C++ Algebra::choice方法代码示例

void Alignment<R,L,AL>::calculateGlobal(const PPForest<L> *ppfx, const PPForest<L> *ppfy, const Algebra<R,L> &alg, bool noSpeedup)
{
	assert(ppfx != NULL);
	assert(ppfy != NULL);

	Ulong m,n,h,cols;
	long i,k;
	Uint j,l,r;

	R score,h_score;

	// alloc space for the score matrix, backtrack structure  and , if wanted, for the calculation-order-matrix
	m_mtrxSize=ppfx->getNumCSFs()*ppfy->getNumCSFs();

	m_mtrx=new R[m_mtrxSize];
	m_rowStart=new Ulong[ppfx->getNumCSFs()];
	m_ppfx = new PPForest<L>(*ppfx);				// copy the ppforests
	m_ppfy = new PPForest<L>(*ppfy);
	m_alg=&alg;
	m_rnaAlg=NULL;
	m_localOptimum=alg.worst_score();


	// initialize variables
	m=ppfx->size();
	n=ppfy->size();
	cols=ppfy->getNumCSFs();

	m_rowStart[0]=0;
	for(h=1;h<ppfx->getNumCSFs();h++)
		m_rowStart[h]=m_rowStart[h-1]+cols;

	// align forests fx and fy

	// the easiest case .. 
	setMtrxVal(0,0,alg.empty());

	// align fx to the empty forest (fill first row of array)
	for(i=m-1;i>=0;i--)  // for all nodes in fx
	{
		for(j=1;j<=ppfx->getMaxLength(i);j++)  // for all non empty csfs induced by i
		{
			score = alg.del(ppfx->label(i),
				            getMtrxVal(ppfx->down(i),0),
				            getMtrxVal(ppfx->over(i,j),0));	  

			setMtrxVal(ppfx->indexpos(i,j),0,score);
		}
	}

	// align fy to the empty forest (fill first column of array)
	for(k=n-1;k>=0;k--)  // for all nodes in fx
	{
		for(l=1;l<=ppfy->getMaxLength(k);l++)  // for all non empty csfs induced by k
		{
			score = alg.insert(getMtrxVal(0,ppfy->down(k)),
					            ppfy->label(k),
					            getMtrxVal(0,ppfy->over(k,l)));

			setMtrxVal(0,ppfy->indexpos(k,l),score);
		}
	}

	// align the rest
	for(i=m-1;i>=0;i--)  // for all nodes in fx  
		for(k=n-1;k>=0;k--)  // for all nodes in fx
		        {
			        j=ppfx->getMaxLength(i);
				for(l=1;l<=ppfy->getMaxLength(k);l++)  // for all non empty csfs induced by k
				{
					// replace
		  
					score = alg.replace(ppfx->label(i),
							            getMtrxVal(ppfx->down(i),ppfy->down(k)),
							            ppfy->label(k),
							            getMtrxVal(ppfx->over(i,j),ppfy->over(k,l)));
					
					// delete				       
					if(ppfx->noc(i)==0 && !noSpeedup)  // no child
					  {
					    h_score = alg.del(ppfx->label(i),0,
							              getMtrxVal(ppfx->over(i,j),ppfy->indexpos(k,l)));

						score=alg.choice(score,h_score);
					  }
					else					  
					  {	
					    if(ppfx->rb(i)==0 && !noSpeedup) // no right brother
					      {
						h_score = alg.del(ppfx->label(i),
								  getMtrxVal(ppfx->down(i),ppfy->indexpos(k,l)),
								  0);
						
						score=alg.choice(score,h_score);
					      }
					    else
					      {
						h=k;               // h is the node where the suffix of the split begins		   					
						for(r=0;r<=l;r++)  // for all splits of fy
						  {
//.........这里部分代码省略.........

//.........这里部分代码省略.........
							AlignmentLinear<double,RNA_Alphabet_Profile,RNA_Alphabet_Profile> * ali = new AlignmentLinear<double,RNA_Alphabet_Profile,RNA_Alphabet_Profile>(f1,f2,*alg,topdown,anchored,local,printBT);
							if (local)
								  score_mtrx->setAt(x-1,y-1,ali->getLocalOptimum());
							else
								  score_mtrx->setAt(x-1,y-1,ali->getGlobalOptimumRelative());

							std::cout << x << "," << y << ": " << score_mtrx->getAt(x-1,y-1) << std::endl;
							delete ali;
						}
        }
    }
    std::cout << std::endl;

    std::vector<RNAProfileAliKeyPairType> inputListMult;
    long bestx = 0, besty = 0;  // keys of stuctures in inputMapProfile
    RNAProfileAlignment *f = NULL;
    int level = 1;


    while (inputMapProfile.size()>1) {
        // find the best score of all pairwise alignments
				if (options.has(Options::Affine))
					bestScore = alg_affine->worst_score();
				else
					bestScore = alg->worst_score();
        for (it=inputMapProfile.begin(); it!=inputMapProfile.end(); it++) {
            x = it->first;
            for (it2=inputMapProfile.begin(); it2->first < it->first; it2++) {
                double old_bestScore = bestScore;

                y = it2->first;

								if (options.has(Options::Affine))
									bestScore = alg_affine->choice(bestScore,score_mtrx->getAt(x-1,y-1));
								else
									bestScore = alg->choice(bestScore,score_mtrx->getAt(x-1,y-1));

                if (bestScore != old_bestScore) {
                    bestx = it->first;
                    besty = it2->first;
                    old_bestScore = bestScore;
                }
            }
        }

        std::cout << "joining alignments:" << std::endl;

        // test, if score is better than the threshold value
        // if threshold is set generate a vector of best pairs within threshold
				bool scoreBetterThanThreshold = false;
				if (options.has(Options::Affine))
					scoreBetterThanThreshold = (alg_affine->choice(bestScore,threshold)!= threshold);
				else
					scoreBetterThanThreshold = (alg->choice(bestScore,threshold)!= threshold);
        if (scoreBetterThanThreshold) {

            int maximize;

            Graph graph;
						if (options.has(Options::Affine))
							graph = makePairsGraph(inputMapProfile,alg_affine,score_mtrx,threshold);
						else
							graph = makePairsGraph(inputMapProfile,alg,score_mtrx,threshold);
            if (options.has(Options::CalculateDistance))
                maximize = 0;
            else