sequencejpanel.java

emboss的linux版本的源代码

  /**
  *
  * Find all occurences of the pattern in the sequence between
  * the start and stop positions. Returning all positions of these
  * in a vector.
  * @param istart	start search from
  * @param istop	stop search from
  * @param seqS		sequence string to search
  * @return		vector of all positions which match 
  *
  */
  private Vector getPatternPositions(int istart, int istop,
                                     String seqS)
  {
    Vector pvec = new Vector();
    int patlen = pattern.length();
    int pstart = istart-patlen;
    int pstop  = istop+patlen;
    if(pstart < 0)
      pstart = 0;
    if(pstop > seqLength)
      pstop = seqLength;

    int ipat;
    while( (ipat = seqS.substring(pstart,pstop).indexOf(pattern)) > -1)
    {
      for(int i=0;i<patlen;i++)
        pvec.add(new Integer(ipat+pstart+i));
      pstart = ipat+pstart+1;
    }
//  System.out.println("Showing "+pattern+" :: "+ipat+pstart+" :: "+
//                     "istart "+istart+" istop "+istop);
    return pvec;
  }


  /**
  *
  * Find all occurences of the pattern in the sequence between
  * the start and stop positions. Returning all positions of these
  * in a vector.
  * @param subseqStart	index of the start of the (sub)sequence
  * @param subseq       sequence string to search
  * @return             vector of all positions which match
  *
  */
  private Vector getPatternPositions(int subseqStart,
                                     String subseq)
  {
    subseq = subseq.toLowerCase();
    Vector pvec = new Vector();
    int patlen = pattern.length();
    int pstart = 0;
    int ipat;
    while( (ipat = subseq.substring(pstart).indexOf(pattern)) > -1)
    {
      for(int i=0;i<patlen;i++)
        pvec.add(new Integer(ipat+pstart+subseqStart+i));
      pstart = ipat+pstart+1;
    }
//  System.out.println("Showing "+pattern+" :: "+ipat+pstart+" :: "+
//                     "istart "+istart+" istop "+istop);
    return pvec;
  }


  /**
  *
  * Set pattern to high light
  * @param pattern	pattern to high light
  *
  */
  protected void showPattern(String pattern)
  {
    highlightPattern = true;
    this.pattern = pattern.toLowerCase();
  }
 
 
  /**
  *
  * Set prettyplot display
  * @param prettyPlot	true if the prettyplot display is to
  *			be used
  */
  public void setPrettyPlot(boolean prettyPlot)
  {
    this.prettyPlot = prettyPlot;
  }

 
  /**
  *
  * Determine if using prettyplot display
  * @return  	true if the prettyplot display is to
  *           	be used
  */
  public boolean isPrettyPlot()
  {
    return prettyPlot;
  }


  /**
  *
  * Determine the tool tip to display
  * @param e	mouse event
  * @return	tool tip
  *
  */
  public String getToolTipText(MouseEvent e)
  {
    Point loc = e.getPoint();
    int resPos = (int)(loc.x/resWidth);
    if(resPos < 0)
      return null;

    if(resPos > seq.getSequence().length()-1)
      return null;

    String res = seq.getSequence().substring(resPos,resPos+1);
    String ls = System.getProperty("line.separator");

    if(seq.getID() != null)
      return seq.getID()+"\nResidue: "+res+ls+
           "Position: "+Integer.toString(resPos+1);

    return seq.getName()+"\nResidue: "+res+ls+
           "Position: "+Integer.toString(resPos+1);
  }


  /**
  *
  * Get the tool tip location
  * @param e    mouse event
  * @return     point on the display
  *
  */
  public Point getToolTipLocation(MouseEvent e)
  {
    Point loc = e.getPoint();
    int x = (int)((loc.x+resWidth)/resWidth)*resWidth;
    int y = seqHeight-(resWidth/2);
    return new Point(x,y);
  }


