buildprogrammenu.java

emboss的linux版本的源代码

/********************************************************************
*
*  This library is free software; you can redistribute it and/or
*  modify it under the terms of the GNU Library General Public
*  License as published by the Free Software Foundation; either
*  version 2 of the License, or (at your option) any later version.
* 
*  This library 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
*  Library General Public License for more details.
* 
*  You should have received a copy of the GNU Library General Public
*  License along with this library; 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.gui;

import java.awt.*;
import javax.swing.*;
import javax.swing.event.*;
import java.awt.event.*;
import java.io.*;
import java.util.*;

import org.emboss.jemboss.JembossJarUtil;
import org.emboss.jemboss.JembossParams;
import org.emboss.jemboss.programs.*;      // running EMBOSS programs
import org.emboss.jemboss.gui.startup.*;   // finds progs, groups, docs & db's
import org.emboss.jemboss.soap.*;
import org.emboss.jemboss.gui.form.*;      // prog forms constructed from ACD

/**
*
* BuildProgramMenu class construct the program menus.
*
*/
public class BuildProgramMenu
{
  /** database names */
  private static String db[] = {"",""};
  /** matrices */
  private static Vector matrices = new Vector();
  /** codons usage tables  */
  private static Vector codons = new Vector();
  /** acd files cache */
  private Hashtable acdStore = new Hashtable();   
  /** login window */
  private AuthPopup splashing;
  /** thread for progress monitor on the login window */
  private SplashThread splashThread;
  /** environment vars */
  private String[] envp;
  /** current appliction loaded */
  private int currentApp = -1;
  /** favorite menu */
  private Favorites favorites;

  /**
  *
  *  @param  p1 		menu pane
  *  @param  p2 		form pane
  *  @param  pform 		pane containing emboss form and job manager
  *  @param  scrollProgForm 	EMBOSS form scroll pane 
  *  @param  mysettings		Jemboss settings
  *  @param  withSoap 		true if using SOAP server
  *  @param  mainMenu		Jemboss main menu bar
  *  @param  f			Jemboss frame
  *  @param  jform 		form pane dimension
  *
  */
  public BuildProgramMenu(final JPanel p1, final ScrollPanel p2, 
           final JPanel pform, final JScrollPane scrollProgForm,
           final JembossParams mysettings,
           final boolean withSoap, final SetUpMenuBar mainMenu,
           final JFrame f, final Dimension jform)
  {
  
    final String fs = new String(System.getProperty("file.separator"));
    final String cwd = new String(System.getProperty("user.dir") + fs);
    final Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
    final Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
  
    if(withSoap)
    {  
      splashing = new AuthPopup(mysettings,400);
      if(mysettings.getUseAuth())
      splashing.setBottomPanel();
      splashing.setSize(380,200);
      splashing.pack();
      splashing.setVisible(true);

      splashThread = new SplashThread(splashing,400-4);
      splashThread.start();
    }
    else 
    {
      String[] env = null;
      
      if(mysettings.isCygwin())
        env = new String[4];  /* environment vars */
      else
        env = new String[3];
      String ps = new String(System.getProperty("path.separator"));
      String embossBin  = mysettings.getEmbossBin();
      String embossPath = mysettings.getEmbossPath();
      embossPath = new String("PATH" + ps +
                      embossPath + ps + embossBin + ps);
      env[0] = "PATH=" + embossPath;
      env[1] = "PLPLOT_LIB=" + mysettings.getPlplot();
//    env[2] = "EMBOSS_DATA=" + mysettings.getEmbossData();
      env[2] = "HOME=" + System.getProperty("user.home") + fs;
      if(mysettings.isCygwin())
        env[3] = "EMBOSSCYGROOT=" + mysettings.getCygwinRoot();

      envp = mysettings.getEmbossEnvironmentArray(env);
    }

    
    SwingWorker groupworker = new SwingWorker() 
    {
      String woss = "";

      public Object construct() 
      {
        if(withSoap) 
        {
          mainMenu.setEnableFileManagers(false);
          mainMenu.setEnableShowResults(false);

          if(mysettings.getPublicSoapURL().startsWith("https") &&
             !mysettings.getUseHTTPSProxy())
          {
            System.setProperty("https.proxyHost", "");
            System.setProperty("http.proxyHost", "");
            System.setProperty("proxyHost", "");  
            String settings[] = new String[1];
            settings[0] = new String("proxy.override=true");
            mysettings.updateJembossPropStrings(settings);
          }

          SwingWorker databaseworker = new SwingWorker()
          {
            public Object construct()
            {
              ShowDB showdb = null;
              try
              {
                showdb  = new ShowDB(mysettings);
              }
              catch (Exception ex)
              {
                splashing.doneSomething("Cannot connect!");
                ServerSetup ss = new ServerSetup(mysettings);
                int sso = JOptionPane.showConfirmDialog(f,ss,
                           "Check Settings",
                           JOptionPane.OK_CANCEL_OPTION,
                           JOptionPane.ERROR_MESSAGE,null);
                if(sso == JOptionPane.OK_OPTION)
                  ss.setNewSettings();
                else
                  System.exit(0);

                try
                {
                  showdb  = new ShowDB(mysettings);
                }
                catch (Exception exp)
                {
                  exp.printStackTrace();
                }
              }
              String showdbOut = showdb.getDBText();

