SeqFunctionMask.java

package org.seqcode.genome.sequence.seqfunctions;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

public class SeqFunctionMask implements SeqFunction {

	SeqFunction function;
	List<Integer> posList; //relative coordinates w.r.t scoring array centers
	Map<Integer, Integer> rel2compactindex; //mapping of relative coord to index in compact representation
	
	public SeqFunctionMask(SeqFunction function, List<Integer> posList){
		this.function = function;
		this.posList = posList;
		
		rel2compactindex = new HashMap<Integer, Integer>();
		int index=0;
		for(Integer i : posList){
			rel2compactindex.put(i,  index);
			index++;
		}
	}
	
	//Returns compact/compressed masked representation
	public double[][] score(String seq) throws SeqFunctionException {
		double[][] fScores = function.score(seq);
		double[][] maskScores = new double[function.scoreDimension()][posList.size()];
		
		for(int d=0; d<function.scoreDimension(); d++){
			for(int i=0; i<seq.length(); i++){
				int rel = i-(seq.length()/2);
				if(posList.contains(rel))
					maskScores[d][rel2compactindex.get(rel)] = fScores[d][i];
			}
		}
		return maskScores;
	}
	
	public List<Integer> getRelPosList(){return posList;}
	
	//score dimensionality (per base)
	public int scoreDimension(){return function.scoreDimension();}
	//offset from initial base position to first score. 
	public int scoringOffset(){return 0;}
	//Window size is the window of sequence that each score is based on 
	public int scoreWindowSize(){return function.scoreWindowSize();}
	//the score is defined between nucleotide positions (i.e. first score defined at offset+0.5bp)
	public boolean isBetweenNucleotides(){return function.isBetweenNucleotides();}
	
	//Score max & min
	public double getMaxScore(){return function.getMaxScore();}
	public double getMinScore(){return function.getMinScore();}
	
	//Labels on each dimension
	public String[] dimensionLabels(){return function.dimensionLabels();}
	//Description of the score
	public String scoreDescription(){return function.scoreDescription();}
}