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//==============================Sequence Analysis==============================
#define ANALYSIS
cursize=maxsize;
//==================Initialize head and set pointers to NULL===================
head=new matchnode*[maxsize-minsize+1];
curr=new matchnode*[maxsize-minsize+1];
if(!head||!curr)
{
cout<<"could not allocate memory for operation, terminating"<<endl;
return MEM_ALLOC_ERROR;
}
num1=0;
while(num1<=(maxsize-minsize+1))
{
head[num1]=NULL;
curr[num1]=NULL;
num1++;
}
while(!(cursize<minsize))
{
for(num1=0;num1<(size1-cursize);num1++)
{
temp=0;
temp2=size2-cursize;
if(flags&0x200&&(num1-leeway)<=num1)
{
temp=num1-leeway;
}
else
{
temp=0;
}
if(flags&0x200&&(num1+leeway)>=num1&&(num1+leeway)<size2-cursize)
{
temp2=leeway+num1;
}
else
{
temp2=size2-cursize;
}
for(num2=temp;num2<temp2;num2++)
{
//==========Check if regions are homologous==========
if(flags&0x100)
{
for(count=0,homnum=0;(count<cursize);count++)
{
homnum+=D_equiv(seq1[num1+count],seq2[num2+count]);
}
matchpercent=(homnum*100)/(cursize);
}
else
{
for(count=0,homnum=0;(count<cursize);count++)
{
homnum+=equiv(seq1[num1+count],seq2[num2+count]);
}
matchpercent=(homnum*100)/cursize;
}
//==========Check if regions are encompassed by Larger regions already found==========
if(!(matchpercent<percent)&&(cursize<maxsize))
{
#if 1
ch=backcheck(head,curr,&num1,&num2,cursize,maxsize);
#else
ch=1;
#endif
}
//==========Store info about region in a matchnode==========
if(ch)
{
newmatchnode=new matchnode();
if(!newmatchnode)
{
puts("could not allocate memory for operation, terminating\n ");
return MEM_ALLOC_ERROR;
}
newmatchnode->next=NULL;
newmatchnode->start1=num1;
newmatchnode->start2=num2;
if(head[maxsize-cursize]==NULL)
{
head[maxsize-cursize]=newmatchnode;
curr[maxsize-cursize]=newmatchnode;
}
else
{
curr[maxsize-cursize]->next=newmatchnode;
curr[maxsize-cursize]=newmatchnode;
}
//num1=num1+count;
num2=num2+count;
ch=0;
}
}
}
#ifdef HOMOLOGY_TEST
cout<<"cursize: "<<cursize<<",num1: "<<num1<<",num2: "<<num2<<endl;
#endif
curr[maxsize-cursize]=head[maxsize-cursize];
cursize--;
}
for(count=0;count<(maxsize-minsize+1);count++)
{
#ifdef HOMOLOGY_TEST
if(!curr[count])
{
cout<<"Nothing found at size: "<<maxsize-count;
}
#endif
while(curr[count])
{
#ifdef HOMOLOGY_TEST
cout<<"Homology found, size: "<<maxsize-count<<", start1: "<<curr[count]->start1+1<<",start2: "<<curr[count]->start2+1<<endl;
#endif
curr[count]=curr[count]->next;
}
curr[count]=head[count];
#ifdef HOMOLOGY_TEST
ch=0;
cin >> noskipws;
while(ch!='\n')
{
cin >> ch;
}
cin >> skipws;
#endif
}
//==============================File Writing==============================
#define FILE_WRITE
#ifndef NO_FSTREAM_WRITING
//equalline:"================================================================================\n"
// hashline:"################################################################################\n"
file.open(argv[output],ios::out|ios::trunc);
delete[] curr;
curr=NULL;
count=0;
num1=0;
num2=0;
selector=0;
file<<starline;
file<<"Results of Comparison Between "<<argv[input1]<<" and "<<argv[input2]<<"\n";
file<<starline;
file<<"Size of "<<argv[input1]<<": "<<size1<<"\tSize of "<<argv[input2]<<": "<<size2<<"\n";
file<<starline;
file<<"Settings Used\n";
file<<" minsize: "<<minsize<<"\n";
file<<" maxsize: "<<maxsize<<"\n";
file<<" percent: "<<(int)percent<<"\n";
if(flags&0x100)
{
file<<"degeneracy: "<<"YES"<<"\n";
}
else
{
file<<"degeneracy: "<<"NO"<<"\n";
}
if(flags&0x200)
{
file<<" leeway: "<<leeway<<"\n";
}
else
{
file<<" leeway: N/A\n";
}
file<<starline;
while(selector<maxsize-minsize+1)
{
file<<hashline;
file<<"Region Size: "<<maxsize-selector<<"\n";
newmatchnode=head[selector];
if(!newmatchnode)
{
file<<"No matching sequences of this size were found.\n";
}
while(newmatchnode)
{
file<<equalline;
for(count=0;count<maxsize-selector;count++)
{
file<<seq1[newmatchnode->start1+count];
}
file<<'\n';
file<<"Start1: "<<newmatchnode->start1+1<<"\t"<<"End1: "<<newmatchnode->start1+maxsize-selector<<"\n";
for(count=0;count<maxsize-selector;count++)
{
file<<seq2[newmatchnode->start2+count];
}
file<<'\n';
file<<"Start2: "<<newmatchnode->start2+1<<"\t"<<"End2: "<<newmatchnode->start2+maxsize-selector<<"\n";
newmatchnode=newmatchnode->next;
delete head[selector];
head[selector]=newmatchnode;
}
selector++;
}
delete [] head;
delete [] seq1;
delete [] seq2;
file<<flush;
file.close();
return 0;
#else
return 0;
#endif
}
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