/*
* 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., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* HierarchicalClusterer.java
* Copyright (C) 2009 University of Waikato, Hamilton, New Zealand
*/
package weka.gui.hierarchyvisualizer;
/**
* Shows cluster trees represented in Newick format as dendrograms.
*
* @author Remco Bouckaert (rrb@xm.co.nz, remco@cs.waikato.ac.nz)
* @version $Revision: 5996 $
*/
import java.awt.Color;
import java.awt.Container;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.event.ComponentEvent;
import java.awt.event.ComponentListener;
import java.util.Vector;
import javax.swing.JFrame;
import weka.gui.visualize.PrintablePanel;
public class HierarchyVisualizer extends PrintablePanel implements ComponentListener {
private static final long serialVersionUID = 1L;
String m_sNewick;
Node m_tree;
int m_nLeafs;
double m_fHeight;
double m_fScaleX = 10;
double m_fScaleY = 10;
public HierarchyVisualizer(String sNewick) {
try {
parseNewick(sNewick);
} catch (Exception e) {
e.printStackTrace();
System.exit(0);
}
addComponentListener(this);
} // c'tor
int positionLeafs(Node node, int nPosX) {
if (node.isLeaf()) {
node.m_fPosX = nPosX + 0.5;
nPosX++;
return nPosX;
} else {
for (int i = 0; i < node.m_children.length; i++) {
nPosX = positionLeafs(node.m_children[i], nPosX);
}
}
return nPosX;
}
double positionRest(Node node) {
if (node.isLeaf()) {
return node.m_fPosX;
} else {
double fPosX = 0;
for (int i = 0; i < node.m_children.length; i++) {
fPosX += positionRest(node.m_children[i]);
}
fPosX /= node.m_children.length;
node.m_fPosX = fPosX;
return fPosX;
}
}
double positionHeight(Node node, double fOffSet) {
if (node.isLeaf()) {
node.m_fPosY = fOffSet + node.m_fLength;
return node.m_fPosY;
} else {
double fPosY = fOffSet + node.m_fLength;
double fYMax = 0;
for (int i = 0; i < node.m_children.length; i++) {
fYMax = Math.max(fYMax, positionHeight(node.m_children[i], fPosY));
}
node.m_fPosY = fPosY;
return fYMax;
}
}
//Vector<String> m_sMetaDataNames;
/** class for nodes in building tree data structure **/
class Node {
double m_fLength = -1;
double m_fPosX = 0;
double m_fPosY = 0;
String m_sLabel;
//Vector<String> m_sMetaDataValues;
String m_sMetaData;
/** list of children of this node **/
Node[] m_children;
/** parent node in the tree, null if root **/
Node m_Parent = null;
Node getParent() {
return m_Parent;
}
void setParent(Node parent) {
m_Parent = parent;
}
/** check if current node is root node **/
boolean isRoot() {
return m_Parent == null;
}
boolean isLeaf() {
return m_children == null;
}
/** return nr of children **/
int getChildCount() {
// }
if (m_children == null) {return 0;}
return m_children.length;
}
Node getChild(int iChild) {
return m_children[iChild];
}
/** count number of nodes in tree, starting with current node **/
int getNodeCount() {
if (m_children == null) {
return 1;
}
int n = 1;
for (int i = 0; i < m_children.length; i++) {
n += m_children[i].getNodeCount();
}
return n;
}
public String toString() {
StringBuffer buf = new StringBuffer();
if (m_children != null) {
buf.append("(");
for (int i = 0; i < m_children.length-1; i++) {
buf.append(m_children[i].toString());
buf.append(',');
}
buf.append(m_children[m_children.length - 1].toString());
buf.append(")");
} else {
buf.append(m_sLabel);
}
if (m_sMetaData != null) {
buf.append('[');
buf.append(m_sMetaData);
buf.append(']');
}
buf.append(":" + m_fLength);
return buf.toString();
}
double draw(Graphics g) {
if (isLeaf()) {
int x = (int)(m_fPosX * m_fScaleX);
int y = (int)(m_fPosY * m_fScaleY);
g.drawString(m_sLabel, x, y);
g.drawLine((int)(m_fPosX * m_fScaleX), (int)(m_fPosY * m_fScaleY), (int)(m_fPosX * m_fScaleX), (int)((m_fPosY - m_fLength) * m_fScaleY));
} else {
double fPosX1 = Double.MAX_VALUE;
double fPosX2 = -Double.MAX_VALUE;
for (int i = 0; i < m_children.length; i++) {
double f = m_children[i].draw(g);
if (f < fPosX1) {fPosX1 = f;}
