dnadraw.java

emboss的linux版本的源代码

   
        current_dna = new DNADraw(block,restrictionEnzyme,
                                  lineAttr,0,100,100);
        jsp.setViewportView(current_dna);
      }
    });
    fileMenu.add(openMenu);
    fileMenu.add(new JSeparator());
 
// print
    JMenu printMenu = new JMenu("Print");
    fileMenu.add(printMenu);

    JMenuItem print = new JMenuItem("Print postscript");
    print.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        doPrintActions();
      }
    });
    printMenu.add(print);

    JMenuItem printImage = new JMenuItem("Print png/jpeg Image...");
    printImage.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PrintDNAImage pdnai = new PrintDNAImage(current_dna);
        pdnai.print();
      }
    });
    printMenu.add(printImage);

// print preview
    JMenuItem printPreview = new JMenuItem("Print Preview...");
    printPreview.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PrintDNAImage pdnai = new PrintDNAImage(current_dna);
        pdnai.printPreview();
      }
    });
    fileMenu.add(printPreview);
    fileMenu.add(new JSeparator());


    JMenuItem fileMenuExit = new JMenuItem("Exit");
    fileMenuExit.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        if(!close)
          System.exit(0);
        else
        {
          mainFrame.setVisible(false);
          mainFrame.dispose();
        }
      }
    });
    fileMenu.add(fileMenuExit);

// view menu
    JMenu viewMenu = new JMenu("View");
    menuBar.add(viewMenu);
  
    JMenuItem zoomIn = new JMenuItem("Zoom In");
    zoomIn.setAccelerator(KeyStroke.getKeyStroke(
                    KeyEvent.VK_I, ActionEvent.CTRL_MASK));
    zoomIn.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zoomIn();
      }
    });
    viewMenu.add(zoomIn);

    JMenuItem zoomOut = new JMenuItem("Zoom Out");
    zoomOut.setAccelerator(KeyStroke.getKeyStroke(
                    KeyEvent.VK_O, ActionEvent.CTRL_MASK));
    zoomOut.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zoomOut();
      }
    });
    viewMenu.add(zoomOut);

// options menu
    JMenu optionMenu = new JMenu("Options");
    menuBar.add(optionMenu);


    JMenuItem wizard = new JMenuItem("DNA Wizard");
    wizard.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {   
        Wizard wiz = new Wizard(current_dna);
        current_dna = wiz.getDNADraw();
        jsp.setViewportView(current_dna);
      }
    });
    optionMenu.add(wizard);
    optionMenu.add(new JSeparator());

    JMenuItem line = new JMenuItem("DNA attributes");
    line.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        JFrame f = new JFrame("DNA Attributes");
        LineAttribute la = new LineAttribute(current_dna);
        JScrollPane laScroll = new JScrollPane(la);
        JPanel laPane = (JPanel)f.getContentPane();
        laPane.add(laScroll,BorderLayout.CENTER);
        f.setJMenuBar(la.createMenuBar(f));
        f.pack();
        f.setVisible(true);
      }
    });
    optionMenu.add(line);

    
    JMenuItem tickMarks = new JMenuItem("Tick marks");
    tickMarks.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        JFrame f = new JFrame("Tick Marks");
        Ticks tk = new Ticks(current_dna,true);
        JScrollPane tkScroll = new JScrollPane(tk);
        JPanel tkPane = (JPanel)f.getContentPane();
        tkPane.add(tkScroll,BorderLayout.CENTER);
        f.setJMenuBar(tk.createMenuBar(f));
        f.pack();
        f.setVisible(true);
      }
    });
    optionMenu.add(tickMarks);


    JMenuItem gmarker = new JMenuItem("Genetic Features");
    gmarker.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        JFrame f = new JFrame("Genetic Features");
        GeneticMarker gm = new GeneticMarker(current_dna,
                                             block);
        JScrollPane gmScroll = new JScrollPane(gm);
        JPanel gmPane = (JPanel)f.getContentPane();
        gmPane.add(gmScroll,BorderLayout.CENTER);
        f.setJMenuBar(gm.createMenuBar(f));
        f.pack();
        f.setVisible(true);
      }
    });
    optionMenu.add(gmarker);

    JMenuItem reSites = new JMenuItem("Restriction Enzyme");
    reSites.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        JFrame f = new JFrame("Restriction Enzyme");
        RestrictionEnzyme re = new RestrictionEnzyme(current_dna,
                                              restrictionEnzyme);
        JScrollPane reScroll = new JScrollPane(re);
        JPanel rePane = (JPanel)f.getContentPane();
        rePane.add(reScroll,BorderLayout.CENTER);
        f.setJMenuBar(re.createMenuBar(f));
        f.pack();
        f.setVisible(true);
      }
    });
    optionMenu.add(reSites);

// help manu
    JMenu helpMenu = new JMenu("Help");
    menuBar.add(helpMenu);
   
