graphicsequencecollection.java

emboss的linux版本的源代码

    }
    return Color.black;
  }


  /**
  *
  * Determine the colour of a residue background
  *
  */
  protected Color getPrettyBackground(Color textColour)
  {
    if(textColour.equals(prettyPlot.getIDColour()))
      return prettyPlot.getIDBackgroundColour();
    else if(textColour.equals(prettyPlot.getMatchColour()))
      return prettyPlot.getMatchBackgroundColour();
    else
      return null;
  }

 
  /**
  *
  * Determine if the identities are to be boxed
  * @return 	true if to draw boxes
  *
  */ 
  protected boolean isPrettyBox()
  {
    return prettyPlot.isPrettyBox();
  }

  
  /**
  *
  * 
  *
  */
  protected int testUpAndDown(int pos, Sequence seq)
  {
    int seqIndex = seqs.indexOf(seq);

    int testUp = -1;
    if(seqIndex == 0)
      testUp = 1;
    else
    {
      Sequence seqUp = (Sequence)seqs.get(seqIndex-1);
      String res = seqUp.getSequence().substring(pos,pos+1);
      Color col = getColor(res,pos,seqUp.getName());
      if(col.equals(Color.black))
        testUp = 1;
    }

    int testDown = -1;
    if(seqIndex+1 == seqs.size())
      testDown= 1;
    else
    {
      Sequence seqDown = (Sequence)seqs.get(seqIndex+1);
      SequenceJPanel seqPanelDown = (SequenceJPanel)graphicSequence.get(seqIndex+2);
      String res = seqDown.getSequence().substring(pos,pos+1);
      Color col = getColor(res,pos,seqDown.getName());
      if(col.equals(Color.black) || !seqPanelDown.isPrettyPlot())   
        testDown = 1;
    }

    if(testUp > -1 && testDown > -1)
      return 3;
    else if(testDown > -1)
      return 2;
    else if(testUp > -1)
      return 1;
    return -1;
  }


  /**
  *
  * Remove a sequence from the editor display
  * @param name		name of sequence to remove
  *
  */
  private Sequence removeSequence(String name)
  {
    boolean removed = false;
    int index = 0;
    Enumeration enumer = seqs.elements();
    Sequence seq = null;

    while(enumer.hasMoreElements())
    {
      seq = (Sequence)enumer.nextElement();
      if(seq.getName().equals(name))
      {
        removedSeqs.add(seq);
        removed = true;
        seqs.remove(seq);
        break;
      }
      index++;
    }

    if(!removed)
      return null;
    if(drawNumber)
      index++;

    seqBox.remove(index);
    seqNameBox.remove(index);
    graphicName.removeElementAt(index);
    graphicSequence.removeElementAt(index);
    return seq;
  }

  /**
  *
  *  Delete a sequence from the sequence collection display
  *  and resize the sequence panel display
  *  @param name	name of sequence to remove
  *
  */
  protected void deleteSequence(String name)
  {
    removeSequence(name);
    setMaxSeqLength();
    numberDraw.setSequenceLength(MAXSEQLENGTH);
    Dimension dpane = getPanelSize();
    setMinimumSize(dpane);
    setPreferredSize(dpane);
    numberDraw.setMaximumSize(numberDraw.getPreferredSize());
    numberDraw.setMinimumSize(numberDraw.getPreferredSize());
    setJScrollPaneViewportView();
  }

  /**
  *
  * Move a sequence to a new position
  * @param name		name of sequence to remove
  * @param i		new position in the sequence editor
  *
  */
  protected void moveSequence(String name, int i)
  {
    Sequence seq = removeSequence(name);
    addSequence(seq,true,0,0,i);
  }

  /**
  *
  * Sorts the sequences and displays them by their id's
  *
  */
  protected void idSort()
  {
    int nseqs = 0;

// get no. of sequences excl. consensus
    Enumeration enumer = seqs.elements();
    while(enumer.hasMoreElements())
    {  
      String name = ((Sequence)enumer.nextElement()).getName();
      if(!name.equals("Consensus"))
        nseqs++;
    }

