/**
 ** Copyright (c) Solexa 2005, 2006
 ** Copyright (c) 2007-2010 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 include/common/Tiling.h
 **
 ** \brief Tiling structure and runfolder names for a data analysis run
 **
 ** Set the tiling structure and runfolder names for a data analysis run.
 ** This object is used to generate suitable filenames for output files,
 ** according to the run-folder specification. Internally, the image
 ** analysis does not need to know about these conventions; tiles (positions
 ** on the chip) are simply numbered sequentially.
 **
 ** \author Klaus Maisinger
 **/

#ifndef _TILING_H_
#define _TILING_H_

#include <string>
#include <map>


class RunFolderFileName {
    std::string path;
    int *channelidx, *channelcount, nchannel, tileoffset;
public:
    typedef enum {
        POSITION_FILE,
        INDEX_FILE,
        INTENSITY_FILE,
        NOISE_FILE,
        HEADER_FILE,
        OFFSET_FILE,
        CLUSTER_FILE,
        QC_FILE,
        SIGNAL_FILE,
        Q_SEQUENCE_FILE,
        SEQUENCE_FILE,
        PROBABILITY_FILE,
        SIGNAL2_FILE,
        SCORE_FILE,
        RESCORE_FILE
    } filename_type;
private:
    std::map<filename_type,std::string> typestring; 

public:
    RunFolderFileName(const char prefix[]);
    ~RunFolderFileName();
    void setLanes(const int *laneIndex, 
                  const int *laneNumTiles,
                  const int  numLanes); 
    void setLane(const int lane,
                 const int tileIndex,
                 const int numTiles = 1);
    std::string getIndexFilename(const filename_type type,
                                 const int idx = 0,
                                 const int cycle = -1,
                                 const int channel = -1) const;
    std::string getTileFilename(const filename_type type,
                                const int lane,
                                const int tile, 
                                const int cycle = -1,
                                const int channel = -1) const;
    // Possibly temporary method pending file distinction by subdirectory.
    std::string getQualifiedTileFilename(const filename_type type,
                                         const std::string& qualifier_str,
                                         const int lane,
                                         const int tile) const;
    int getLane(const int idx) const;
    int getTile(const int idx) const;
    int getIndex(const int lane,
                 const int tile) const;
    std::string getFilePrefix() const;
};

#endif // _TILING_H_