    JMenuItem aboutMenu = new JMenuItem("About");
    helpMenu.add(aboutMenu);
    aboutMenu.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        ClassLoader cl = this.getClass().getClassLoader();
        try
        {
          URL inURL = cl.getResource("resources/readmeDNADraw.html");
          new Browser(inURL,"resources/readmeAlign.html");
        }
        catch (Exception ex)
        {
          JOptionPane.showMessageDialog(null,
                              "Jemboss Alignment Viewer Guide not found!",
                              "Error", JOptionPane.ERROR_MESSAGE);
        }
      }
    });

    return menuBar;
  }

  
  public void setCloseAndDispose(boolean close, JFrame mainFrame)
  {
    this.mainFrame = mainFrame;
    this.close = close;
  }

  protected Vector getGeneticMarker()
  {
    return block;
  }


  protected Vector getRestrictionEnzyme()
  {
    return restrictionEnzyme;
  }


  protected int getStart()
  {
    return ((Integer)lineAttr.get("start")).intValue();
  }

 
  protected int getEnd()
  {
    return ((Integer)lineAttr.get("end")).intValue();
  }

  
  protected void setStart(int start)
  {
    lineAttr.put("start",new Integer(start));
    calculateTickPosistions();
  }


  protected void setEnd(int end)
  {
    lineAttr.put("end",new Integer(end));
    calculateTickPosistions();
  }

////////////////////
// DRAG AND DROP
////////////////////
// drag source
  public void dragGestureRecognized(DragGestureEvent e)
  {
    // ignore if mouse popup trigger
    InputEvent ie = e.getTriggerEvent();
    if(ie instanceof MouseEvent)
      if(((MouseEvent)ie).isPopupTrigger())
        return;

    Point loc = e.getDragOrigin();
    Component c = getComponentAt(loc);
 
    if(c instanceof Block)
    {
//    System.out.println("BLOCK DRAG GESTURE");
    
      for(int i=0; i<getComponentCount(); i++)
      {
        if(getComponent(i) instanceof Block)
        {
          Block drawBlock = (Block)getComponent(i);
          if(drawBlock.isOverMe(loc.x,loc.y))
             e.startDrag(DragSource.DefaultCopyDrop,  // cursor
                   (Transferable)drawBlock,           // transferable data
                   this);                             // drag source listener
        }
      }
    }
  }

  public void dragDropEnd(DragSourceDropEvent e) {}
  public void dragEnter(DragSourceDragEvent e) {}
  public void dragExit(DragSourceEvent e) {}
  public void dragOver(DragSourceDragEvent e) {}
  public void dropActionChanged(DragSourceDragEvent e) {}

// drop sink
  public void dragEnter(DropTargetDragEvent e)
  {
    if(e.isDataFlavorSupported(Block.BLOCK))
      e.acceptDrag(DnDConstants.ACTION_COPY_OR_MOVE);
  }

  public void drop(DropTargetDropEvent e)
  {
    Transferable t = e.getTransferable();
    if(t.isDataFlavorSupported(Block.BLOCK))
    {
      try
      {
        Point loc = e.getLocation();
        Block drawBlock = (Block)t.getTransferData(Block.BLOCK);
        
        for(int i=0; i<getComponentCount(); i++)
          if(getComponent(i) instanceof Block)
          {
            Block c = (Block)getComponent(i);
            if( c.getLabel().equals(drawBlock.getLabel()) &&
                c.getStart() == drawBlock.getStart() &&
                c.getEnd() == drawBlock.getEnd() )
              c.setBlockLocation(loc.x,loc.y);
          }
      }
      catch(Exception ufe){} 
    }
  }

  public void dragOver(DropTargetDragEvent e)
  {
  }

  public void dropActionChanged(DropTargetDragEvent e) {}
  public void dragExit(DropTargetEvent e){}

  public static void main(String arg[])
  {
    Wizard wiz = new Wizard(null);
    DNADraw dna = wiz.getDNADraw();

    JFrame f = new JFrame("DNA Viewer");

    Dimension d = f.getToolkit().getScreenSize();

    Vector minTicks = new Vector();
    minTicks.add(new Integer(1200));
    minTicks.add(new Integer(1600));
    minTicks.add(new Integer(2000));
    minTicks.add(new Integer(2500));
    minTicks.add(new Integer(3000));
    minTicks.add(new Integer(3500));
    minTicks.add(new Integer(4070));
    minTicks.add(new Integer(4500));
    minTicks.add(new Integer(5070));
    Vector majTicks = new Vector();

    Vector marker = new Vector();
    Vector block = new Vector();
    marker.add(new String("CDS"));
    marker.add(new Integer(1200));
    marker.add(new Integer(1600));
    marker.add(Color.red);
    marker.add(new Float(10.0f));
    marker.add(new Boolean(false));
    marker.add(new Boolean(true));
    block.add(marker);

    Vector restrictionEnzyme = new Vector(); 
    Vector re = new Vector();
    re.add(new String("EcoR1"));
    re.add(new Integer(2555));
    re.add(Color.blue);
    restrictionEnzyme.add(re);
    re = new Vector();
    re.add(new String("EcoR1"));
    re.add(new Integer(3444));
    re.add(Color.blue);
    restrictionEnzyme.add(re);

  
    if(dna == null)
      dna = new DNADraw(minTicks,majTicks,block,restrictionEnzyme);
    jsp = new JScrollPane(dna);
    jsp.getViewport().setBackground(Color.white);
    f.getContentPane().add(jsp);
    f.setJMenuBar(dna.createMenuBar());
    
    f.pack();
    f.setLocation(((int)d.getWidth()-f.getWidth())/4,
                  ((int)d.getHeight()-f.getHeight())/2);

    f.setVisible(true);
  }

}