private List<NWRecord> makeAlignment(double[][] simMatrix,
			double[][] pathMatrix, String[] chunksSrc, String[] chunksTrg) {
		// TODO Auto-generated method stub
		
		List<NWRecord> alignResults = new ArrayList<NWRecord>();
		List<String> tmpMatchSrc = new ArrayList<String>();
		List<String> tmpMatchTrg = new ArrayList<String>();
		
		int i = chunksSrc.length;
		int j = chunksTrg.length;
		
		while(i > 0 && j > 0){
			double score = pathMatrix[i][j];
			double scoreDiagInv = pathMatrix[i-1][j-1];
			double scoreLeft = pathMatrix[i-1][j];
			
			if(score==scoreDiagInv + simMatrix[i-1][j-1]){
				tmpMatchSrc.add(chunksSrc[i-1]);
				tmpMatchTrg.add(chunksTrg[j-1]);
				i = i-1;
				j = j-1;
			}
			else if (score == scoreLeft + getGapPenality()) {
				tmpMatchSrc.add(chunksSrc[i-1]);
				tmpMatchTrg.add(gapChar);
				i = i-1;
			}
			else {
				tmpMatchSrc.add(gapChar);
				tmpMatchTrg.add(chunksTrg[j-1]);
				j = j-1;
			}
				
			
		}
		
		while(i>0){
			tmpMatchSrc.add(chunksSrc[i-1]);
			tmpMatchTrg.add(gapChar);
			i = i-1;
		}
		while(j>0){
			
			tmpMatchSrc.add(gapChar);
			tmpMatchTrg.add(chunksTrg[j-1]);
			j = j-1;
			
		}
		
		return alignResults;
	}