{		it->second->printFastaAli(false);		cout << endl;	      }	    else	      {  		it->second->printSeqAli();#ifdef HAVE_LIBRNA  // This features require the ViennaRNA library				// print alignment		it->second->printStrAli();		cout << endl;#endif			      }	    // save profile	    if(options.has(RNAforesterOptions::SaveProfile))	    {	      string filename;	      filename=options.generateFilename(RNAforesterOptions::SaveProfile,".pro", "rna.pro",clusterNr);	      it->second->save(filename);	    }	    		// print consensus structure		cout << "Consensus sequence/structure:" << endl;		it->second->printConsensus(minPairProb);		cout << endl;#ifdef HAVE_LIBG2  // This features require the g2 library				// generate squiggle plots			if(options.has(RNAforesterOptions::MakeSquigglePlot))			{				RNAProfileAlignment::SquigglePlotOptions sqOptions;				string filename;				// plot showing full base information				filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,".ps", "rnaprofile.ps",clusterNr);				sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors);				sqOptions.minPairProb=minPairProb;				sqOptions.mostLikelySequence=false;				it->second->squigglePlot(filename,sqOptions);				// plot showing consensus sequence				filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,"_cons.ps", "rnaprofile_cs.ps",clusterNr);				sqOptions.mostLikelySequence=true;				it->second->squigglePlot(filename,sqOptions);			}#endif		      		clusterNr++;	  }	/*	if(!options.has(RNAforesterOptions::ShowOnlyScore))	{		cout << "global optimal score: ";	}	cout << optScore << endl;	list<RNAProfileAlignment*>::iterator it=inputMapProfile.begin();	RNAProfileAlignment *ppf=it;	if(!options.has(RNAforesterOptions::ShowOnlyScore))	{
		// generate dot file		makeDotFileAli(*ppf,options);
		ppf->print();
		cout << endl;		ppf->printConsensus();	}	*/	// save profile alignment to binary file	/*	      if(options.has(RNAforesterOptions::SaveMultipleAliFile))	{	string filename;	filename=generateFilename(options,RNAforesterOptions::SaveMultipleAliFile,".mta", "unknown.dot");	ofstream s(filename.c_str());	f1->save(s);	}	*/	/*	// generate squiggle plots	if(options.has(RNAforesterOptions::MakeSquigglePlot))	{		RNAProfileAlignment::SquigglePlotOptions sqOptions;		string filename;		// plot showing full base information		filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,".ps", "rnaprofile.ps");		sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors);		sqOptions.mostLikelySequence=false;		ppf->squigglePlot(filename,sqOptions);		// plot showing consensus sequence		filename=options.generateFilename(RNAforesterOptions::MakeSquigglePlot,"_cons.ps", "rnaprofile_cons.ps");		sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors);		sqOptions.mostLikelySequence=true;		ppf->squigglePlot(filename,sqOptions);	}	*/		delete alg;}void alignPairwise(deque<RNAForest*> &inputListPW,Score &score,const RNAforesterOptions &options){	IntScoreRNA_AlgebraType *alg;	Uint xbasepos,ybasepos,xlen,ylen;	list<pair<Uint,Uint> > xsubopts;	list<pair<Uint,Uint> > ysubopts;	string seq1,seq2,str1,str2;	char s[8];	int suboptPercent;	Uint count=1;	RNAFuncs::SquigglePlotOptions sqOptions;	tms tmsStart, tmsEnd;	// read options	options.get(RNAforesterOptions::LocalSubopts,suboptPercent,100);#ifdef HAVE_LIBG2  // This features require the g2 library		// generate squiggle plot	if(options.has(RNAforesterOptions::MakeSquigglePlot))	{	      		// get sq options		sqOptions.hideBaseNumbers=options.has(RNAforesterOptions::SquiggleHideBaseNumbers);		options.get(RNAforesterOptions::SquiggleBaseNumberInterval,sqOptions.baseNumInterval,(Uint)20);		sqOptions.greyColors=options.has(RNAforesterOptions::SquiggleGreyColors);		options.get(RNAforesterOptions::SquiggleScaleFactor,sqOptions.scale,1.0);		sqOptions.generateFIG=options.has(RNAforesterOptions::SquiggleGenerateFIG);		#ifdef HAVE_LIBGD		sqOptions.generatePNG=options.has(RNAforesterOptions::SquiggleGeneratePNG);		sqOptions.generateJPG=options.has(RNAforesterOptions::SquiggleGenerateJPG);#endif			}#endif	// distance or similarity	if(options.has(RNAforesterOptions::CalculateDistance))		alg=new IntDistRNA_Algebra(score);	else	{		if(options.has(RNAforesterOptions::RIBOSUMScore))			alg=new RIBOSUM8560(score);		else			alg=new IntSimiRNA_Algebra(score);	}	RNAForest *f1=inputListPW.front();	RNAForest *f2=inputListPW.back();	if(options.has(RNAforesterOptions::SpaceTimeInfo))	  {	    IntScore_AlgebraType *algGlobClassic;	    algGlobClassic=new IntDist_Algebra(score);
