(i); column.setCellRenderer(new DataRowRenderer(rowNum,genename,mapdistance,phaseinfo,onerow,ploidy,recessiveallele)); } } table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); table.setPreferredScrollableViewportSize(new Dimension(650, 420)); JScrollPane scrollPane = new JScrollPane(table); dataframe = new JInternalFrame("Project Data", true, true, true, true); dataframe.setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); dataframe.addInternalFrameListener(framelistener); dataframe.getContentPane().add(scrollPane); dataframe.setSize(650,450); dataframe.setVisible(true); rightPane.add(dataframe); try { dataframe.setSelected(true); dataframe.setMaximum(true); } catch (java.beans.PropertyVetoException e) {} } public void loadSummaryFrame(JInternalFrame sp,String title){ hideAllFrames(); if(summaryframe != null ) summaryframe.dispose(); summaryframe = sp; summaryframe.setTitle(title); summaryframe.setSize(650,450); summaryframe.setVisible(true); rightPane.add(summaryframe); try { summaryframe.setSelected(true); summaryframe.setMaximum(true); } catch (java.beans.PropertyVetoException e) {} return; } public int getCurrState(){ return app.getCurrState(); } public void loadDataFrame(String type, String title, String content){ if(type.equals("proj")){ hideAllFrames(); if(projframe == null ){ projframe = new JInternalFrame(title,true, true, true, true); projframe.setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); projframe.addInternalFrameListener(framelistener); JTextArea ta = new JTextArea(content); ta.setFont(new Font("TimesRoman", Font.PLAIN, 15)); ta.setLineWrap(true); ta.setWrapStyleWord(true); JScrollPane scrollPane = new JScrollPane(ta); ta.setCaretPosition(0); ta.setEditable(false); projframe.getContentPane().add(scrollPane); projframe.setSize(650,450); projframe.setVisible(true); rightPane.add(projframe); } if(!projframe.isVisible()) projframe.setVisible(true); try { projframe.setSelected(true); projframe.setMaximum(true); } catch (java.beans.PropertyVetoException e) {} return ; } if(type.equals("data")){ hideAllFrames(); if(!dataframe.isVisible()){ dataframe.setVisible(true); } try{ dataframe.setSelected(true); dataframe.setMaximum(true); } catch (java.beans.PropertyVetoException e) { System.err.println(e);} return; } if(type.equals("sim")){ hideAllFrames(); if(simframe != null ) simframe.dispose(); simframe = new JInternalFrame(title,true, true, true, true); JTextArea ta = new JTextArea(content); ta.setFont(new Font("TimesRoman", Font.PLAIN, 15)); ta.setLineWrap(true); ta.setWrapStyleWord(true); JScrollPane sp = new JScrollPane(ta); ta.setCaretPosition(0); ta.setEditable(false); simframe.getContentPane().add(sp); simframe.setSize(650,450); simframe.pack(); simframe.setVisible(true); rightPane.add(simframe); try { simframe.setSelected(true); simframe.setMaximum(true); } catch (java.beans.PropertyVetoException e) {} return; } if(type.equals("result")){ hideAllFrames(); if(resultframe != null ) resultframe.dispose(); resultframe = new JInternalFrame(title,true, true, true, true); JTextArea ta = new JTextArea(content); content = null; ta.setFont(new Font("TimesRoman", Font.PLAIN, 15)); ta.setMargin(new Insets(0,25,0,10)); ta.setLineWrap(true); ta.setWrapStyleWord(true); JScrollPane sp = new JScrollPane(ta); ta.setCaretPosition(0); ta.setEditable(false); resultframe.setJMenuBar(rst_mbar); resultframe.getContentPane().setLayout(new BorderLayout()); resultframe.getContentPane().add(sp,BorderLayout.CENTER); resultframe.pack(); resultframe.setVisible(true); rightPane.add(resultframe); try { resultframe.setSelected(true); resultframe.setMaximum(true); } catch (java.beans.PropertyVetoException e) {} return; } } void hideAllFrames(){ if(dataframe!=null) dataframe.setVisible(false); if(projframe!=null) projframe.setVisible(false); if(simframe!=null) simframe.setVisible(false); if(resultframe!=null) resultframe.setVisible(false); if(rstplotframe!=null) rstplotframe.setVisible(false); if(summaryframe!=null) summaryframe.setVisible(false); } /***********************************************************/ /********** Internal Frame Window Event Listener ***********/ class FrameSetListener implements InternalFrameListener{ public void internalFrameClosing(InternalFrameEvent e) { JInternalFrame frame = (JInternalFrame)e.getSource(); frame.setVisible(false); } public void internalFrameClosed(InternalFrameEvent e) { /* JInternalFrame frame = e.getInternalFrame(); frame.setVisible(false); */ } public void internalFrameOpened(InternalFrameEvent e) { } public void internalFrameIconified(InternalFrameEvent e) { } public void internalFrameDeiconified(InternalFrameEvent e) { } public void internalFrameActivated(InternalFrameEvent e) { } public void internalFrameDeactivated(InternalFrameEvent e) { } } } class DataRowRenderer extends DefaultTableCellRenderer { Color[] rowColor; public DataRowRenderer(int rowNum, boolean genename , boolean mapdist , boolean phaseinfo, boolean onerow, int ploidy,boolean recessiveallel){ super(); int data_start_row = 0; if(genename) data_start_row++; if(mapdist) data_start_row++; if(recessiveallel) data_start_row++; int interval = 0; if(phaseinfo){ if(onerow) interval=1; else interval=ploidy; } rowColor = new Color[rowNum]; for(int i=0;i