buildprogrammenu.java

emboss的linux版本的源代码

                    currentApp = setForm(e,f,scrollProgForm,numProgs,p2,
                             mysettings,cwd,allAcd,allDes,withSoap);
                    f.setCursor(cdone);
                  }
                });
              }
              else if(e.getActionCommand().equals("EDIT"))
                favorites.edit(allAcd);
              else
                currentApp = setForm(e,f,scrollProgForm,numProgs,p2,
                             mysettings,cwd,allAcd,allDes,withSoap);
              f.setCursor(cdone);
            }
          });
        }

// main menu
        JMenuItem mi[] = new JMenuItem[numProgs];
        mi = progs.getMenuItems();
        int nm = progs.getNumberMenuItems();

// create action listeners into menu to build Jemboss program forms
        for(int i=0; i<nm;i++)
        {
          mi[i].addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              f.setCursor(cbusy);
              currentApp= setForm(e,f,scrollProgForm,numProgs,p2,
                          mysettings,cwd,allAcd,allDes,withSoap);
              f.setCursor(cdone);
            }
          });

          if(withSoap)
          {
            JFrame splashf = splashing.getSplashFrame();
            if(splashf.isVisible())
              splashf.toFront();
          }
        }

// program scroll list
        final JList progList = new JList(allAcd);
        JScrollPane scrollPane = new JScrollPane(progList);

        Box alphaPane = new Box(BoxLayout.Y_AXIS);
        Box alphaTextPane = new Box(BoxLayout.X_AXIS);
        alphaPane.add(Box.createRigidArea(new Dimension(0,10)));
        alphaTextPane.add(new JLabel("GoTo:"));
        alphaTextPane.add(Box.createRigidArea(new Dimension(5,0)));

        final JTextField alphaTextPaneEntry = new JTextField(12);
        alphaTextPaneEntry.setMaximumSize(new Dimension(100,20));
        //scroll program list on typing 
        alphaTextPaneEntry.getDocument().addDocumentListener(new DocumentListener()
        {
          public void insertUpdate(DocumentEvent e)
          {
            updateScroll();
          }
          public void removeUpdate(DocumentEvent e) 
          {
            updateScroll();
          }
          public void changedUpdate(DocumentEvent e) {}
          public void updateScroll()
          {
            for(int k=0;k<numProgs;k++)
              if(allAcd[k].startsWith(alphaTextPaneEntry.getText()))
              {
                progList.ensureIndexIsVisible(k);
                progList.setSelectionBackground(Color.cyan);
                progList.setSelectedIndex(k);
                break;
              }
          }
        });
        //load program form on carriage return
        alphaTextPaneEntry.addActionListener(new ActionListener()
        {
          public void actionPerformed(ActionEvent e)
          {
            f.setCursor(cbusy);
            int index = progList.getSelectedIndex();
            p2.removeAll();
            currentApp = index;
            String acdText = getAcdText(allAcd[index],mysettings,
                                                       withSoap);
            BuildJembossForm bjf = new BuildJembossForm(allDes[index],
                                  db,allAcd[index],envp,cwd,
                                  acdText,withSoap,p2,mysettings,f);
            scrollProgForm.setViewportView(p2);   
            JViewport vp = scrollProgForm.getViewport();
            vp.setViewPosition(new Point(0,0));
            f.setCursor(cdone);
          }
        });

        alphaTextPane.add(alphaTextPaneEntry);
        alphaPane.add(alphaTextPane);
        alphaPane.add(scrollPane);

        p1.add(alphaPane, BorderLayout.CENTER);

        Dimension dp1 = p1.getMinimumSize();
        dp1 = new Dimension((int)dp1.getWidth()-10,(int)dp1.getHeight());
        p1.setPreferredSize(dp1);
        p1.setMaximumSize(dp1);
        p1.setMinimumSize(dp1);


// search tool bar
        final JRadioButton radioAND = new JRadioButton("AND");
        JRadioButton radioOR  = new JRadioButton("OR");
        Font fnt = new Font("SansSerif", Font.BOLD, 10);
        radioAND.setFont(fnt);
        radioOR.setFont(fnt);
        radioAND.setSelected(true);
                                                                                            
        ButtonGroup group = new ButtonGroup();
        group.add(radioAND);
        group.add(radioOR);

        JToolBar toolBar = new JToolBar(JToolBar.VERTICAL);
        final JTextField search = new JTextField(12);
        search.addActionListener(new ActionListener()
        {
          public void actionPerformed(ActionEvent e)
          {
            new KeywordSearch(search,woss,mysettings,withSoap,
                              radioAND.isSelected());
          }
        });

        Box bacross = Box.createHorizontalBox();
        JLabel keyw = new JLabel("Keyword Search");
        keyw.setFont(fnt);
        bacross.add(keyw);
        JButton go = new JButton("GO");
        go.setFont(new Font("monospaced", Font.BOLD, 10));
        go.setMargin(new Insets(0,0,0,0));
        go.setForeground(new Color(0,51,102));
        go.addActionListener(new ActionListener()
        {
          public void actionPerformed(ActionEvent e)
          {
            new KeywordSearch(search,woss,mysettings,withSoap,
                              radioAND.isSelected());
          }
        });
        bacross.add(Box.createHorizontalStrut(2));
        bacross.add(go);
        bacross.add(Box.createHorizontalGlue());
        toolBar.add(bacross);
        toolBar.add(search);

        bacross = Box.createHorizontalBox();
        bacross.add(radioAND);
        bacross.add(radioOR);
        bacross.add(Box.createHorizontalGlue());
        toolBar.add(bacross);

        p1.add(toolBar, BorderLayout.SOUTH);

