Java Code Examples for org.biojava.nbio.structure.align.model.AFPChain#setBlockScore()

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Example 1

Source File: AFPOptimizer.java From biojava with GNU Lesser General Public License v2.1

4 votes

/**
 * to update the chaining score after block delete and merge processed
 * the blockScore value is important for significance evaluation
 */
public static void updateScore(FatCatParameters params, AFPChain afpChain)
{
	int     i, j, bknow, bkold, g1, g2;


	afpChain.setConn(0d);
	afpChain.setDVar(0d);

	int blockNum = afpChain.getBlockNum();
	int alignScoreUpdate = 0;
	double[] blockScore = afpChain.getBlockScore();
	int[] blockGap = afpChain.getBlockGap();
	int[] blockSize =afpChain.getBlockSize();
	int[] afpChainList = afpChain.getAfpChainList();
	List<AFP>afpSet = afpChain.getAfpSet();
	int[] block2Afp = afpChain.getBlock2Afp();

	double torsionPenalty = params.getTorsionPenalty();


	bkold = 0;
	for(i = 0; i < blockNum; i ++)  {
		blockScore[i] = 0;
		blockGap[i] = 0;
		for(j = 0; j < blockSize[i]; j ++)      {
			bknow = afpChainList[block2Afp[i] + j];
			if(j == 0)      {
				blockScore[i] = afpSet.get(bknow).getScore();
			}
			else    {
				AFPChainer.afpPairConn(bkold, bknow, params, afpChain); //note: j, i
				Double conn = afpChain.getConn();
				blockScore[i] += afpSet.get(bknow).getScore() + conn;
				g1 = afpSet.get(bknow).getP1() - afpSet.get(bkold).getP1() - afpSet.get(bkold).getFragLen();
				g2 = afpSet.get(bknow).getP2() - afpSet.get(bkold).getP2() - afpSet.get(bkold).getFragLen();
				blockGap[i] += (g1 > g2)?g1:g2;
			}
			bkold = bknow;
		}
		alignScoreUpdate += blockScore[i];
	}
	if(blockNum >= 2)       {
		alignScoreUpdate += (blockNum - 1) * torsionPenalty;
	}

	afpChain.setBlockGap(blockGap);
	afpChain.setAlignScoreUpdate(alignScoreUpdate);
	afpChain.setBlockScore(blockScore);
	afpChain.setBlockSize(blockSize);
	afpChain.setAfpChainList(afpChainList);
	afpChain.setBlock2Afp(block2Afp);
}