001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 * Created on Aug 3, 2007 021 */ 022package org.biojava.nbio.structure.gui.util.color; 023 024/** 025 * Performs a log10 transform on input before passing the values off to another 026 * colorMapper. 027 * 028 * For instance, to map [10^0, 10^10] to a rainbow gradient, use 029 * 030 * new LogColorMapper(GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)) 031 * 032 * @author Spencer Bliven 033 * 034 */ 035public class LogColorMapper extends ContinuousColorMapperTransform { 036 037 private int base; 038 039 /** 040 * Creates a new LogColorMapper with base 10. 041 * @param logspaceMapper 042 */ 043 public LogColorMapper(ContinuousColorMapper logspaceMapper) { 044 this(logspaceMapper, 10); 045 } 046 047 /** 048 * If logspaceMapper maps values x1 to x2, this creates a 049 * mapper for values base^x1 to base^x2 050 * 051 * @param logspaceMapper logspace mapper 052 * @param base The base of the logorithm 053 */ 054 public LogColorMapper(ContinuousColorMapper logspaceMapper, int base) { 055 super(logspaceMapper); 056 this.base = base; 057 } 058 059 /** 060 * Apply log transform. 061 * @param value 062 * @return log_b(value) 063 * @see org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform#transform(double) 064 */ 065 @Override 066 public double transform(double value) { 067 double logValue = Math.log(value>0?value:0)/Math.log(base); 068 return logValue; 069 } 070 071}