              Database d = new Database(showdbOut);
              db = d.getDB();
              mainMenu.setEnableFileManagers(true);
              mainMenu.setEnableShowResults(true);
              splashing.doneSomething("");
              splashThread.setInterval(0);

              matrices = showdb.getMatrices();  // get the available matrices
              codons   = showdb.getCodonUsage();

              JLabel jl = new JLabel("<html>"); // not used but speeds first
                                                // ACD form loading which
                                                // uses html
              return null;
            }
          };
          databaseworker.start();
          
          splashing.doneSomething("");

          int iloop = 0;

          try
          {
            try
            {
              Hashtable hwoss = (new JembossJarUtil("resources/wossname.jar")).getHash();
              if(hwoss.containsKey("wossname.out"))
                woss = new String((byte[])hwoss.get("wossname.out"));

//            mainMenu.setEnableFileManagers(false);
//            mainMenu.setEnableShowResults(false);

//            Hashtable hshowdb = (new JembossJarUtil("resources/showdb.jar")).getHash();
//            mainMenu.setEnableFileManagers(false);
//            mainMenu.setEnableShowResults(false);   

//            if(hshowdb.containsKey("showdb.out"))
//            {
//              String showdbOut = new String((byte[])hshowdb.get("showdb.out"));
//              Database d = new Database(showdbOut);
//              db = d.getDB();
//            }
            }
            catch (Exception ex){ System.out.println("calling the server"); }

            if(woss.equals(""))
            {
              GetWossname ewoss = new GetWossname(mysettings);
              woss = ewoss.getWossnameText(); 
              mainMenu.setEnableFileManagers(true);
              mainMenu.setEnableShowResults(true);
            }
            
            splashing.doneSomething("");
          } 
          catch(Exception e)
          {
            splashing.doneSomething("Cannot connect!");
            ServerSetup ss = new ServerSetup(mysettings);
            int sso = JOptionPane.showConfirmDialog(f,ss,
                           "Check Settings",
                           JOptionPane.OK_CANCEL_OPTION,
                           JOptionPane.ERROR_MESSAGE,null);
            if(sso == JOptionPane.OK_OPTION)
              ss.setNewSettings();
            else
              System.exit(0);
          }
        } 
        else 
        {
          String embossBin = mysettings.getEmbossBin();
          String embossCommand = new String(embossBin + "wossname -colon -gui -auto");
          RunEmbossApplication2 rea = new RunEmbossApplication2(
                                      embossCommand,envp,null);
          rea.waitFor();
          woss = rea.getProcessStdout();

          embossCommand = new String(embossBin + "showdb -auto");
          rea = new RunEmbossApplication2(embossCommand,envp,null);
          rea.waitFor();
          String showdbOut = rea.getProcessStdout();

          Database d = new Database(showdbOut);
          db = d.getDB();

          // get the available matrices
          String dataFile[] = (new File(mysettings.getEmbossData())).list(new FilenameFilter()
          {
            public boolean accept(File dir, String name)
            {
              File fileName = new File(dir, name);
              return !fileName.isDirectory();
            };
          });

          matrices = new Vector();
          for(int i=0;i<dataFile.length;i++)
            matrices.add(dataFile[i]);
          
          // get the available codon usage tables
          dataFile = (new File(mysettings.getEmbossData()+
                                  "/CODONS")).list(new FilenameFilter()
          {
            public boolean accept(File dir, String name)
            {
              File fileName = new File(dir, name);
              return !fileName.isDirectory();
            };
          });

          codons = new Vector();
          for(int i=0;i<dataFile.length;i++)
            codons.add(dataFile[i]);
        }

        return woss;
      }


      public void finished() 
      {
// sets the delay for dismissing tooltips
        MultiLineToolTipUI.initialize();
        ToolTipManager toolTipManager = ToolTipManager.sharedInstance();
        toolTipManager.setDismissDelay(80000);

        try
        {
          acdStore = (new JembossJarUtil("resources/acdstore.jar")).getHash();
        }
        catch (Exception ex){}

// program menu
        JMenuBar menuBar = new JMenuBar();
        ProgList progs = new ProgList(woss,menuBar);

        if(withSoap)
          splashing.doneSomething("");

        int npG = progs.getNumPrimaryGroups();
        menuBar.setLayout(new GridLayout(npG,1));
   
        final int numProgs = progs.getNumProgs();
        final String allAcd[] = progs.getProgsList();
        final String allDes[] = progs.getProgDescription();

        p1.add(menuBar, BorderLayout.NORTH);
        f.setVisible(true);

// favorites
        favorites = new Favorites(mainMenu.getFavoriteJMenu());
        JMenuItem favItems[] = favorites.getFavorites();
        for(int i=0; i<favItems.length;i++)
        {
          favItems[i].addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              f.setCursor(cbusy);
              if(e.getActionCommand().equals("ADD") &&
                 currentApp > -1)
              {
                JMenuItem favItem = favorites.add(allAcd[currentApp],
                                              allDes[currentApp]);
                favItem.addActionListener(new ActionListener()
                {
                  public void actionPerformed(ActionEvent e)
                  {
                    f.setCursor(cbusy);