	    if(!options.has(RNAforesterOptions::ShowOnlyScore))	      {		cout << "F1_NUMNODES" << ";";		cout << "F2_NUMNODES" << ";";		cout << "F1_DEGREE" << ";";		cout << "F2_DEGREE" << ";";		cout << "F1_LEAVES" << ";"; 		cout << "F2_LEAVES" << ";";		cout << "F1_DEPTH" << ";"; 		cout << "F2_DEPTH" << ";";		cout << "F1_NUMCSFS" << ";";		cout << "F2_NUMCSFS" << ";";		cout << "TABLE_SIZE_4D" << ";";		cout << "TABLE_SIZE_2D" << ";";		cout << "GLOBALI_TIME" << ";";		cout << "GLOBALI_TIME_SPEEDUP" << ";";		cout << "LOCALALI_TIME" << ";";		cout << "LOCALALI_TIME_SPEEDUP" << ";";				cout << endl;	      }	    cout << f1->size() << "\t";	    cout << f2->size() << "\t"; 	    cout << f1->maxDegree() << "\t";	    cout << f2->maxDegree() << "\t";	    cout << f1->numLeaves() << "\t";            cout << f2->numLeaves() << "\t";	    cout << f1->maxDepth() << "\t";	    cout << f2->maxDepth() << "\t";	    cout << f1->getNumCSFs() << "\t";	    cout << f2->getNumCSFs() << "\t";	    cout << f1->size()*f2->size()*f1->maxDegree()*f1->maxDegree() << "\t";	    cout << f1->getNumCSFs()*f2->getNumCSFs() << "\t"; 	    // global alignment	    {	      times(&tmsStart);	      Alignment<int,RNA_Alphabet,RNA_AlphaPair> ali(f1,f2,*algGlobClassic,false,true);	      times(&tmsEnd);	      cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; 	      //	    cerr << "#" << ali.getGlobalOptimum() << "#";	    } 	    // global alignment speedup	    {	      times(&tmsStart);	      Alignment<int,RNA_Alphabet,RNA_AlphaPair> ali(f1,f2,*algGlobClassic,false,false);	      times(&tmsEnd);	      cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; 	      //	    cerr << "#" << ali.getGlobalOptimum() << "#";	    } 	    // local alignment	    {	      times(&tmsStart);	      Alignment<int,RNA_Alphabet,RNA_AlphaPair> ali(f1,f2,*algGlobClassic,true,true);	      times(&tmsEnd);	      cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; 	      //	    cerr << "#" << ali.getLocalOptimum() << "#";	    } 	    // local alignment speedup	    {	      times(&tmsStart);	      Alignment<int,RNA_Alphabet,RNA_AlphaPair> ali(f1,f2,*algGlobClassic,true,false);	      times(&tmsEnd);	      cout <<((double) (tmsEnd.tms_utime - tmsStart.tms_utime))/sysconf(_SC_CLK_TCK) << "\t"; 	      //	    cerr << "#" << ali.getLocalOptimum() << "#";	    }	    	    cout << endl;	    exit(EXIT_SUCCESS);	  }	Alignment<int,RNA_Alphabet,RNA_AlphaPair> ali(f1,f2,*alg);	RNA_Alignment ppfali;	ppfali.setStructureNames(f1->getName(),f2->getName());	if(!options.has(RNAforesterOptions::ShowOnlyScore))	{	  if(options.has(RNAforesterOptions::SmallInLarge))	    {	      cout << "small-in-large optimal score: ";	    }	  else	    {	      if(options.has(RNAforesterOptions::LocalSimilarity))		cout << "local optimal score: ";	      else		cout << "global optimal score: ";	    }	}	if(options.has(RNAforesterOptions::SmallInLarge))	  {	    cout << ali.getSILOptimum() << endl;	  }	else	  {	    if(options.has(RNAforesterOptions::LocalSimilarity))	      {		cout << ali.getLocalOptimum() << endl;	      }  	    else	      {		cout << ali.getGlobalOptimum() << endl;	  	  		if(options.has(RNAforesterOptions::RelativeScore))		  cout << ali.getGlobalOptimumRelative() << endl;	      }	  }	if(!options.has(RNAforesterOptions::ShowOnlyScore))	{	  if(options.has(RNAforesterOptions::SmallInLarge))	    {	      ali.getOptSILAlignment(ppfali,ybasepos);	      cout << "starting at position: " << ybasepos << endl << endl; 	    }	  else	    {	      	      if(options.has(RNAforesterOptions::LocalSimilarity))		{		  ali.resetOptLocalAlignment(suboptPercent);		  ali.getOptLocalAlignment(ppfali,xbasepos,ybasepos);		      		    		  cout << "starting at positions: " << xbasepos << "," << ybasepos << endl << endl; 		}	      else		  		ali.getOptGlobalAlignment(ppfali);		  	    }		// generate dot file
