Alignment.cpp

#include <iostream>
#include <string>
#include <vector>
#include <map>
#include <unordered_map>

using namespace std; 

class Alignment_Data{
public:
	string label;		//the row data, uesd as key
						//ex: 2620178 2620733 6424 6980 6 6 0
	string refid;
	long Rstart;
	long Rend; 
	long Qstart; 
	long Qend; 
	int Error;
	int SimError;		//similar error
	int negNum;			//negative number ( Deletion )
	double pid;
	
	//  Constructor															
	Alignment_Data(string label, long Rstart, long Rend, long Qstart, long Qend, int Error ,int SimError ,int negNum){
		this->label = label;
		this->Rstart = Rstart;
		this->Rend = Rend;
		this->Qstart = Qstart;
		this->Qend = Qend;
		this->Error = Error;
		this->SimError = SimError;
		this->negNum = negNum;
	}
	
	void set_pid (double pid){
		this->pid = pid;
	}
	
	double get_pid(){
		return pid;
	}
	
	long get_left_most_position(){
		if(Rend > Rstart){
			return Rstart;
		}else{
			return Rend;
		}
	}
	
	long get_right_most_position(){
		if(Rend < Rstart){
			return Rstart;
		}else{
			return Rend;
		}
	}
	
	long get_rstart(){
		return Rstart;
	}
	
	long get_rend(){
		return Rend;
	}
	
	long get_qstart(){
		return Qstart;
	}
	
	long get_qend(){
		return Qend;
	}
	
};


class Header{
public:
	string header;	// rname + qname , used as key
					// ex:>000003F|arrow scf7180000001372|quiver
					
	string rname;	// ex:>000003F|arrow
	string qname;	// ex:scf7180000001372|quiver
	long rlen;
	long qlen;
	unordered_map< string , Alignment_Data* > dataMap;	//map sotres key and ptr pair.
	
	//constructor
	Header(string header, long rlen, long qlen){
		this->header = header;
		this->rlen = rlen;
		this->qlen = qlen;
	}
	
	// adding data by information Rstart Rend .......
	void add_alignment( string label, long Rstart, long Rend, long Qstart, long Qend, int Error ,int SimError ,int negNum){
		Alignment_Data *ad = new Alignment_Data(label,  Rstart, Rend,  Qstart, Qend, Error ,SimError ,negNum);
		dataMap.insert( make_pair( label, ad ) );
	}
	
	// adding data by object
	void add_aglinment( string label, Alignment_Data* ad){
		dataMap.insert( make_pair( label, ad ) );
	}
	
	//serach data by label, return ptr of object
	Alignment_Data* get_alignment(string label){
		unordered_map< string , Alignment_Data* >::iterator iter = dataMap.find(label);
		if(iter != dataMap.end()){
			return iter->second;
		}
		else{
			cout<<"Do not Find alignment data: "<<label<<endl;
		}
	}
	
	//remove data from map
	void remove_alignment( string label ){
		unordered_map< string , Alignment_Data* >::iterator iter = dataMap.find(label);
		if (iter != dataMap.end()){
			delete iter->second;	//remove object
			dataMap.erase(iter);	//remove key in map
		}
		else{
			cout<<"Do not Find header:"<< label<<endl;
		}
	}
	
	string get_ref_name(){
		return rname;
	}
	
	string get_query_name(){
		return qname;
	}
	
	long get_rlen(){
		return rlen;
	}
	
	long get_qlen(){
		return qlen;
	}
	
};


class Alignment {
public:	
	string source; 
	string datatype;
	unordered_map< string , Header* > headerMap;

	
	Alignment(string source, string datatype){
		this->source = source;
		this->datatype = datatype;
	}
	
	/*
	void add_header( string header, long rlen, long qlen ){
		Header head( header, rlen, qlen);
		headerMap.insert( make_pair( header , head ) );
	}
	*/
	
	void add_header( string header, Header* h ){
		headerMap.insert( make_pair( header , h ) );
		//headerMap[header] = h;								//need 	empty constructor at begin  :  Header(){}	
	}
	
