/*  Copyright by Matthias Hoechsmann (C) 2002-2004  =====================================                                     You may use, copy and distribute this file freely as long as you  - do not change the file,  - leave this copyright notice in the file,  - do not make any profit with the distribution of this file  - give credit where credit is due  You are not allowed to copy or distribute this file otherwise  The commercial usage and distribution of this file is prohibited  Please report bugs and suggestions to <mhoechsm@TechFak.Uni-Bielefeld.DE>*/#include <algorithm>#include <string>#ifndef WIN32#include "config.h"#endif#include "misc.h"#include "rna_alignment.h"#include "rnafuncs.h"#include "utils.h"/* ****************************************** *//*            Private functions               *//* ****************************************** */void RNA_Alignment::makePairTable(map<Uint,Uint> &pairs, bool first) const{        pair<int,int> *baseIndex;   // stores for each node in the alignment the index position of the left and right base (or -1)	RNA_Alphabet c;	baseIndex=new pair<int,int>[m_size];	// initialize pairs, all gaps	for(int i=size()-1;i>=0;i--)	  {	    baseIndex[i].first=-1;	    baseIndex[i].second=-1;	  }	for(int i=size()-1;i>=0;i--)	{		// first or second component		if(first)			c=m_lb[i].a;		else			c=m_lb[i].b;		if(isLeave(i))		  {			if(c!=ALPHA_GAP)			{			    baseIndex[i].first=i;			    baseIndex[i].second=i;			}		  }		else		{			// internal node			// leftmost and rightmost base			bool lmBaseFound=false;			for(size_type r=0,h=i+1;r<getMaxLength(i+1);r++,h=rb(h))			{					  				// leftmost base				if(!lmBaseFound && baseIndex[h].first != -1)				{					baseIndex[i].first=baseIndex[h].first;					lmBaseFound=true;				}				// rightmost base				if(baseIndex[h].second != -1)				{					baseIndex[i].second=baseIndex[h].second;				}			}			// report pairing bases if P node			if(c==ALPHA_BASEPAIR)			{			        assert(baseIndex[i].first != -1);			        assert(baseIndex[i].second != -1);				assert(baseIndex[i].first < baseIndex[i].second);				pairs[baseIndex[i].first]=baseIndex[i].second;				pairs[baseIndex[i].second]=baseIndex[i].first;			}		}	}	delete[] baseIndex;}/* ****************************************** *//*             Public functions               *//* ****************************************** */void RNA_Alignment::getSequenceAlignments(string &s1, string &s2) const{  s1="";  s2="";  // generate base strings  for(size_type i=0;i<size();i++)    {      if(m_lb[i].a != ALPHA_BASEPAIR && m_lb[i].b != ALPHA_BASEPAIR)	  {		s1 += m_lb[i].a;		s2 += m_lb[i].b;	  }    }}void RNA_Alignment::getStructureAlignment(string &s, bool first) const{  s="";  map<Uint,Uint> pairs;  makePairTable(pairs, first);  // iterate through leaves nodes and use information of pairs  for(size_type i=0;i<size();i++)    {	  RNA_Alphabet c;	  	  if(first)		c=m_lb[i].a;	  else		c=m_lb[i].b;      if(isLeave(i))	  {		if(c != ALPHA_GAP)		{			if(pairs.find(i) != pairs.end())	// is base paired ?			{				size_type j=pairs[i];				if(i<j)					s+='(';				else					s+=')';			}			else				s+='.';		}		else			s+='-';	  }    }}#ifdef HAVE_LIBG2  // This features require the g2 libraryvoid RNA_Alignment::squigglePlot(const string &filename_suffix, const RNAFuncs::SquigglePlotOptions &options) const{  string str1,str2,seq1,seq2;  string filename;  getStructureAlignment(str1,true);  getStructureAlignment(str2,false);  getSequenceAlignments(seq1,seq2);  filename = "x_" + filename_suffix;  RNAFuncs::drawRNAAlignment(str1,str2,seq1,seq2,m_strname1,m_strname2,filename,true,options);  filename = "y_" + filename_suffix;  RNAFuncs::drawRNAAlignment(str2,str1,seq1,seq2,m_strname1,m_strname2,filename,false,options);}#endifvoid RNA_Alignment::setStructureNames(const string &s1,const string &s2){  m_strname1=s1;  m_strname2=s2;}#ifdef HAVE_LIBRNAvoid RNA_Alignment::generateXML(ostream &s) const{  string str1,str2,seq1,seq2;  getStructureAlignment(str1,true);  getStructureAlignment(str2,false);  getSequenceAlignments(seq1,seq2);  RNAFuncs::generateRNAAlignmentXML(str1,str2,seq1,seq2,m_strname1,m_strname2,s);}#endif