Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Nov 8, 2005
*
*/
package org.biojava.nbio.structure.gui.util;
import org.biojava.nbio.structure.*;
import javax.swing.*;
import java.awt.*;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/** A class that draws a Sequence as a rectangle, a scale display over it.
*
* @author Andreas Prlic
* @since 1.7
*/
public class SequenceScalePanel
extends JPanel{
static final long serialVersionUID = 7893248902423l;
//private static final Logger logger = LoggerFactory.getLogger(SequenceScalePanel.class);
public static final int DEFAULT_X_START = 10 ;
public static final int DEFAULT_X_RIGHT_BORDER = 40 ;
public static final int DEFAULT_Y_START = 0 ;
public static final int DEFAULT_Y_STEP = 10 ;
public static final int DEFAULT_Y_HEIGHT = 8 ;// the size of the box
public static final int DEFAULT_Y_BOTTOM = 16 ;
public static final int LINE_HEIGHT = 10 ;
public static final int MINIMUM_HEIGHT = 20;
public static final Color SEQUENCE_COLOR = Color.LIGHT_GRAY;
public static final Color SCALE_COLOR = Color.black;
public static final Color TEXT_SCALE_COLOR = Color.GRAY;
public static final Color IDX_COLOR = Color.yellow;
public static final Color GAP_COLOR = Color.white;
public static final Color BACKGROUND_COLOR;
public static final Font seqFont ;
// the scale value after which to show the sequence as text
private static final int SEQUENCE_SHOW = 9;
// the height of the panel
public static final int SIZE = 20;
Chain chain;
int chainLength;
float scale;
Character[] seqArr;
CoordManager coordManager;
int position;
List apos;
static {
String fontName = "Helvetica";
int fsize = 12;
seqFont = new Font(fontName,Font.PLAIN,fsize);
String col1 = "#FFFFFF";
BACKGROUND_COLOR = Color.decode(col1);
}
public SequenceScalePanel(int position) {
super();
this.position = position;
this.setBackground(BACKGROUND_COLOR);
chain = new ChainImpl();
setDoubleBuffered(true);
seqArr = new Character[0];
chainLength = 0;
scale = 1.0f;
setPrefSize();
coordManager = new CoordManager();
apos = new ArrayList();
}
private void setPrefSize() {
int length = chainLength ;
int l = Math.round(length*scale) + DEFAULT_X_START + DEFAULT_X_RIGHT_BORDER ;
if ( l < 60){
l = 60;
}
this.setPreferredSize(new Dimension(l,SIZE));
}
public void setAligMap(List apos){
this.apos = apos;
if ( apos.size() == 0)
return;
AlignedPosition last = apos.get(apos.size()-1);
//System.out.println("got last aligned:" +last);
if ( last.getPos(position) != -1){
// add the end of the chain...
int idxlast = last.getPos(position);
for (;idxlast < chainLength;idxlast++){
AlignedPosition m = new AlignedPosition();
m.setPos(position,idxlast);
apos.add(m);
}
}
}
public synchronized void setChain(Chain c){
List a = c.getAtomGroups(GroupType.AMINOACID);
seqArr = new Character[a.size()];
chain = new ChainImpl();
Iterator iter = a.iterator();
int i = 0;
while (iter.hasNext()){
AminoAcid aa = (AminoAcid) iter.next();
// preserver original hierarchy ... for highlighting in Jmol
Chain old = aa.getChain();
chain.addGroup(aa);
aa.setChain(old);
seqArr[i] = aa.getAminoType();
i++;
}
chainLength = i;
coordManager.setLength(chainLength);
setPrefSize();
this.repaint();
}
public Chain getChain(){
return chain;
}
public synchronized float getScale(){
return scale;
}
public void setScale(float scale) {
this.scale=scale;
coordManager.setScale(scale);
setPrefSize();
this.repaint();
this.revalidate();
}
/** set some default rendering hints, like text antialiasing on
*
* @param g2D the graphics object to set the defaults on
*/
protected void setPaintDefaults(Graphics2D g2D){
g2D.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
g2D.setFont(seqFont);
}
@Override
public void paintComponent(Graphics g){
g.setColor(BACKGROUND_COLOR);
Rectangle drawHere = g.getClipBounds();
g.fillRect(drawHere.x,drawHere.y, drawHere.width, drawHere.height);
Graphics2D g2D =(Graphics2D) g;
setPaintDefaults(g2D);
int y = 1;
// draw the scale
y = drawScale(g2D,1);
// draw the background for identical residues
drawIdx(g2D,y);
// sequence
y = drawSequence(g2D,y);
}
/** draw the Scale
*
* @param g2D
* @param y the height on which to draw the scale
* @return the new y position
*/
protected int drawScale(Graphics2D g2D, int y){
// only draw within the ranges of the Clip
Rectangle drawHere = g2D.getClipBounds();
g2D.setColor(SCALE_COLOR);
int aminosize = Math.round(1*scale);
if ( aminosize < 1)
aminosize = 1;
int startpos = coordManager.getSeqPos(drawHere.x);
int endpos = coordManager.getSeqPos(drawHere.x+drawHere.width);
if ( endpos > apos.size())
endpos = apos.size();
