groutgraphicsequencecollection.java

emboss的linux版本的源代码

/***************************************************************
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
*
*  @author: Copyright (C) Tim Carver
*
***************************************************************/

package org.emboss.jemboss.editor;

import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.print.*;
import java.util.*;
import java.io.File;
//import ;
import java.awt.event.AdjustmentListener;

import org.emboss.jemboss.gui.form.MultiLineToolTipUI;

/**
*  
* This class can be used to get a grapical representation
* of a collection of sequences.
*
*/
public class GroutGraphicSequenceCollection extends 
		GraphicSequenceCollection implements AdjustmentListener
{

		Vector targets; // = new Vector();

  /**
  *
  * @param seqs		vector of sequences
  * @param colorScheme	sequence colour scheme
  * @param jspSequence 	sequence scrollpane
  * @param drawSequence true to draw the sequence
  * @param drawBlackBox true to draw black square around residues
  * @param drawColorBox true to colour residues
  * @param drawNumber   true to draw sequence position number
  * @param statusField	status field in the editor
  *
  */
  public GroutGraphicSequenceCollection(Vector seqs, Hashtable colorScheme,
                         JScrollPane jspSequence,
                         boolean drawSequence, boolean drawBlackBox,
                         boolean drawColorBox, boolean drawNumber,
                         JTextField statusField)
  {
    super(seqs, colorScheme, jspSequence, drawSequence, drawBlackBox,
					 drawColorBox, drawNumber, statusField);
		jspSequence.getHorizontalScrollBar().addAdjustmentListener(this);
  }
 
  /**
  *
  * @param seqs         vector of sequences
  * @param jspSequence  sequence scrollpane
  * @param drawSequence true to draw the sequence
  * @param drawBlackBox true to draw black square around residues
  * @param drawColorBox true to colour residues
  * @param drawNumber   true to draw sequence position number
  * @param statusField  status field in the editor
  *
  */
  public GroutGraphicSequenceCollection(Vector seqs, JScrollPane jspSequence,
                         boolean drawSequence, boolean drawBlackBox,
                         boolean drawColorBox, boolean drawNumber,
                         JTextField statusField)
  {
    super(seqs,null,jspSequence,drawSequence,
         drawBlackBox,drawColorBox,drawNumber,statusField);
		jspSequence.getHorizontalScrollBar().addAdjustmentListener(this);
  }

  /**
  *
  * @param seqs		      vector of sequences
  * @param indents      vector of indents
  * @param colorScheme	sequence colour scheme
  * @param jspSequence 	sequence scrollpane
  * @param drawSequence true to draw the sequence
  * @param drawBlackBox true to draw black square around residues
  * @param drawColorBox true to colour residues
  * @param drawNumber   true to draw sequence position number
  * @param statusField	status field in the editor
  *
  */
  public GroutGraphicSequenceCollection(Vector seqs, Vector indents,
																				Hashtable colorScheme,
                         JScrollPane jspSequence,
                         boolean drawSequence, boolean drawBlackBox,
                         boolean drawColorBox, boolean drawNumber,
                         JTextField statusField)
  {
    super(seqs, colorScheme, jspSequence, drawSequence, drawBlackBox,
					 drawColorBox, drawNumber, statusField);
		doIndent(indents);
		jspSequence.getHorizontalScrollBar().addAdjustmentListener(this);
  }
 
  /**
  *
  * @param seqs         vector of sequences
  * @param indents      vector of indents
  * @param jspSequence  sequence scrollpane
  * @param drawSequence true to draw the sequence
  * @param drawBlackBox true to draw black square around residues
  * @param drawColorBox true to colour residues
  * @param drawNumber   true to draw sequence position number
  * @param statusField  status field in the editor
  *
  */
  public GroutGraphicSequenceCollection(Vector seqs, Vector indents,
																				JScrollPane jspSequence,
                         boolean drawSequence, boolean drawBlackBox,
                         boolean drawColorBox, boolean drawNumber,
                         JTextField statusField)
  {
    super(seqs,null,jspSequence,drawSequence,
         drawBlackBox,drawColorBox,drawNumber,statusField);
		
		// System.out.println("GroutGraphicSequenceCollection Vector seqs, Vector indents");
		doIndent(indents);
		jspSequence.getHorizontalScrollBar().addAdjustmentListener(this);
  }

	public void doIndent(Vector indents)
		{
				Vector numberSequenceJpanels = new Vector();
				// System.out.println("gsc setIndents to " + indents.elementAt(0) +  " " + indents.elementAt(1));
				int limit = graphicSequence.size();
				/*
				if(seqs.size() < indents.size())
				{
						limit = seqs.size();
				}
				else
				{
						limit = indents.size();
				}
				*/
				int drawNumberJPanels = 0;
				// System.out.println("xclimit = " + limit);
				for(int i = 0; i < limit; ++i)
				{
						// this is the new way
						// System.out.println("xclindenting graphicSequence.elementAt(" + i + ") = " + graphicSequence.elementAt(i));
				// System.out.println("xcligraphicSequence = " + graphicSequence);
				// System.out.println("xclindents = " + indents);
				// System.out.println("indents.elementAt(i - drawNumberJPanels) = " + indents.elementAt(i - drawNumberJPanels));
						if(!((SequenceJPanel) graphicSequence.elementAt
								 (i)).drawNumber)
						{
								((GroutSequenceJPanel) graphicSequence.elementAt
								 (i)).setIndent
										(((Integer) indents.elementAt(i - drawNumberJPanels)).intValue());
								setMaxSequenceLength(((GroutSequence) seqs.elementAt(i - drawNumberJPanels)).getLength());
								// System.out.println("MAXSEQLENGTH = " + MAXSEQLENGTH);
						}
						else
						{
								numberSequenceJpanels.addElement(graphicSequence.elementAt(i));
								((GroutSequenceJPanel) graphicSequence.elementAt
								 (i)).setIndent
										(((Integer) indents.elementAt(drawNumberJPanels)).intValue());
								++drawNumberJPanels;
						}
						// this is the old way
						/*
						((GroutSequence) seqs.elementAt(i)).setIndent
								(((Integer) indents.elementAt(i)).intValue());
						
						setMaxSequenceLength(((GroutSequence) seqs.elementAt(i)).getLength());
						if(getGraphics() != null)
						{
								// I am sure you need something like this
								paintComponent(getGraphics());
								// viewPaneResize();
								((SequenceJPanel)graphicSequence.elementAt(0)).paintComponent(((SequenceJPanel)graphicSequence.elementAt(0)).getGraphics());
								((SequenceJPanel)graphicSequence.elementAt(0)).viewPaneResize();

						}
						*/
						//						((Sequence) seqs.elementAt(i))
						//								.indentSequence(((Integer) indents.elementAt(i)).intValue());
				}
				for(int i = 0; i < numberSequenceJpanels.size(); ++i)
				{
						((SequenceJPanel)numberSequenceJpanels.elementAt(i)).setSequenceLength(MAXSEQLENGTH);
				}
				//				addResidue();
		}


  /**
  *
  *  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++;

    GroutSequenceJPanel gs = new GroutSequenceJPanel(seq,this,
                           drawSequence,drawBlackBox,drawColorBox,
                           colorScheme,ypad);
		// System.out.println("adding new gs = " + gs);
    graphicSequence.add(index,gs);
				for(int i = 0; i < graphicSequence.size(); ++i)
				{
						// System.out.println("as graphicSequence.elementAt(" + i + ") = " + graphicSequence.elementAt(i));
				}

    Box XBox = new Box(BoxLayout.X_AXIS);