alignjframe.java

emboss的linux版本的源代码

      public void actionPerformed(ActionEvent e)
      {
        matFrame.setMatrix(mat);
        matFrame.setVisible(true);
        matFrame.toFront();
      }
    });

// colour display
    JMenuItem showColour = new JMenuItem("Colour Display");
    viewMenu.add(showColour);
    final ColourJFrame colFrame = new ColourJFrame(this);
    showColour.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        Point pos = getLocationOnScreen();
        pos.x = pos.x + getWidth();
        if(pos.x+colFrame.getWidth() > dScreen.getWidth())
          pos.x = (int)(dScreen.getWidth()-colFrame.getWidth());

        colFrame.setLocation(pos);
        colFrame.setCurrentColour(currentColour);
        colFrame.setVisible(true);
        colFrame.toFront();
      }
    });
    viewMenu.add(new JSeparator());
     
    colourMenus(viewMenu);
   
//pretty plot
    final JMenuItem pretty = new JMenuItem("Colour Identical/Matches");
    viewMenu.add(pretty);
    viewMenu.add(new JSeparator());

//draw black box
    final JCheckBoxMenuItem drawBoxes = new JCheckBoxMenuItem("Draw boxes",false);
    drawBoxes.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setDrawBoxes(drawBoxes.isSelected());
      }
    });
    viewMenu.add(drawBoxes);

//draw colored boxes
    final JCheckBoxMenuItem drawColorBox = new JCheckBoxMenuItem("Colour boxes",true);
    drawColorBox.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setDrawColor(drawColorBox.isSelected());
      }
    });
    viewMenu.add(drawColorBox);

    pretty.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        if(ppj == null)
          ppj = new PrettyPlotJFrame(gsc);
        else
          ppj.setGraphicSequenceCollection(gsc);
        gsc.setMatrix(mat);
        ppj.setVisible(true);
      }
    });
    menuBar.add(viewMenu);

// calculate menu
    JMenu calculateMenu = new JMenu("Calculate");
    menuBar.add(calculateMenu);

// consensus sequence
    final ConsensusOptions options = new ConsensusOptions(jspSequence);
    calculateCons.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        setCursor(cbusy);
        gsc.deleteSequence("Consensus");

        float wgt = getTotalWeight(gsc.getSequenceCollection());
        float plu = 0.f;
        try
        {
          plu = options.getPlurality();
        }
        catch(NumberFormatException nfe)
        {
          plu = wgt/2.f;
        }

        float cas = 0.f;
        try
        {
          cas = options.getCase();
        }
        catch(NumberFormatException nfe)
        {
          cas = wgt/2.f;
        }

        Consensus conseq = new Consensus(mat,   
                    gsc.getSequenceCollection(),
                    plu,cas,
                    options.getIdentity());

        int fontSize = gsc.getFontSize();
        gsc.addSequence(conseq.getConsensusSequence(),true,0,fontSize);

//      if(pretty.isSelected())
//        gsc.setPrettyPlot(pretty.isSelected(),ppj);

        Dimension dpane = gsc.getPanelSize();
        gsc.setPreferredSize(dpane);
        gsc.setNamePanelWidth(gsc.getNameWidth());
        jspSequence.setViewportView(gsc);
        setCursor(cdone);
        calculateCons.setText("Recalculate consensus");
      }
    });
    calculateMenu.add(calculateCons);

    
    JMenuItem consOptions = new JMenuItem("Set consensus options...");
    consOptions.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        try
        {
          Vector vseq = gsc.getSequenceCollection();
//        Enumeration enumer = vseq.elements();
          float wgt = getTotalWeight(gsc.getSequenceCollection());
          options.setCase(wgt/2.f);
          options.setPlurality(wgt/2.f);
          options.setGraphicSequenceCollection(gsc);
        }
        catch(NullPointerException npe){}
        options.setMatrix(mat);
        options.setVisible(true);
      }
    });
    calculateMenu.add(consOptions);
    calculateMenu.add(new JSeparator());

// %age identity between pairs
    JMenuItem calculateId = new JMenuItem("Identity table");
    calculateId.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        IDTableJFrame idtab = new IDTableJFrame(gsc.getSequenceCollection());
        idtab.setVisible(true);
      }
    });
    calculateMenu.add(calculateId);
    calculateMenu.add(new JSeparator());

// consensus plot
    calculatePlotCon.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        setCursor(cbusy);
        gsc.showConsensusPlot(mat,2);
        setCursor(cdone);
        calculatePlotCon.setText("Recalculate Consensus plot");
      }
    });
    calculateMenu.add(calculatePlotCon);
    calculateMenu.add(new JSeparator());

// sort by id
    JMenuItem test = new JMenuItem("Sort by ID");
    calculateMenu.add(test);
    test.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.idSort();
        jspSequence.setViewportView(gsc);
      }
    });
    
// font menu
    String sizes[] = {"10", "12", "14", "16", "18"};
    final JComboBox fntSize = new JComboBox(sizes);
    fntSize.setSelectedItem("12");
    menuBar.add(fntSize);
    fntSize.setEditable(true);
    Dimension dfont = new Dimension(50,20);
    fntSize.setPreferredSize(dfont);
    fntSize.setMaximumSize(dfont);
    fntSize.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        String fsize = (String)fntSize.getSelectedItem();
        if(gsc !=null)
          gsc.setFontSizeForCollection(Integer.parseInt(fsize));
      }
    });

    setJMenuBar(menuBar);

