Java tutorial
/* * 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 3 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, see <http://www.gnu.org/licenses/>. */ /* * HierarchicalClusterer.java * Copyright (C) 2009-2012 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 $Revision$ */ 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 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)) || 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 sNewick * @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"); HierarchyVisualizer a = new HierarchyVisualizer("((1:0.4,2:0.6):-0.4,3:0.4)"); 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