// put on the logo
        ClassLoader cl = this.getClass().getClassLoader();
        ImageIcon jlo = new ImageIcon(
                  cl.getResource("images/Jemboss_logo_large.gif"));
        JLabel jlablogo = new JLabel(jlo); 
        JPanel pFront = new JPanel();
        pFront.setBackground(Color.white);
        pFront.add(jlablogo);

// ensure fill the screen here as pform is BorderLayout.WEST
        int pwidth = (int)(f.getSize().getWidth()-p1.getSize().getWidth())-14;
        Dimension d = new Dimension(pwidth,100);
        pform.setPreferredSize(d);
        pform.setMinimumSize(d);
        jlablogo.setPreferredSize(jform);

        p2.add(pFront);

        progList.setSelectionBackground(Color.cyan);

// create listener to build Jemboss program forms
        MouseListener mouseListener = new MouseAdapter()
        {
          public void mouseClicked(MouseEvent e)
          {
//          System.gc();
            f.setCursor(cbusy);
            JList source = (JList)e.getSource();
            source.setSelectionBackground(Color.cyan);
            int index = source.getSelectedIndex();
            p2.removeAll();
            currentApp = index;
            String acdText = getAcdText(allAcd[index],mysettings,
                                                       withSoap);
            BuildJembossForm bjf = new BuildJembossForm(allDes[index],
                                  db,allAcd[index],envp,cwd,
                                  acdText,withSoap,p2,mysettings,f);
            scrollProgForm.setViewportView(p2);
            JViewport vp = scrollProgForm.getViewport();
            vp.setViewPosition(new Point(0,0));
            f.setCursor(cdone);
          }
        };
        progList.addMouseListener(mouseListener);

        p1.setVisible(false);
        p1.setVisible(true);

      }
    };
    groupworker.start();

  }

  private int setForm(ActionEvent e, JFrame f, JScrollPane scrollProgForm,
                      int numProgs, ScrollPanel p2, JembossParams mysettings, 
                      String cwd, String allAcd[], String allDes[],
                      boolean withSoap)
  {
//  JMenuItem source = (JMenuItem)(e.getSource());
                  
    String p = e.getActionCommand();
    int ind = p.indexOf(" ");

    if(ind > -1)
      p = p.substring(0,ind).trim();
                                                                                                     
    for(int k=0;k<numProgs;k++)
    {
      if(p.equalsIgnoreCase(allAcd[k]))
      {
        p2.removeAll();
        currentApp = k;

        String acdText = getAcdText(allAcd[k],mysettings,
                                               withSoap);
        BuildJembossForm bjf = new BuildJembossForm(allDes[k],
                      db,allAcd[k],envp,cwd,acdText,
                      withSoap,p2,mysettings,f);
        scrollProgForm.setViewportView(p2);
        JViewport vp = scrollProgForm.getViewport();
        vp.setViewPosition(new Point(0,0));
        break;
      }
    }
    return currentApp;
  }

  /**
  *
  * List of available EMBOSS databases
  * @return 	list of databases
  *
  */
  protected static String[] getDatabaseList()
  {
    return db;
  }

  /**
  *
  * Contains all scoring matrix files
  *
  */
  public static Vector getMatrices()
  {
    return matrices;
  }

  /**
  *
  * Contains all codon usage tables
  *
  */
  public static Vector getCodonUsage()
  {
    return codons;
  }

  /**
  *
  * Get the contents of an ACD file in the form of a String
  * @param applName		application name
  * @param mysettings		jemboss properties
  * @param withSoap		true if in client-server mode
  * @return	 		String representation of the ACD
  *
  */
  private String getAcdText(String applName, JembossParams mysettings, 
                            boolean withSoap)
  {

    String acdText = new String("");
    String line;

    if(!withSoap)
    {
      String acdDirToParse = mysettings.getAcdDirToParse();
      String acdToParse = acdDirToParse.concat(applName).concat(".acd");
      try
      {
        BufferedReader in = new BufferedReader(new FileReader(acdToParse));
        StringBuffer buff = new StringBuffer();
        
        while((line = in.readLine()) != null)
          buff = buff.append(line + "\n");

        in.close();
        acdText = buff.toString();
      }
      catch (IOException e)
      {
        System.out.println("BuildProgramMenu: Cannot read acd file " + acdText);
      }
    }
    else 
    {
      if(acdStore.containsKey(applName+".acd"))
      {
        Object obj = acdStore.get(applName+".acd");

        if(obj.getClass().getName().equals("java.lang.String"))
          acdText = (String)obj;
        else
          acdText = new String((byte[])obj);
 
//      System.out.println("Retrieved "+applName+" acd file from cache");
      }
      else
      {
        GetACD progacd = new GetACD(applName,mysettings);
        acdText = progacd.getAcd();
//      System.out.println("Retrieved "+applName+" acd file via soap");
        acdStore.put(applName+".acd",acdText);
      }
    }
    return acdText;
  }

}