    String seqName[] = new String[nseqs];
    int i = 0;
    enumer = seqs.elements(); 
    while(enumer.hasMoreElements())
    {
      String name = ((Sequence)enumer.nextElement()).getName();
      if(!name.equals("Consensus"))
      {
        seqName[i] = new String(name);
        i++;
      }
    }

    Arrays.sort(seqName);
    for(i=0;i<nseqs;i++)
      moveSequence(seqName[i],i);
  }

  /**
  *
  *  Add a sequence at a particular index to the sequence 
  *  collection display and to the collection of sequences 
  *  (seqs) with a specified y-padding.
  *  @param seq			sequence to add to the editor display
  *  @param addToSequences	true to add seq to the vector of sequences
  *  @param ypad		sequence panel height padding
  *  @param fontSize		font size
  *  @param index		sequence index
  *
  */
  protected void addSequence(Sequence seq, boolean addToSequences, 
                             int ypad, int fontSize, int index)
  {
    if(addToSequences)
      seqs.add(index,seq);
    if(drawNumber)
      index++;

    SequenceJPanel gs = new SequenceJPanel(seq,this,
                           drawSequence,drawBlackBox,drawColorBox,
                           colorScheme,ypad);
    graphicSequence.add(index,gs);

    Box XBox = new Box(BoxLayout.X_AXIS);
    XBox.add(gs);
    XBox.add(Box.createHorizontalGlue());
    seqBox.add(XBox,index);
    gs.setToolTipText("");   //enable tooltip display

    SequenceNameJButton snj = new SequenceNameJButton(seq,ypad);
    graphicName.add(index,snj);
    XBox = new Box(BoxLayout.X_AXIS);
    XBox.add(Box.createHorizontalGlue());
    XBox.add(snj);
    seqNameBox.add(XBox,index);

    if(seq.getLength()>MAXSEQLENGTH)
      MAXSEQLENGTH = seq.getLength();

    Dimension actual = gs.getMaximumSize();
    int slen = gs.getResidueWidth()*(int)(MAXSEQLENGTH*1.2);
    gs.setMaximumSize(new Dimension(slen,(int)actual.getHeight()));
  }



  /**
  *
  *  Add a sequence to the sequence collection display and
  *  to the collection of sequences (seqs) with a specified
  *  y-padding.
  *  @param seq                 sequence to add to the editor display
  *  @param addToSequences      true to add seq to the vector of sequences
  *  @param ypad                sequence panel height padding
  *  @param fontSize            font size
  *
  */
  protected void addSequence(Sequence seq, boolean addToSequences,
                             int ypad, int fontSize)
  {
    if(addToSequences)
      seqs.add(seq);
    SequenceJPanel gs = new SequenceJPanel(seq,this,
                           drawSequence,drawBlackBox,drawColorBox,
                           colorScheme,fontSize,ypad);
    graphicSequence.add(gs);

    Box XBox = new Box(BoxLayout.X_AXIS);
    XBox.add(gs);
    XBox.add(Box.createHorizontalGlue());
    seqBox.add(XBox);
    gs.setToolTipText("");   //enable tooltip display

    SequenceNameJButton snj = new SequenceNameJButton(seq,ypad);
    graphicName.add(snj);
    XBox = new Box(BoxLayout.X_AXIS);
    XBox.add(Box.createHorizontalGlue());
    XBox.add(snj);
    seqNameBox.add(XBox);

    if(seq.getLength()>MAXSEQLENGTH)
      MAXSEQLENGTH = seq.getLength();

    Dimension actual = gs.getMaximumSize();
    int slen = gs.getResidueWidth()*(int)(MAXSEQLENGTH*1.2);
    gs.setMaximumSize(new Dimension(slen,(int)actual.getHeight()));
  }


  /**
  *
  * Get the sequence view size
  * @return 	sequence view dimension
  *
  */
  public Dimension getViewSize()
  {
    hgt = 1;
    len = 0; 
    Enumeration enumer = graphicSequence.elements();
    while(enumer.hasMoreElements())
    {
      SequenceJPanel gs = (SequenceJPanel)enumer.nextElement();
      hgt = hgt+gs.getSequenceHeight();
      if(len<gs.getSequenceWidth())
        len = gs.getSequenceWidth();
    }

    if(pc !=null) 
    {
      Dimension dplot = pc.getPreferredSize();
      hgt = hgt + (int)dplot.getHeight() + plotConStrut;
    }
    return new Dimension(len,hgt);
  }


  public String getName(int i)
  {
    return ((Sequence)seqs.get(i)).getName();
  }

