📄 alignmentclass.cpp.bak
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// aligmentClass.cpp: implementation of the AligmentClass class.
//
//////////////////////////////////////////////////////////////////////
#include "math.h"
#include "AlignmentClass.h"
//#include <fstream>
//#include <math.h>
//const double s[5][5]={{1,0.5,0.5,0,0},{0.5,1,0.5,0,0},{0,0.5,1,0.5,0},{0.5,0,0.5,1,0},{0,0,0,0,0}};//打分矩阵
const double s[5][5]={{1.0,-1,-2.0,-1,-2.0},{-1,1.0,-1,-2.0,-2.0},{-2.0,-1,1.0,-1,-2.0},{0,-2.0,0,1.0,-2.0},{-2.0,-2.0,-2.0,-2.0,0}};//打分矩阵
const double K = 1.23891;
const double L = 1.386294;
double tmpArray[PSS4LineLength][PSS4LineLength];
double ArrayMax(int a,int rang);
double ShowMax(double a,double b,double c);
double S(char a,char b);
const double reducematrix=0;
const double gap=0.1;
float ExtAlign(AlignmentResult &rar,int tb,int te,int pb,int pe)
{
int i,j;
float score=0;
std::ofstream log("log1");
log<<"Seed:"<<std::endl;
for(i=rar.TBegin;i<rar.TEnd;i++)
log<<rar.Text[i];
log<<std::endl;
for(i=rar.PBegin;i<rar.PEnd;i++)
log<<rar.Pattern[i];
log<<std::endl;
log<<std::endl;
for(i=tb;i<te;i++)
log<<rar.Text[i];
log<<std::endl;
for(i=pb;i<pe;i++)
log<<rar.Pattern[i];
log<<std::endl;
for(i=0;i<=(te-tb);i++)
{
for(j=0;j<=(te-tb);j++)
{
log<<tmpArray[i][j]<<" ";
}
log<<std::endl;
}
for(i=0;i<=(te-tb);i++)
{
int j1=(i-(int)(reducematrix*(te-tb)))>0?(i-(int)(reducematrix*(te-tb))):0;
int j2=(i+(int)(reducematrix*(te-tb))<(te-tb))?(i+(int)(reducematrix*(te-tb))):(te-tb);
for(j=j1;j<=j2;j++)
{
if(i==0||j==0)
tmpArray[i][j]=0;
else
tmpArray[i][j]=ShowMax(tmpArray[i-1][j-1]+S(rar.Text[tb+j-1],rar.Pattern[pb+i-1]),tmpArray[i][j-1]+gap,tmpArray[i-1][j]+gap);
}
}
for(i=0;i<=(te-tb);i++)
{
for(j=0;j<=(te-tb);j++)
{
log<<tmpArray[i][j]<<" ";
}
log<<std::endl;
}
score=ArrayMax(te-tb,(int)(reducematrix*(te-tb)));
log.close();
return score;
}
float AlignmentClass::FinalAlign(AlignmentResult &rar,int tb,int te,int pb,int pe)
{
int i,j;
float score=0;
int tgapcount=0;
int pgapcount=0;
//int tmpArray[PSS4LineLength][PSS4LineLength];
std::ofstream log("log1");
for(i=0;i<=(pe-pb);i++)
{
for(j=0;j<=(te-tb);j++)
{
log<<tmpArray[i][j]<<" ";
}
log<<std::endl;
}
for(i=0;i<=(pe-pb);i++)
{
//int j1=(i-(int)(reducematrix*(te-tb)))>0?(i-(int)(reducematrix*(te-tb))):0;
//int j2=(i+(int)(reducematrix*(te-tb))<(te-tb))?(i+(int)(reducematrix*(te-tb))):(te-tb);
for(j=0;j<=(te-tb);j++)
{
if(i==0||j==0)
tmpArray[i][j]=0;
else
tmpArray[i][j]=ShowMax(tmpArray[i-1][j-1]+S(rar.Text[tb+j-1],rar.Pattern[pb+i-1]),tmpArray[i][j-1]+gap,tmpArray[i-1][j]+gap);
