/* * 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.search; import org.biojava.bio.symbol.AlphabetIndex; import org.biojava.bio.symbol.AlphabetManager; import org.biojava.bio.symbol.AtomicSymbol; import org.biojava.bio.symbol.FiniteAlphabet; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.IllegalSymbolException; import org.biojava.bio.symbol.SymbolList; /** * A pattern that can be used to find regions with given sequence content. * *
* Regular expressions can be used to find sequence patterns. However, some * things can't be easily expressed as a regular expression. For example, * a region of length 10 that contains at least 8 Gs and up to two Ts and no * other symbols. A SeqContentPattern can be built that does represent this. *
*
*
*
*
* SeqContentPattern scp = new SeqContentPattern(DNATools.getDNA());
* scp.setLength(10);
* scp.setMinCounts(DNATools.g(), 8);
* scp.setMaxCounts(DNATools.t(), 2);
* scp.setMaxCounts(DNATools.c(), 0);
* scp.setMaxCounts(DNATools.a(), 0);
*
* The minimum counts default to 0, and the maximum counts default to the * length. If you have not manually set the maximum count for a symbol, it will * continue to adjust while you change the length. Once you have set it, it will * not vary, even if you do set the length. To re-set a maximum count to track * the length, set it to -1. *
* ** All regions of the defined length for which all constraints are satisfied * will potentialy be found. At the moment we have not defined what will * happen for multiple regions that overlap all of which satisfy the * constraints. *
* * @author Matthew Pocock * @since 1.4 */ public class SeqContentPattern implements BioPattern { private final AlphabetIndex index; private final int[] minCounts; private final int[] maxCounts; private int length; /** * Create a new SeqContentPattern over an alphabet. * * @param alpha the FiniteAlphabet for this pattern */ public SeqContentPattern(FiniteAlphabet alpha) { index = AlphabetManager.getAlphabetIndex(alpha); this.minCounts = new int[alpha.size()]; this.maxCounts = new int[alpha.size()]; for(int i = 0; i < minCounts.length; i++) { minCounts[i] = 0; maxCounts[i] = -1; } } /** * Get the current length. * * @return the length */ public int getLength() { return length; } /** * Set the pattern length. * * @param length the new length */ public void setLength(int length) { this.length = length; } /** * Set the minimum counts required for a symbol. * * @param as the AtomicSymbol to check * @param count the minimum number of counts it must have * @throws IllegalSymbolException if as is not known in this alphabet */ public void setMinCounts(AtomicSymbol as, int count) throws IllegalSymbolException { minCounts[index.indexForSymbol(as)] = count; } /** * Get the minimum counts required for a symbol. * * @param as the AtomicSymbol to check * @return the minimum number of counts it must have * @throws IllegalSymbolException if as is not known in this alphabet */ public int getMinCounts(AtomicSymbol as) throws IllegalSymbolException { return minCounts[index.indexForSymbol(as)]; } /** * Set the maximum counts required for a symbol. * Use -1 to reset it to track the length. * * @param as the AtomicSymbol to check * @param count the maximum number of counts it must have * @throws IllegalSymbolException if as is not known in this alphabet */ public void setMaxCounts(AtomicSymbol as, int count) throws IllegalSymbolException { maxCounts[index.indexForSymbol(as)] = count; } /** * Get the maximum counts required for a symbol. * * @param as the AtomicSymbol to check * @return the maximum number of counts it must have * @throws IllegalSymbolException if as is not known in this alphabet */ public int getMaxCounts(AtomicSymbol as) throws IllegalSymbolException { int c = maxCounts[index.indexForSymbol(as)]; if(c == -1) { return length; } else { return c; } } public BioMatcher matcher(SymbolList symList) throws IllegalAlphabetException { if(symList.getAlphabet() != index.getAlphabet()) { throw new IllegalAlphabetException( "Attempted to search symbol list over " + symList.getAlphabet() + " but the search parameters only accept " + index.getAlphabet() ); } int[] minCounts = new int[this.minCounts.length]; int[] maxCounts = new int[this.maxCounts.length]; for(int i = 0; i < minCounts.length; i++) { minCounts[i] = this.minCounts[i]; int c = this.maxCounts[i]; maxCounts[i] = (c == -1) ? length : c; } return new SeqContentMatcher( symList, index, minCounts, maxCounts, length ); } }