  /**
  *
  * Get the sequence name view size
  * @return	sequence name dimension
  *
  */
  public Dimension getNameViewSize()
  {
    int hgtName = getNameHeight();
    int lenName = getNameWidth();
    return new Dimension(lenName,hgtName);
  }

  /**
  *
  * Get the sequence view size
  * @return     sequence view dimension
  *
  */
  public Dimension getPanelSize()
  {
    getViewSize();
    return new Dimension(len,hgt);
  }

  /**
  *
  * Get the sequence name panel height 
  * @return     sequence name panel height
  *
  */
  public int getNameHeight()
  {
    int hgtName = 0;
    Enumeration enumer = graphicName.elements();
    while(enumer.hasMoreElements())
      hgtName = hgtName+
          ((SequenceNameJButton)enumer.nextElement()).getPanelHeight();
    return hgtName;
  }

  /**
  *
  * Get the sequence name panel width
  * @return     sequence name panel width
  *
  */
  public int getNameWidth()
  {
    int lenName = 0;
    Enumeration enumer = graphicName.elements();
    while(enumer.hasMoreElements())
    {
      SequenceNameJButton gs = (SequenceNameJButton)enumer.nextElement();
      if(lenName<gs.getPanelWidth())
        lenName = gs.getPanelWidth();
    }
    return lenName;
  }
 
  /**
  *
  * Set the sequence name panel width
  * @param x	sequence name panel  width
  *
  */
  public void setNamePanelWidth(int x)
  {
    seqNamePanel.setPreferredSize(new Dimension(x,1000));
  }

  /**
  *
  * Get the sequence panel height
  * @return     sequence panel height
  *
  */
  public int getPanelHeight()
  {
    getViewSize();
    return hgt;
  }

  /**
  *
  * Get the sequence panel width
  * @return     sequence panel width
  *
  */
  public int getPanelWidth()
  {
//  getNameViewSize();
    getViewSize();
    return len;
  }

  /**
  *
  * Get the vector containing the SequenceJPanel objects
  * @return	vector containing the SequenceJPanel objects
  *
  */
  public Vector getGraphicSequence()
  {
    return graphicSequence;
  }

  /**
  *
  * Draw the boxes around the residues of each sequence
  * @param	true to draw boxes, false not to display
  *		boxes
  *
  */
  public void setDrawBoxes(boolean drawBlackBox)
  {
    this.drawBlackBox = drawBlackBox;
    Enumeration enumer = graphicSequence.elements();
    while(enumer.hasMoreElements())
      ((SequenceJPanel)(enumer.nextElement())).setDrawBoxes(drawBlackBox);
    setJScrollPaneViewportView();
  }

  /**
  *
  * Draw the residue colours in each sequence
  * @param      true to display colour, false not to display
  *             colour
  *
  */
  public void setDrawColor(boolean drawColorBox)
  {
    this.drawColorBox = drawColorBox;
    Enumeration enumer = graphicSequence.elements();
    while(enumer.hasMoreElements())
      ((SequenceJPanel)(enumer.nextElement())).setDrawColor(drawColorBox);
    setJScrollPaneViewportView();
  }

  /**
  *
  * Set the font size of the sequences in the editor
  * @param	font size to use
  *
  */
  public void setFontSizeForCollection(int fs)
  {
    Enumeration enumer = graphicSequence.elements();

    while(enumer.hasMoreElements())
    {
      SequenceJPanel gs = (SequenceJPanel)enumer.nextElement();
      gs.setFontSize(fs);
      Dimension actual = gs.getMaximumSize();
      int slen = gs.getResidueWidth()*(int)(MAXSEQLENGTH*1.2);
      gs.setMaximumSize(new Dimension(slen,(int)actual.getHeight()));
    }

    Enumeration enumName = graphicName.elements();
    while(enumName.hasMoreElements())
    {
      SequenceNameJButton snjp = (SequenceNameJButton)enumName.nextElement();
      snjp.setFontSize(fs);
      snjp.setMaximumSize(snjp.getPreferredSize());
    }