		makeDotFileAli(ppfali,options);
		// print alignment		ppfali.getSequenceAlignments(seq1,seq2);						ppfali.getStructureAlignment(str1,true);		ppfali.getStructureAlignment(str2,false);		if(options.has(RNAforesterOptions::FastaOutput))		  {		    cout << ppfali.getStructureNameX() << endl;		    cout << seq1 << endl;		    cout << str1 << endl;		    cout << ppfali.getStructureNameY() << endl;		    cout << seq2 << endl;		    cout << str2 << endl;		    cout << endl;		  }		else				  RNAFuncs::printAli(ppfali.getStructureNameX(),ppfali.getStructureNameY(),seq1,seq2,str1,str2);  		xlen=seq1.size();		ylen=seq2.size();
		if(options.has(RNAforesterOptions::LocalSimilarity))
		{			xsubopts.push_back(pair<Uint,Uint>(xbasepos,xlen));			ysubopts.push_back(pair<Uint,Uint>(ybasepos,ylen));
		}#ifdef HAVE_LIBG2  // This features require the g2 library				if(options.has(RNAforesterOptions::MakeSquigglePlot))		  {		    sprintf(s,"%d",count);		    ppfali.squigglePlot(s,sqOptions);      		  }#endif	       		// suboptimal alignments		if(options.has(RNAforesterOptions::LocalSubopts))		{			while(ali.nextLocalSuboptimum())			{				count++;				cout << "local optimal score: ";				cout << ali.getLocalOptimum() << endl;				ali.getOptLocalAlignment(ppfali,xbasepos,ybasepos);				cout << "starting at positions: " << xbasepos << "," << ybasepos << endl << endl; 				// print alignment				ppfali.getSequenceAlignments(seq1,seq2);				ppfali.getStructureAlignment(str1,true);				ppfali.getStructureAlignment(str2,false);				RNAFuncs::printAli(ppfali.getStructureNameX(),ppfali.getStructureNameY(),seq1,seq2,str1,str2);  				xlen=seq1.size();				ylen=seq2.size();				xsubopts.push_back(pair<Uint,Uint>(xbasepos,xlen));				ysubopts.push_back(pair<Uint,Uint>(ybasepos,ylen));	#ifdef HAVE_LIBG2  // This features require the g2 library				                if(options.has(RNAforesterOptions::MakeSquigglePlot))		  				{				  sprintf(s,"%d",count);								  ppfali.squigglePlot(s,sqOptions);      	    	  				}#endif			       			}		}	}#ifdef HAVE_LIBRNA  // This features require the ViennaRNA library		// generate xml	if(options.has(RNAforesterOptions::GenerateXML))	{		string filename;		filename=options.generateFilename(RNAforesterOptions::GenerateXML,".xml", "ali.xml");		ofstream s(filename.c_str());		ppfali.generateXML(s);	}#endif	#ifdef HAVE_LIBG2  // This features require the g2 library	// generate squiggle plot	if(options.has(RNAforesterOptions::MakeSquigglePlot))	{		f1->plot2d("x_str", xsubopts, sqOptions);		f2->plot2d("y_str", ysubopts, sqOptions);  	}#endif		// clear input list	deque<RNAForest*>::const_iterator it;	for(it = inputListPW.begin(); it!=inputListPW.end(); it++)		delete *it;	inputListPW.clear();	delete alg;}
void editPairwise(list<RNAForestSZ*> &inputListSZ,Score &score,RNAforesterOptions &options){  //  timeb t1,t2;  IntScoreSZAlgebraType *alg;//  if(options.has(RNAforesterOptions::CalculateDistance))    alg=new IntDistSZAlgebra(score);//  else//    alg=new IntSimiSZAlgebra(score);    RNAForestSZ *f1=inputListSZ.front();  RNAForestSZ *f2=inputListSZ.back();  //  ftime(&t1);  Mapping<int,RNA_Alphabet> mapping(f1,f2,*alg);  //  ftime(&t2);
//	f1->printParameters("F1");//	f2->printParameters("F2");  cout << "Global optimum: " << mapping.getGlobalOptimum() << endl;  //  cout << "Calculation Time ms: " << (t2.time*1000+t2.millitm) - (t1.time*1000+t1.millitm) << endl;}void alignPairwiseSimple(deque<RNAForest*> &inputListPW,Score &score,RNAforesterOptions &options)
{
  //  timeb t1,t2;
  IntScore_AlgebraType *alg;
//  if(options.has(RNAforesterOptions::CalculateDistance))
    alg=new IntDist_Algebra(score);
//  else
//    alg=new ScoreAlgebraSimple(score);

  RNAForest *f1=inputListPW.front();
  RNAForest *f2=inputListPW.back();

  //  ftime(&t1);
  Alignment<int,RNA_Alphabet,RNA_AlphaPair> ali(f1,f2,*alg,false);
  //  ftime(&t2);
//	f1->printParameters("F1");  //f2->printParameters("F2");
  cout << "Global optimum: " << ali.getGlobalOptimum() << endl;
  //  cout << "Calculation Time ms: " << (t2.time*1000+t2.millitm) - (t1.time*1000+t1.millitm) << endl;
}