reader should have no knowledge of writer functionality

io/TomahawkOutput/TomahawkOutputReader.cpp

@@ -46,11 +46,15 @@ bool TomahawkOutputReader::view(const std::string& input){
 }
 
 bool TomahawkOutputReader::__viewRegion(void){
-	if(this->writer_output_type == WRITER_TYPE::natural)
+	if(this->writer_output_type == WRITER_TYPE::natural){
 		this->writer = new TomahawkOutputWriterNatural();
+		TomahawkOutputWriterNatural* temp = reinterpret_cast<TomahawkOutputWriterNatural*>(this->writer);
+		temp->setContigs(this->contigs);
+	}
 	else this->writer = new TomahawkOutputWriter();
+
 	this->writer->open();
-	this->__writeOutputHeaders();
+	this->writer->writeHeader();
 
 	if(this->interval_tree != nullptr){
 		const entry_type*  entry;
@@ -60,31 +64,8 @@ bool TomahawkOutputReader::__viewRegion(void){
 		} // end while next variant
 	}
 
-	this->writer->flush();
-	this->__writeOutputEOF();
-	this->writer->close();
-
 	return true;
 }
-
-bool TomahawkOutputReader::__writeOutputHeaders(void){
-	if(this->writer_output_type == WRITER_TYPE::binary){
-		return true;
-	} else {
-		const std::string header = "FLAG\tAcontigID\tAposition\tBcontigID\tBpositionID\tp1\tp2\tq1\tq2\tD\tDprime\tR2\tP\tchiSqFisher\tchiSqModel\n";
-		this->writer->write(&header[0], header.length());
-		return true;
-	}
-}
-
-bool TomahawkOutputReader::__writeOutputEOF(void){
-	if(this->writer_output_type == WRITER_TYPE::binary){
-		return true;
-	} else {
-		return true;
-	}
-}
-
 bool TomahawkOutputReader::__checkRegion(const entry_type* const entry){
 	// If iTree for contigA exists
 	if(this->interval_tree[entry->AcontigID] != nullptr){

io/TomahawkOutput/TomahawkOutputReader.h

@@ -71,9 +71,6 @@ class TomahawkOutputReader {
 	bool __viewRegion(void);
 	bool __checkRegion(const entry_type* const entry);
 
-	bool __writeOutputHeaders(void);
-	bool __writeOutputEOF(void);
-
 public:
 	U64 filesize;	// input file size
 	U32 position;

io/TomahawkOutput/TomahawkOutputWriter.h

@@ -26,6 +26,7 @@ class TomahawkOutputWriterInterface {
 		if(this->stream->open()){
 			return false;
 		}
+
 		return true;
 	}
 
@@ -38,19 +39,22 @@ class TomahawkOutputWriterInterface {
 		if(this->stream->open(output)){
 			return false;
 		}
+
 		return true;
 	}
 
 	virtual inline void flush(void){ this->stream->flush(); }
 	virtual inline bool close(void){ this->stream->close(); return true; }
 	virtual void operator<<(const entry_type* const entryentry) =0;
-	virtual void write(const entry_type* const entry, const void* support) =0;
 	inline void write(const char* data, const U32 length){ this->stream->write(&data[0], length); }
 
 	template<class T> void write(const T& data){
 		*reinterpret_cast<std::ofstream*>(&this->stream->getStream()) << data;
 	}
 
+	virtual void writeHeader(void) =0;
+	virtual void writeEOF(void) =0;
+
 protected:
 	std::string outFile;
 	stream_type* stream;
@@ -74,15 +78,14 @@ class TomahawkOutputWriter : public TomahawkOutputWriterInterface {
 	~TomahawkOutputWriter(){
 		// Flush upon termination
 		this->flush();
+		this->writeEOF();
 		this->close();
 		this->buffer.deleteAll();
 	}
 
 	inline void flush(void){ this->stream->flush(); }
 	inline bool close(void){ this->stream->close(); return true; }
 
-	void write(const entry_type* const entry, const void* support){}
-
 	void operator<<(const entry_type* const entry){
 		this->buffer.Add(reinterpret_cast<const char*>(entry), sizeof(entry_type));
 		if(this->buffer.size() > this->flush_limit){
@@ -93,6 +96,9 @@ class TomahawkOutputWriter : public TomahawkOutputWriterInterface {
 		}
 	}
 
+	void writeHeader(void){	};
+	void writeEOF(void){};
+
 private:
 	U32 flush_limit;
 	buffer_type buffer;
@@ -102,24 +108,30 @@ class TomahawkOutputWriter : public TomahawkOutputWriterInterface {
 // case binary
 class TomahawkOutputWriterNatural : public TomahawkOutputWriterInterface {
 	typedef TomahawkOutputWriterNatural self_type;
+	typedef Totempole::TotempoleContigBase contig_type;
 
 public:
-	TomahawkOutputWriterNatural(){}
+	TomahawkOutputWriterNatural() : contigs(nullptr){}
 	~TomahawkOutputWriterNatural(){
 		// Flush upon termination
 		this->flush();
+		this->writeEOF();
 		this->close();
 	}
 
-	void write(const entry_type* const entry, const void* support){
-		*reinterpret_cast<std::ofstream*>(&this->stream->getStream()) << *entry;
-		this->stream->getStream() << '\n';
-	}
-
 	void operator<<(const entry_type* const entry){
-		*reinterpret_cast<std::ofstream*>(&this->stream->getStream()) << *entry;
-		this->stream->getStream() << '\n';
+		entry->write(*reinterpret_cast<std::ofstream*>(&this->stream->getStream()), this->contigs);
 	}
+
+	void setContigs(const contig_type* const contigs){ this->contigs = contigs; }
+	void writeHeader(void){
+		const std::string header = "FLAG\tAcontigID\tAposition\tBcontigID\tBpositionID\tp1\tp2\tq1\tq2\tD\tDprime\tR2\tP\tchiSqFisher\tchiSqModel\n";
+		this->stream->getStream() << header;
+	};
+	void writeEOF(void){};
+
+private:
+	const contig_type* contigs;
 };
 
 }