if (f > fPosX2) {fPosX2 = f;}
}
g.drawLine((int)(m_fPosX * m_fScaleX), (int)(m_fPosY * m_fScaleY), (int)(m_fPosX * m_fScaleX), (int)((m_fPosY - m_fLength) * m_fScaleY));
g.drawLine((int)(fPosX1 * m_fScaleX), (int)(m_fPosY * m_fScaleY), (int)(fPosX2 * m_fScaleX), (int)(m_fPosY* m_fScaleY));
}
return m_fPosX;
}
} // class Node
/** helper method for parsing Newick tree **/
int nextNode(String sStr, int i) {
int nBraces = 0;
char c = sStr.charAt(i);
do {
i++;
if (i < sStr.length()) {
c = sStr.charAt(i);
// skip meta data block
if (c == '[') {
while (i < sStr.length() && sStr.charAt(i)!=']') {
i++;
}
i++;
if(i < sStr.length()) {
c = sStr.charAt(i);
}
}
switch (c) {
case '(':
nBraces++;
break;
case ')':
nBraces--;
break;
default:
break;
}
}
} while (i < sStr.length()
&& (nBraces > 0 || (c != ','&&c != ')'&&c != '(')));
if (i >= sStr.length() || nBraces < 0) {
return -1;
} else if (sStr.charAt(i) == ')') {
i++;
if (sStr.charAt(i) == '[') {
while (i < sStr.length() && sStr.charAt(i)!=']') {
i++;
}
i++;
if (i >= sStr.length()) {
return -1;
}
}
if (sStr.charAt(i) == ':') {
i++;
c = sStr.charAt(i);
while (i < sStr.length() && (c=='.' || Character.isDigit(c))) {
i++;
if (i < sStr.length()) {
c = sStr.charAt(i);
}
}
}
}
return i;
}
/**
* convert string containing Newick tree into tree datastructure but only in
* the limited format as contained in m_sTrees
*
* @param sStr
* @return tree consisting of a Node
*/
void parseNewick(String sNewick) throws Exception {
m_sNewick = sNewick;
int i = m_sNewick.indexOf('(');
if (i > 0) {
m_sNewick = m_sNewick.substring(i);
}
System.err.println(m_sNewick);
m_tree = parseNewick2(m_sNewick);
System.err.println(m_tree.toString());
m_nLeafs = positionLeafs(m_tree, 0);
positionRest(m_tree);
m_fHeight = positionHeight(m_tree, 0);
}
Node parseNewick2(String sStr) throws Exception {
// System.out.println(sStr);
if (sStr == null || sStr.length() == 0) {
return null;
}
Node node = new Node();
if (sStr.startsWith("(")) {
int i1 = nextNode(sStr, 0);
int i2 = nextNode(sStr, i1);
node.m_children = new Node[2];
node.m_children[0] = parseNewick2(sStr.substring(1, i1));
node.m_children[0].m_Parent = node;
String sStr2 = sStr.substring(i1+1, (i2>0?i2:sStr.length()));
node.m_children[1] = parseNewick2(sStr2);
node.m_children[1].m_Parent = node;
if (sStr.lastIndexOf('[') > sStr.lastIndexOf(')')) {
sStr = sStr.substring(sStr.lastIndexOf('['));
i2 = sStr.indexOf(']');
if (i2 < 0) {
throw new Exception("unbalanced square bracket found:" + sStr);
}
sStr2 = sStr.substring(1, i2);
node.m_sMetaData = sStr2;
}
if (sStr.lastIndexOf(':') > sStr.lastIndexOf(')')) {
sStr = sStr.substring(sStr.lastIndexOf(':'));
sStr = sStr.replaceAll("[,\\):]", "");
node.m_fLength = new Double(sStr);
} else {
node.m_fLength = 1;
}
} else {
// it is a leaf
if (sStr.contains("[")) {
// grab metadata
int i1 = sStr.indexOf('[');
int i2 = sStr.indexOf(']');
if (i2 < 0) {
throw new Exception("unbalanced square bracket found:" + sStr);
}
String sStr2 = sStr.substring(i1+1, i2);
sStr = sStr.substring(0, i1) +sStr.substring(i2+1);
node.m_sMetaData = sStr2;
}
if (sStr.indexOf(')') >= 0) {
sStr = sStr.substring(0, sStr.indexOf(')'));
}
sStr = sStr.replaceFirst("[,\\)]", "");
// System.out.println("parsing <<"+sStr+">>");
if (sStr.length() > 0) {
if (sStr.indexOf(':') >= 0) {
int iColon = sStr.indexOf(':');
node.m_sLabel = sStr.substring(0, iColon);
if (sStr.indexOf(':', iColon+1) >= 0) {
int iColon2 = sStr.indexOf(':', iColon+1);
node.m_fLength = new Double(sStr.substring(iColon+1, iColon2));
m_fTmpLength = new Double(sStr.substring(iColon2+1));
} else {
node.m_fLength = new Double(sStr.substring(iColon+1));
}
} else {
node.m_sLabel = sStr;
node.m_fLength = 1;
}
} else {
return null;
}
}
return node;
}
double m_fTmpLength;
/**
* Fits the tree to the current screen size. Call this after window has been
* created to get the entire tree to be in view upon launch.