//tmpArray[i][j]=ShowMax(tmpArray[i-1][j-1]+S(rar.Text[tb+j-1],rar.Pattern[pb+i-1]),tmpArray[i][j-1]-gap,tmpArray[i-1][j]-gap);
}
}
log<<"\t\t";
for(j=0;j<(te-tb);j++)
log<<rar.Text[j]<<"\t";
log<<std::endl;
for(i=0;i<=(pe-pb);i++)
{
if(i>0)
log<<rar.Pattern[i-1]<<"\t";
else
log<<"\t";
for(j=0;j<=(te-tb);j++)
{
log<<tmpArray[i][j]<<"\t";
}
log<<std::endl;
}
log.close();
for(i=(pe-pb),j=(te-tb);i>0&&j>0;)
{
double ttt=S(rar.Text[tb+j-1],rar.Pattern[pb+i-1]);
if(tmpArray[i][j]==tmpArray[i-1][j-1]+ttt)
{
i--;
j--;
}
else if(tmpArray[i][j]==tmpArray[i-1][j]+gap)
{
rar.TGapRecord.push_back(i-2);
tgapcount++;
j--;
}
else if(tmpArray[i][j]==tmpArray[i][j-1]+gap)
{
rar.PGapRecord.push_back(j-2);
pgapcount++;
i--;
}
else
{
i--;
j--;
}
}
score=tmpArray[pe-pb][te-tb];
rar.SimScore=score;
rar.Similarity=rar.SimScore/double(te-tb+pgapcount+tgapcount);
rar.TGapCount=tgapcount;
rar.PGapCount=pgapcount;
return score;
}
void AlignmentClass::MainAlignment(AlignmentResult &rar)
{
/*char *T=tar.Text;
char *P=tar.Pattern;
AlignmentResult rar;
ResultAsignMent(&rar,&tar);*/
bool RFlag=true,LFlag=true;
int extcount=0;
while(RFlag==true)//while(LFlag==TRUE||RFlag==TRUE)
{
if(LFlag==true)
{
//LeftExtend
if(rar.IsPbegin()||rar.IsTbegin())
{
LFlag=false;
}
else
{
double Score=0;
int Lext=rar.Lextern();
Score=ExtAlign(rar,rar.TBegin-Lext,rar.TBegin,rar.PBegin-Lext,rar.PBegin);
//int t1=(Score+rar.SimScore),t2=(Lext+(rar.PEnd-rar.PBegin)),t3=(rar.SimScore)+t1,t4=(rar.PEnd-rar.PBegin)+t2;
if(Score/Lext<LocalSimDomain)
LFlag=false;
else
{
extcount++;
//RFlag=true;
rar.TBegin=rar.TBegin-Lext;
rar.PBegin=rar.PBegin-Lext;
//rar.SimScore=Score;
//rar.Similarity=rar.SimScore/(rar.PEnd-rar.PBegin);
}
}
if(RFlag==true)
{
//RExtend
if(rar.IsPend()||rar.IsTend())
{
RFlag=false;
}
else
{
int Score=0;
int Rext=rar.Rextern();
Score=ExtAlign(rar,rar.TEnd,rar.TEnd+Rext,rar.PEnd,rar.PEnd+Rext);
if(Score/Rext<LocalSimDomain)
RFlag=false;
else
{
extcount++;
//LFlag=true;
rar.TEnd=rar.TEnd+Rext;
rar.PEnd=rar.PEnd+Rext;
//rar.SimScore=Score;
//rar.Similarity=rar.SimScore/(rar.PEnd-rar.PBegin);
}
}
}
}
else
{
if(RFlag==true)
{
// RExtend();
if(rar.IsPend()||rar.IsTend())
{
RFlag=false;
}
else
{
int Score=0;
int Rext=rar.Rextern();
Score=ExtAlign(rar,rar.TEnd,rar.TEnd+Rext,rar.PEnd,rar.PEnd+Rext);
if(Score/Rext<LocalSimDomain)
RFlag=false;
else
{
extcount++;
//LFlag=true;
rar.TEnd=rar.TEnd+Rext;
rar.PEnd=rar.PEnd+Rext;
//rar.SimScore=Score;
//rar.Similarity=rar.SimScore/(rar.PEnd-rar.PBegin);
}
}
}
}
}
if(extcount>=3)
{
