void fillArr( vector<int> &arr, MSVS &mp ){
arr.push_back( 0 );
for( MSVS::iterator p = mp.begin(); p != mp.end() ; ++p ){
string key;
key = p->first;
arr.push_back( getStart( key ) );
arr.push_back( getEnd( key ) );
}
}
// MSVS:map(START$END, set<Gene> ) , there is only one Gene in set
void block ( MSVS &mp ){
MSVS::iterator p, pNext, pTmp;
int pStart, pEnd, nextStart, nextEnd ; // two old
int leftEnd, midStart, midEnd, rightStart; // three new
string leftKey, midKey, rightKey;
stringstream ss;
if( mp.size() < 2 )
return;
p = mp.begin();
pNext = p;
++pNext ;
while( pNext != mp.end() ) {
pStart = getStart( p->first );
pEnd = getEnd( p->first );
nextStart = getStart( pNext->first );
nextEnd = getEnd( pNext->first );
//cout << "Enter loop: p is ( " << pStart << ", " << pEnd << "), pNext is ( " << nextStart << ", " << nextEnd << " )." << endl;
if( nextStart > pEnd ){
//cout << "no overlap " << endl; // (3,8 ) (9, 12 ) 9 > 8
p = pNext;
++pNext;
continue;
}
if( nextStart > pStart ){
//cout << "insert left " << endl;
leftEnd = nextStart - 1;
ss.str("");
ss << pStart << "$" << leftEnd;
leftKey = ss.str();
//cout << "leftKey is : " << leftKey << endl;
mp.insert( MSVS::value_type ( leftKey, p->second ) );
}
if( nextEnd > pEnd ){ // ( 3,10) (3,7) 10 > 7
//cout << "insert right" << endl;
rightStart = pEnd + 1;
ss.str("");
ss << rightStart << "$" << nextEnd ;
rightKey = ss.str();
//cout << "rightKey is : " << rightKey << endl;
pTmp = mp.find( rightKey );
if ( pTmp != mp.end() )
pTmp->second.insert( pNext->second.begin(), pNext->second.end() );
else
mp.insert( MSVS::value_type( rightKey, pNext->second ) );
if( nextStart > pStart ){
//cout << "insert middle" << endl;
midStart = nextStart;
midEnd = pEnd;
ss.str("");
ss << midStart << "$" << midEnd ;
midKey = ss.str();
//cout << "midKey is : " << midKey << endl;
mp.insert( MSVS::value_type( midKey, p->second ) );
mp.erase( p );
pTmp = mp.find( midKey );
pTmp->second.insert( pNext->second.begin(), pNext->second.end() );
p = pTmp;
}
else if ( nextStart == pStart )
p->second.insert( pNext->second.begin(), pNext->second.end() );
mp.erase( pNext );
pNext = p;
++pNext;
}
// when nextEnd <= pEnd
else {
pNext->second.insert( p->second.begin(), p->second.end() ); // nextStart > pStart , nextEnd <= pEnd, pNext is middle
if ( nextEnd < pEnd ){ // (4,6 ) (3,8)
//cout << "insert right " << endl;
rightStart = nextEnd + 1;
ss.str("");
ss << rightStart << "$" << pEnd ;
rightKey = ss.str();
//cout << "rightKey is : " << rightKey << endl;
pTmp = mp.find( rightKey );
if( pTmp != mp.end() )
pTmp->second.insert( p->second.begin(),p->second.end() );
else
mp.insert( MSVS::value_type ( rightKey, p->second ) );
}
mp.erase ( p ) ;
p = pNext;
++pNext;
}
}
}