	Header* get_header( string header){
		unordered_map< string , Header* >::iterator iter = headerMap.find(header);
		if(iter != headerMap.end()){
			return iter->second;
		}
		else{
			cout<<"Do not Find header: "<<header<<endl;
		}
	}
	
	void remove_header( string header ){
		unordered_map< string , Header* >::iterator iter = headerMap.find(header);	//iterator
		if (iter != headerMap.end()){
			delete iter->second;
			headerMap.erase(iter);
		}
		else{
			cout<<"Do not Find header:"<< header<<endl;
		}
	}
};



//  test Alignment.cpp

/*
int main(){
	
//	test Alignment_data
	Alignment_Data ad1("1 2 3 4 5 6 0",1,2,3,4,5,6,7);
	cout<<"test Alignment data:" << endl<<endl;
	cout<<"  label: " <<ad1.label<<endl;
	cout<<"  Rstart:" <<ad1.Rstart<<endl;
	cout<<"  get R: " <<ad1.get_rstart()<<endl;
	cout<<"  Rend: "  <<ad1.Rend<<endl;
	cout<<"  Qstart:" <<ad1.Qstart<<endl;
	cout<<"  Qend: "  <<ad1.Qend<<endl;
	cout<<"  error: " <<ad1.Error<<endl;
	cout<<"  negative numbers:"<<ad1.negNum<<endl<<endl<<endl;
	
	Alignment_Data ad2("11 22 33 44 55 66 00",11,22,33,44,55,66,77);
	
	
//	test Header
	Header h( ">000003F|arrow scf7180000001372|quiver" , 9085994 , 21655);
	cout<<"test Header:" << endl<<endl;
	h.add_alignment("1 2 3 4 5 6 0",1,2,3,4,5,6,7);
	h.add_alignment("11 22 33 44 55 66 00",11,22,33,44,55,66,77);
	cout<< "  get info from map:" <<h.get_alignment("1 2 3 4 5 6 0")->Rend<<endl;
	cout<< "  get info from map:" <<h.get_alignment("11 22 33 44 55 66 00")->Qstart<<endl;
	cout<<endl<<endl;
	
	
//	test Alignment
	Alignment a( "/data/users/yuanhunl/Lab/self_oneline.fa /data/users/yuanhunl/Lab/hybrid_oneline.fa" ,
				 "NUCMER" );
	cout<< "  test Alignment: "<<endl<<endl;
	cout<< "  data source: "<<a.source<<endl;
	cout<< "  data type: " <<a.datatype<<endl<<endl;
	
	Header *h1  = new Header( ">000010F|arrow scf7180000001375|quiver" ,  2187667 , 18219 );
	Alignment_Data *a1 = new Alignment_Data("8373859 8395578 21655 1 72 72 0" , 8373859, 8395578, 21655, 1, 72, 72, 15);
	
	h1->add_aglinment("8373859 8395578 21655 1 72 72 0", a1);
	a.add_header(">000010F|arrow scf7180000001375|quiver" , h1);
	a.get_header(">000010F|arrow scf7180000001375|quiver")->add_alignment("8373859 8395578 21655 1 72 72 0" , 8373859, 8395578, 21655, 1, 72, 72, 15);
	
	cout<<a.get_header(">000010F|arrow scf7180000001375|quiver")->get_alignment("8373859 8395578 21655 1 72 72 0")->Rstart<<endl;
	
	
	h1  = new Header( ">000010F|arrow scf7180000001375|quiver" ,  2187667 , 18219 );
	a1 = new Alignment_Data("8373859 8395578 21655 1 72 72 0" , 8373859, 8395578, 21655, 1, 72, 72, 15);
	h1->add_aglinment("8373859 8395578 21655 1 72 72 0", a1);
	a.add_header(">000010F|arrow scf7180000001375|quiver" , h1);
	a.get_header(">000010F|arrow scf7180000001375|quiver")->add_alignment("8373859 8395578 21655 1 72 72 0" , 8373859, 8395578, 21655, 1, 72, 72, 15);
	
	cout<<a.get_header(">000010F|arrow scf7180000001375|quiver")->get_alignment("8373859 8395578 21655 1 72 72 0")->Rstart<<endl;
	
	
	system("pause");
	return 0;
}

*/