rar.SimScore=FinalAlign(rar,rar.TBegin,rar.TEnd,rar.PBegin,rar.PEnd);
rar.Similarity=rar.SimScore/(rar.PEnd-rar.PBegin);
double m=rar.PatternCount;
double n=rar.TextCount;
double x=rar.SimScore;
rar.p_value=1-exp(-K*m*n*exp(-L*x));
}
else
{
rar.SimScore=-1;
rar.Similarity=-1;
rar.p_value=-1;
}
//return rar;
}
int AlignmentResult::Lextern()
{
int i=(TBegin-ExtendStep)>0?ExtendStep:TBegin;
int j=(PBegin-ExtendStep)>0?ExtendStep:PBegin;
i=(i<=j?i:j);
return i;
}
int AlignmentResult::Rextern()
{
int i=(TEnd+ExtendStep)<TextCount?ExtendStep:TextCount-TEnd;
int j=(PEnd+ExtendStep)<PatternCount?ExtendStep:PatternCount-PEnd;
i=(i<=j?i:j);
return i;
}
bool AlignmentResult::IsTbegin()
{
if(TBegin==0)
return true;
else
return false;
}
bool AlignmentResult::IsTend()
{
if(TEnd==TextCount)
return true;
else
return false;
}
bool AlignmentResult::IsPend()
{
if(PEnd==PatternCount)
return true;
else
return false;
}
bool AlignmentResult::IsPbegin()
{
if(PBegin==0)
return true;
else
return false;
}
void AlignmentClass::ResultAsignMent(AlignmentResult& rar,AlignmentResult& tar)
{
rar.PBegin=tar.PBegin;
rar.PEnd=tar.PEnd;
rar.TBegin=tar.TBegin;
rar.TEnd=tar.TEnd;
rar.Similarity=tar.Similarity;
rar.SimScore=tar.SimScore;
rar.PatternCount=tar.PatternCount;
rar.TextCount=tar.TextCount;
rar.Text=tar.Text;
rar.Pattern=tar.Pattern;
}
double S(char a,char b)//打分矩阵
{
int a1,b1;
switch(a)
{
case '0':
a1=0;break;
case '1':
a1=1;break;
case '2':
a1=2;break;
case '3':
a1=3;break;
case ' ':
a1=4;break;
}
switch(b)
{
case '0':
b1=0;break;
case '1':
b1=1;break;
case '2':
b1=2;break;
case '3':
b1=3;break;
case ' ':
b1=4;break;
}
if(a1==-1||b1==-1)
return 0;
double t=s[a1][b1];
return t;
}
double ShowMax(double a,double b,double c)
{
double tmp=a>b?a:b;
tmp=tmp>c?tmp:c;
return tmp;
}
void AlignmentClass::test(AlignmentResult &tmpAR)
{
std::ofstream OutFile;
OutFile.open("odata\\test.out",std::ios::out|std::ios::app);
//int tmpExt=Result.PEnd-Result.PBegin;
int i,j;
for(i=tmpAR.PBegin;i<tmpAR.PEnd;i++)
{
for(j=tmpAR.TBegin;j<tmpAR.TEnd;j++)
{
if(tmpArray[i][j]>=0)
OutFile<<tmpArray[i][j]<<" ";
else
OutFile<<"*"<<" ";
}
OutFile<<std::endl;
}
}
double ArrayMax(int a,int range)
{
double max;
int rangei,rangej;
if(a<=0)
{
rangei=0;
rangej=0;
return max=tmpArray[0][0];
}
else
{
max=tmpArray[a][a];
rangei=a;
rangej=a;
for(int i=1;i<(range<a?range:a);i++)
{
if(max<tmpArray[a][a-i])
{
rangei=a;
rangej=a-i;
max=tmpArray[a][a-i];
}
if(max<tmpArray[a-i][a])
{
rangei=a-i;
rangej=a;
max=tmpArray[(a-i)>i?(a-i):i][a];
}
}
return max;
}
}
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