  /**
  *
  * Get a residue colour
  * @param s	residue
  * @return	colour of the residue s
  *
  */
  private Color getColor(String s)
  {
    s = s.toUpperCase();
    if(colorTable.containsKey(s))
      return (Color)colorTable.get(s);
       
    return getBackground();
  }
 

  /**
  *
  * Set a default colour scheme 
  *
  */ 
  public void setDefaultColorHashtable()
  {
    colorTable = new Hashtable();
    colorTable.put("A",Color.green);
    colorTable.put("T",Color.red);
    colorTable.put("C",Color.blue);
    colorTable.put("G",Color.white);
  }


  /**
  *
  * Set whether to draw boxes around residues
  * @param drawBlackBox	true to draw boxes
  *
  */
  public void setDrawBoxes(boolean drawBlackBox)
  {
    if(drawNumber)
      return;
    this.drawBlackBox = drawBlackBox;
//  paintComponent(getGraphics());
  }


  /**
  *
  * Set whether to colour residues
  * @param drawColorBox true to colour residues
  *
  */
  public void setDrawColor(boolean drawColorBox)
  {
    if(drawNumber)
      return;
    this.drawColorBox = drawColorBox;
//  paintComponent(getGraphics());
  }


  /**
  *
  * Set the font size and set the size
  * @param size		font size
  *
  */
  public void setFontSize(int size)
  {
    fontSize = size;
    font = new Font("Monospaced",
                      Font.PLAIN, fontSize);
    FontMetrics metrics = getFontMetrics(font);
    boundWidth = metrics.stringWidth("A");
    resWidth = metrics.stringWidth("A")+boundWidth/2;
    seqHeight = metrics.stringWidth("A")+boundWidth;
    setPreferredSize(getPreferredSize());
    repaint();
//  paintComponent(getGraphics());
  }
 

  /**
  *
  * Get the width of a residue
  * @return	residue width
  *
  */
  public int getResidueWidth()
  {
    return resWidth;
  }


  /**
  *
  * Set the colour scheme 
  * @param colorHash	colour scheme to use
  *
  */
  public void setColorScheme(Hashtable colorHash)
  {
    this.colorTable = colorHash;
    setPrettyPlot(false);
  }


  /**
  *
  * Get the font size
  * @return font size
  *
  */
  public int getFontSize()
  {
    return fontSize;
  }


  /**
  *
  * Get the preferred size dimension
  * @return 	preferred dimension for this component
  *
  */
  public Dimension getPreferredSize()
  {
    return new Dimension(getSequenceWidth(),getSequenceHeight());
  }


  /**
  *
  * Re-size the sequence alignment panel if the width of 
  * this sequence pane increases
  *
  */
  protected void viewPaneResize()
  {
    Dimension dpane = viewPane.getPreferredSize();
    GraphicSequenceCollection gsc = (GraphicSequenceCollection)viewPane;
    
    int xpane = (int)dpane.getWidth();
    int xsize = gsc.getPanelWidth();
    if(xsize > xpane)
      viewPane.setPreferredSize(new Dimension(xsize,
                              gsc.getPanelHeight()));
    gsc.setJScrollPaneViewportView();
  }


  /**
  *
  * Get the sequence panel height
  * @return 	sequence height
  *
  */
  public int getSequenceHeight()
  {
    return seqHeight+ypad;
  }


  /**
  *
  * Get the sequence panel width
  * @return     sequence width
  *
  */
  public int getSequenceWidth()
  {
    return resWidth*seqLength;
  }


  /**
  *
  * Get the width of a residue
  * @return 	residue width
  *
  */
  public int getSequenceResidueWidth()
  {
    return resWidth;
  }


  /**
  *
  * Set the sequence length
  * @param s	sequence length
  *
  */
  public void setSequenceLength(int s)
  {
    seqLength = s;
  }


  /**
  *
  * Get the sequence name associated with this display
  * @return	sequence name
  *
  */
  public String getName()
  {
    return seq.getName();
  }