*/
public void fitToScreen() {
m_fScaleX = 10;
int nW = getWidth();
if (m_nLeafs > 0) {
m_fScaleX = nW / m_nLeafs;
}
m_fScaleY = 10;
int nH = getHeight();
if (m_fHeight > 0) {
m_fScaleY = (nH - 10) / m_fHeight;
}
repaint();
}
/**
* Updates the screen contents.
*
* @param g
* the drawing surface.
*/
public void paintComponent(Graphics g) {
Color oldBackground = ((Graphics2D) g).getBackground();
// if (m_BackgroundColor != null)
((Graphics2D) g).setBackground(Color.WHITE);
g.clearRect(0, 0, getSize().width, getSize().height);
((Graphics2D) g).setBackground(oldBackground);
g.setClip(3, 7, getWidth() - 6, getHeight() - 10);
m_tree.draw(g);
g.setClip(0, 0, getWidth(), getHeight());
}
public void componentHidden(ComponentEvent e) {}
public void componentMoved(ComponentEvent e) {}
public void componentResized(ComponentEvent e) {
fitToScreen();
}
public void componentShown(ComponentEvent e) {}
/**
* Main method for testing this class.
*/
public static void main(String[] args) {
//HierarchyVisualizer a = new HierarchyVisualizer("((((human:2.0,(chimp:1.0,bonobo:1.0):1.0):1.0,gorilla:3.0):1.0,siamang:4.0):1.0,orangutan:5.0)");
//HierarchyVisualizer a = new HierarchyVisualizer("(((human:2.0,(chimp:1.0,bonobo:1.0):1.0):1.0,gorilla:3.0):1.0,siamang:4.0)");
HierarchyVisualizer a = new HierarchyVisualizer(" (((5[theta=0.121335,lxg=0.122437]:0.00742795,3[theta=0.0972485,lxg=0.152762]:0.00742795)[theta=0.490359,lxg=0.0746703]:0.0183076,((2[theta=0.0866056,lxg=0.2295]:0.00993801,4[theta=0.135512,lxg=0.146674]:0.00993801)[theta=0.897783,lxg=0.0200762]:0.00901206,1[theta=0.200265,lxg=0.18925]:0.0189501)[theta=0.0946195,lxg=0.143427]:0.00678551)[theta=0.185562,lxg=0.139681]:0.0129598,(7[theta=0.176022,lxg=0.364039]:0.0320395,((0[theta=0.224286,lxg=0.156485]:0.0175487,8[theta=0.223313,lxg=0.157166]:0.0175487)[theta=0.631287,lxg=0.024042]:0.00758871,6[theta=0.337871,lxg=0.148799]:0.0251374)[theta=0.33847,lxg=0.040784]:0.00690208)[theta=0.209238,lxg=0.0636202]:0.00665587)[theta=0.560453,lxg=-0.138086]:0.01");
//HierarchyVisualizer a = new HierarchyVisualizer(" ((5[theta=0.121335,lxg=0.122437]:0.00742795,3[theta=0.0972485,lxg=0.152762]:0.00742795)[theta=0.490359,lxg=0.0746703]:0.0183076,2[theta=0.0866056,lxg=0.2295]:0.00993801)[theta=0.897783,lxg=0.0200762]:0.00901206");
a.setSize(800 ,600);
JFrame f;
f = new JFrame();
Container contentPane = f.getContentPane();
contentPane.add(a);
f.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
f.setSize(800,600);
f.setVisible(true);
a.fitToScreen();
}
} // class HierarchyVisualizer