int l = endpos - startpos + 1 ;
int drawStart = coordManager.getPanelPos(startpos);
int drawEnd = coordManager.getPanelPos(l) - DEFAULT_X_START + aminosize;
// System.out.println("SeqScalePanel drawing scale s:" + startpos + " e: " + endpos +
// " ps: " + drawStart + " pe:" + drawEnd + " draw.x " + drawHere.x + " draw.w " + drawHere.width +
// " scale " + scale);
// the frame around the sequence box
if ( scale < SEQUENCE_SHOW){
g2D.setColor(SEQUENCE_COLOR);
//g2D.setColor(Color.blue);
Rectangle seqline = new Rectangle(drawStart, y, drawEnd, LINE_HEIGHT);
//g2D= (Graphics2D)g;
g2D.fill(seqline);
//g2D.setColor(Color.blue);
//g2D.draw(seqline);
}
// the top line for the scale
g2D.setColor(SCALE_COLOR);
Rectangle baseline = new Rectangle(drawStart, y, drawEnd, 2);
g2D.fill(baseline);
// draw the vertical ticks
int lineH = 11;
if ( scale <= 3)
lineH = 8;
for (int gap =startpos ; ((gap<= endpos) && ( gap < apos.size())); gap++){
int xpos = coordManager.getPanelPos(gap) ;
AlignedPosition m = apos.get(gap);
if ( m.getPos(position) == -1 ){
// a gap position
g2D.setColor(GAP_COLOR);
g2D.fillRect(xpos, y+2, aminosize+1, y+lineH);
g2D.setColor(GAP_COLOR);
continue;
}
int i = m.getPos(position);
if ( ((i+1)%100) == 0 ) {
if ( scale> 0.1) {
g2D.setColor(TEXT_SCALE_COLOR);
g2D.fillRect(xpos, y+2, aminosize, y+lineH);
g2D.setColor(SCALE_COLOR);
if ( scale < SEQUENCE_SHOW)
g2D.drawString(String.valueOf(i+1), xpos, y+DEFAULT_Y_STEP);
}
}else if ( ((i+1)%50) == 0 ) {
if ( scale>1.4) {
g2D.setColor(TEXT_SCALE_COLOR);
g2D.fillRect(xpos,y+2, aminosize, y+lineH);
g2D.setColor(SCALE_COLOR);
if ( scale < SEQUENCE_SHOW)
g2D.drawString(String.valueOf(i+1), xpos, y+DEFAULT_Y_STEP);
}
} else if ( ((i+1)%10) == 0 ) {
if ( scale> 3) {
g2D.setColor(TEXT_SCALE_COLOR);
g2D.fillRect(xpos, y+2, aminosize, y+lineH);
g2D.setColor(SCALE_COLOR);
if ( scale < SEQUENCE_SHOW)
g2D.drawString(String.valueOf(i+1), xpos, y+DEFAULT_Y_STEP);
}
}
}
int length = chainLength;
if ( endpos >= length-1) {
int endPanel = coordManager.getPanelPos(endpos);
g2D.drawString(String.valueOf(length), endPanel+10,y+DEFAULT_Y_STEP);
}
return y ;
}
protected void drawIdx(Graphics2D g2D, int y){
int aminosize = Math.round(1*scale);
if ( aminosize < 1)
aminosize = 1;
// only draw within the ranges of the Clip
Rectangle drawHere = g2D.getClipBounds();
int startpos = coordManager.getSeqPos(drawHere.x);
//int endpos = coordManager.getSeqPos(drawHere.x+drawHere.width-2);
Composite oldComp = g2D.getComposite();
g2D.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,0.8f));
//logger.info("paint l " + l + " length " + length );
if ( startpos < 0)
startpos = 999;
g2D.setColor(IDX_COLOR);
int lineH = 11;
if ( scale <= 3)
lineH = 8;
int i = startpos;
// display the actual sequence!;
for ( int gap = startpos ; gap < apos.size() ;gap++){
int xpos = coordManager.getPanelPos(gap) ;
AlignedPosition m = apos.get(gap);
if ( m.getEquivalent() == AlignedPosition.NOT_ALIGNED){
// a gap position
continue;
}
i = m.getPos(position);
for (AlignedPosition xi : apos ) {
if (xi.getPos(position)!= -1)
if ( i == xi.getPos(position)){
g2D.fillRect(xpos, y+2, aminosize, y+lineH);
break;
}
}
// TODO:
// color amino acids by hydrophobicity
}
g2D.setComposite(oldComp);
}
/** draw the Amino acid sequence
*
* @param g2D
* @param y .. height of line to draw the sequence onto
* @return the new y value
*/
protected int drawSequence(Graphics2D g2D, int y){
//g2D.drawString(panelName,10,10);
g2D.setColor(SEQUENCE_COLOR);
int aminosize = Math.round(1*scale);
if ( aminosize < 1)
aminosize = 1;
// only draw within the ranges of the Clip
Rectangle drawHere = g2D.getClipBounds();
int startpos = coordManager.getSeqPos(drawHere.x);
//int endpos = coordManager.getSeqPos(drawHere.x+drawHere.width-2);
Composite oldComp = g2D.getComposite();
g2D.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,0.8f));
//logger.info("paint l " + l + " length " + length );
if ( startpos < 0)
startpos = 999;
if ( scale > SEQUENCE_SHOW){
g2D.setColor(Color.black);
//g2D.setColor(SCALE_COLOR);
int i = startpos;
// display the actual sequence!;
for ( int gap = startpos ; gap < apos.size() ;gap++){
int xpos = coordManager.getPanelPos(gap) ;
AlignedPosition m = apos.get(gap);
if (m.getPos(position) == -1){
// a gap position
g2D.drawString("-",xpos+1,y+2+DEFAULT_Y_STEP);
continue;
}
i = m.getPos(position);
// TODO:
// color amino acids by hydrophobicity
g2D.drawString(seqArr[i].toString(),xpos+1,y+2+DEFAULT_Y_STEP);
}
// in full sequence mode we need abit more space to look nice
y+=2;
}
g2D.setComposite(oldComp);
y+= DEFAULT_Y_STEP + 2;
return y;
}
}
