/* * 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.symbol; import java.util.HashMap; import java.util.Map; import org.biojava.bio.seq.DNATools; /** *
* A factory that is used to maintain associations between alphabets and * preferred bit-packings for them. *
* ** There are many ways to pack the symbols for an alphabet as binary. * Different applications will wish to have different representations for * reasons such as integration with external formats, whether to store * ambiguity or not and what algorithms may be used on the bit-packed * representation. Also, it has utility methods to arrange the bit-strings * for symbols within a Java int primitive. *
* * @author Matthew Pocock * @author Thomas Down */ public class PackingFactory { private final static Map packForAlpha; static { packForAlpha = new HashMap(); } /** * Get the default packing for an alphabet. * * @param alpha the FiniteAlphabet that will be bit-packed * @param ambiguity true if the packing should store ambiguity and false * if it can discard ambiguity information * @throws IllegalAlphabetException if this combination of alphabet and * ambiguity can not be handled **/ public static Packing getPacking(FiniteAlphabet alpha, boolean ambiguity) throws IllegalAlphabetException { Packing pack = (Packing) packForAlpha.get(alpha); if(pack == null) { if(alpha == DNATools.getDNA()) { if(ambiguity) { pack = new DNAAmbPack(); } else { pack = new DNANoAmbPack(DNATools.a()); } } else { if(ambiguity) { // can't handle this in the general case throw new IllegalAlphabetException(); } else { pack = new IndexedNoAmbPack(AlphabetManager.getAlphabetIndex(alpha)); } } } return pack; } public static int primeWord( SymbolList symList, int wordLength, Packing packing ) throws IllegalSymbolException { int word = 0; for(int i = 0; i < wordLength; i++) { int p = packing.pack(symList.symbolAt(i+1)); word |= (int) ((int) p << (int) (i * packing.wordSize())); } return word; } public static int nextWord( SymbolList symList, int word, int offset, int wordLength, Packing packing ) throws IllegalSymbolException { word = word >> (int) packing.wordSize(); int p = packing.pack(symList.symbolAt(offset)); word |= (int) p << ((int) (wordLength - 1) * packing.wordSize()); return word; } public static void binary(long val) { for(int i = 63; i >= 0; i--) { System.out.print( ((((val >> i) & 1) == 1) ? 1 : 0) ); } System.out.println(); } public static void binary(int val) { for(int i = 31; i >= 0; i--) { System.out.print( ((((val >> i) & 1) == 1) ? 1 : 0) ); } System.out.println(); } }