  /**
  *
  * Render the sequence name graphic
  * @param g2d	graphic
  *
  */
  public void getNamePrintGraphic(Graphics g2d)
  {
    if(seq == null)
      return;

    String name = seq.getName();
    if(seq.getID() != null)
      name = seq.getID();

    g2d.setFont(font);
    g2d.setColor(Color.black);
    g2d.drawString(name,0,seqHeight-boundWidth2);
  }
 

  /**
  *
  * Render the sequence graphic
  * @param g2d  	graphic
  * @param MAXSEQNAME	maximum size for a sequence name
  * @param istart	sequence start position for graphic
  * @param istop	sequence stop position for graphic
  *
  */
  public void getSequencePrintGraphic(Graphics g2d, int MAXSEQNAME, 
                                      int istart, int istop) 
  {
    String sName = null;
    String seqS  = null; 

    g2d.setFont(font);
    if(drawSequence)
    {
      sName = seq.getName();
      if(seq.getID() != null)
        sName = seq.getID();

      seqS  = seq.getSequence();
      int seqLength = seq.getLength();
      if(seqLength < istop)
        istop = seqLength;
    }

    int boundWidth4 = boundWidth2/2;
    boolean leftResidue = false;
    FontMetrics metrics = getFontMetrics(font);
    for(int i=istart;i<istop;i++)
    {
      int ipos = (i-istart)*(resWidth)+MAXSEQNAME;
      if(drawColorBox)
      {
        g2d.setColor(getColor(seqS.substring(i,i+1)));
        g2d.fillRect(ipos,0,resWidth,seqHeight);
      }
      g2d.setColor(Color.black);
      if(drawBlackBox)
        g2d.drawRect((i-istart)*(resWidth)+MAXSEQNAME,0,resWidth,seqHeight);


      if(drawSequence)
      {
        String res = seqS.substring(i,i+1);
        if(prettyPlot)
          leftResidue = prettyDraw(i,ipos,istop,res,seqHeight,
                                   resWidth,leftResidue,g2d);

        g2d.drawString(res,
                      ((i-istart)*resWidth)+boundWidth4+MAXSEQNAME,
                      seqHeight-boundWidth2);
      
      }
      else if(drawNumber && (int)((i+1-istart)%interval) == 0)
      {
        String snum = Integer.toString(i+1);
        int numWidth = metrics.stringWidth(snum);
        g2d.drawString(snum,
                     ((int)((i-istart+0.5)*resWidth)-(numWidth/2))+MAXSEQNAME,
                     seqHeight-boundWidth2);
      }
    }
  }
 

  /**
  *
  * Override actionPerformed for popup menu actions
  * @param e	action event
  * 
  */
  public void actionPerformed(ActionEvent e)
  {
    JMenuItem source = (JMenuItem)(e.getSource());
    if(source.getText().startsWith("Delete "))
    {
      ((GraphicSequenceCollection)viewPane).deleteSequence(seq.getName());
    }
    else if(source.getText().startsWith("Reverse Complement"))
    {
      seq.reverseComplementSequence();
      paintComponent(getGraphics());
    }
    else if(source.getText().startsWith("Reverse "))
    {
      seq.reverseSequence();
      paintComponent(getGraphics());
    }
    else if(source.getText().startsWith("Complement "))
    {
      seq.complementSequence();
      paintComponent(getGraphics());
    }
  }


  /**
  *
  * Popup listener
  *
  */
  class PopupListener extends MouseAdapter
  {
    public void mousePressed(MouseEvent e)
    {
      maybeShowPopup(e);
    }

    public void mouseReleased(MouseEvent e)
    {
      maybeShowPopup(e);
    }

    private void maybeShowPopup(MouseEvent e)
    {
      if(e.isPopupTrigger())
        popup.show(e.getComponent(),
                e.getX(), e.getY());
    }
  }

}