/* * 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/ * */ package org.biojava.bio; import java.util.regex.Matcher; import java.util.regex.Pattern; /** * An ec (enzyme classification) number. * * * Implementations of this interface should be imutable. This makes them much * more usefull as keys in maps. * * it is a good idea to validate that the data being passed in is a sane ec * number. * * @author Matthew Pocock * @since 1.4 */ public interface EcNumber { /** * A Pattern that can be used to parse EC strings into the indiidual numbers. */ public static final Pattern EC_PATTERN = Pattern.compile("((\\d*)|(-))\\.((\\d*)|(-))\\.((\\d*)|(-))\\.((\\d*)|(-))"); /** * Constant that represents EC number components that are not defined. This * is often represented as a '-' in EC strings. */ public static final int UNDEFINED = -1; /** * Constant that represents EC number components that are as yet unclassified. * This is often represented as 99 in EC strings. */ public static final int UNCLASSIFIED = 99; /** * Get the class number associated with the particular level of the ec number. * *
The index can be between 0 and 3 inclusive. 0 correxpons to the top * level class, 1 to the sub-class and so on. A return value of UNDEFINED * indicates that this field is not populated.
* * @param level the level in the ec classification to return the number for * @return the value at that level */ public int getClassNumber(int level); /** * A simple implementation of EcNumber. * * @author Matthew Pocock * @since 1.4 */ public static class Impl implements EcNumber { private int[] classes; /** * Make a new EcNumber.Impl with the data provided. * * @param mainClass the main class number * @param subClass the sub class number * @param subSubClass the sub-sub class number * @param group the group number */ public Impl(int mainClass, int subClass, int subSubClass, int group) { this.classes = new int[] { mainClass, subClass, subSubClass, group }; } private Impl(String ecString) { Matcher matcher = EC_PATTERN.matcher(ecString); if(!matcher.matches()) { throw new IllegalArgumentException( "Can't parse ec string: " + ecString ); } classes = new int[] { process(matcher.group(1)), process(matcher.group(4)), process(matcher.group(7)), process(matcher.group(10)) }; } private int process(String s) { if(s.length() > 0) { if(s.equals("-")) { return UNDEFINED; } else { return Integer.parseInt(s); } } else { return UNDEFINED; } } public int getClassNumber(int level) { return classes[level]; } public String toString() { StringBuffer sBuf = new StringBuffer(); sBuf.append(process(getClassNumber(0))); for(int i = 1; i < 4; i++) { sBuf.append("."); sBuf.append(process(getClassNumber(i))); } return sBuf.toString(); } private String process(int val) { if(val == UNDEFINED) { return ""; } else { return Integer.toString(val); } } public boolean equals(Object obj) { if(obj instanceof EcNumber) { EcNumber that = (EcNumber) obj; for(int i = 0; i < 4; i++) { if(this.getClassNumber(i) != that.getClassNumber(i)) { return false; } } return true; } return false; } public int hashCode() { return getClassNumber(0) * 1000000 + getClassNumber(1) * 10000 + getClassNumber(2) * 100 + getClassNumber(3); } /** * Process a string into an EcNumber. * ** This method uses the {@link EcNumber#EC_PATTERN} regular expression. *
* * @param ecString String to parse * @return a new EcNumber * @throws IllegalArgumentException if ecString could not be parsed */ public static Impl valueOf(String ecString) { return new Impl(ecString); } } }