// 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/readmeAlign.html");
          new Browser(inURL,"resources/readmeAlign.html");
        }
        catch (Exception ex)
        {
          JOptionPane.showMessageDialog(null,
                              "Jemboss Alignment Viewer Guide not found!",
                              "Error", JOptionPane.ERROR_MESSAGE);
        }
      }
    });

// set size of sequence panel
    Dimension d = new Dimension(700,300);
    jspSequence.setPreferredSize(d);

    JPanel seqNamePanel = new JPanel(new BorderLayout());
    seqNamePanel.add(jspSequence,BorderLayout.CENTER);

    mainPane.add(jspSequence,BorderLayout.CENTER);

    Border loweredbevel = BorderFactory.createLoweredBevelBorder();
    Border raisedbevel = BorderFactory.createRaisedBevelBorder();
    Border compound = BorderFactory.createCompoundBorder(raisedbevel,loweredbevel);
    statusField.setBorder(compound);
    statusField.setEditable(false);
    statusField.setText("Current matrix: "+mat.getCurrentMatrixName());
    mainPane.add(statusField,BorderLayout.SOUTH);

    addWindowListener(new winExit());
    pack();
    setLocation( (int)(dScreen.getWidth()-getWidth())/3,
                 (int)(dScreen.getHeight()-getHeight())/3 );
  }


  public static float getTotalWeight(Vector vseq)
  {
    float wgt = 0.f;
    vseq = gsc.getSequenceCollection();
    Enumeration enumer = vseq.elements();
    while(enumer.hasMoreElements())
    {
      Sequence s = (Sequence)enumer.nextElement();
      if(!s.getName().equals("Consensus"))
        wgt+=s.getWeight();
    }
    return wgt;
  }


  /**
  *
  * Set the scoring matrix
  * @param mat 	scoring matrix to use
  *
  */
  public void setMatrix(Matrix mat)
  {
    this.mat = mat;
  }

  /**
  *
  * Force a re-display of the sequences with a new colour
  * scheme.
  * @param hash		hash of the colour scheme
  *
  */
  public void repaintSequences(Hashtable hash)
  {
    gsc.setColorScheme(hash);
    gsc.repaint();
  }

  /**
  *
  * Given a Vector of Sequence display them in the editor
  * @param seqVector	vector containing Sequence objects
  *
  */
  protected void openMethod(Vector seqVector)
  {
    gsc = new GraphicSequenceCollection(seqVector,
                                   jspSequence,true,false,true,true,
                                   statusField);
// set colour scheme
    gsc.setColorScheme(SequenceProperties.residueColor);
    currentColour = (Hashtable)SequenceProperties.residueColor.clone();
    residueColor.setSelected(true);
    jspSequence.setViewportView(gsc);

    colourScheme("Residue colour");
  }


  /**
  *
  * Update the status bar with the selected colour scheme
  * being used.
  * @param colScheme 	name of colour scheme
  *
  */
  protected void colourScheme(String colScheme)
  {
    String status = statusField.getText();
    int ncol = status.indexOf("Colour Scheme: ");
    if(ncol > -1)
      statusField.setText(status.substring(0,ncol)+
                          "Colour Scheme: "+colScheme);
    else
      statusField.setText(status+"              "+
                          "Colour Scheme: "+colScheme);
  }

  /**
  *
  * Constructs the colour menus
  *
  */
  private void colourMenus(JMenu viewMenu)
  {
    ButtonGroup group = new ButtonGroup();

// property colour menus
    JMenu propertyMenu = new JMenu("Colour by Property");
    viewMenu.add(propertyMenu);

    JCheckBoxMenuItem acidColor =
                new JCheckBoxMenuItem("Red=acidic, Blue=basic");
    propertyMenu.add(acidColor);
    group.add(acidColor);
    acidColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.acidColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.acidColor;
        colourScheme("Red=acidic, Blue=basic");
      }
    });

    JCheckBoxMenuItem polarColor =
                new JCheckBoxMenuItem("Red=polar");
    propertyMenu.add(polarColor);
    group.add(polarColor);
    polarColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.polarColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.polarColor;
        colourScheme("Red=polar");
      }
    });

    JCheckBoxMenuItem hydrophobicColor = 
               new JCheckBoxMenuItem("Red=Hydrophobic");
    propertyMenu.add(hydrophobicColor);
    group.add(hydrophobicColor);
    hydrophobicColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.hydrophobicColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.hydrophobicColor;
        colourScheme("Red=Hydrophobic");
      }
    });

    JCheckBoxMenuItem aromaticColor = 
               new JCheckBoxMenuItem("Red=Aromatic, Blue=Aliphatic");
    propertyMenu.add(aromaticColor);
    group.add(aromaticColor);
    aromaticColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.aromaticColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.aromaticColor;
        colourScheme("Red=Aromatic, Blue=Aliphatic");
      }
    });

    JCheckBoxMenuItem surfaceColor =
               new JCheckBoxMenuItem("Red=Surface, Blue=Buried");
    propertyMenu.add(surfaceColor);
    group.add(surfaceColor);
    surfaceColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.surfaceColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.surfaceColor;
        colourScheme("Red=Surface, Blue=Buried");
      }
    });

    JCheckBoxMenuItem chargeColor  =
               new JCheckBoxMenuItem("Red=Positive, Blue=Negative");
    propertyMenu.add(chargeColor);
    group.add(chargeColor);
    chargeColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.chargeColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.chargeColor;
        colourScheme("Red=Positive, Blue=Negative");
      }
    });