/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 ** \file SignalMeansTile.hh
 **
 ** \brief I/O API for signal means files (_all files).
 **
 ** \author Mauricio Varea
 **/

#ifndef CASAVA_COMMON_SIGNAL_MEANS_TILE_HH
#define CASAVA_COMMON_SIGNAL_MEANS_TILE_HH

#include <iostream>
#include <string>
#include <vector>
#include <list>

#include "common/SignalMeans.hh"

namespace casava
{
namespace common
{

class SignalMeansTile
{
public:
    // use this one to read from file:
    SignalMeansTile();
    // use either of these one to populate directly:
    SignalMeansTile(const SignalMeansTile &ref);
    SignalMeansTile(const unsigned int numberOfCycles);

    SignalMeansTile &operator=(const SignalMeansTile &ref);
    unsigned int getNumFilteredClusters() {return passFilter_.first;}
    unsigned int getNumOriginalClusters() {return passFilter_.second;}
    void setNumFilteredClusters(const unsigned int &n) {passFilter_.first = n;}
    void setNumOriginalClusters(const unsigned int &n) {passFilter_.second = n;}
    void incNumFilteredClusters() {passFilter_.first++;}
    void incNumOriginalClusters() {passFilter_.second++;}
    unsigned int getNumberOfCycles() {return baseCalls_.size();}

    void clear(const std::list<unsigned int> &remove);
    void readHeader(std::istream &is);
    unsigned int read(std::istream &is);
    void writeHeader(std::ostream &os);
    unsigned int write(std::ostream &os);
    void incrementallyPopulate(std::string seq);
    // a SignalMeansTile is valid when baseCalls_[i] contains cycle i+1 (and there are no gaps)
    bool isValid();
    void makeValid();
private:
    // first -> Filtered, second -> Original.  (PF == 0  is  second - first)
    std::pair<unsigned int, unsigned int> passFilter_;
    std::vector<SignalMeans> baseCalls_;
};




} // namespace common
} // namespace casava

#endif // #ifndef CASAVA_COMMON_SIGNAL_MEANS_TILE_HH