// ***************************************************************************
// SamHeaderValidator.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 13 January 2011 (DB)
// ---------------------------------------------------------------------------
// Provides functionality for validating SamHeader data
// ***************************************************************************

#ifndef SAM_HEADER_VALIDATOR_P_H
#define SAM_HEADER_VALIDATOR_P_H

//  -------------
//  W A R N I N G
//  -------------
//
// This file is not part of the BamTools API.  It exists purely as an
// implementation detail. This header file may change from version to version
// without notice, or even be removed.
//
// We mean it.

#include <string>
#include <vector>

namespace BamTools {

class SamHeader;
class SamReadGroup;
class SamSequence;

namespace Internal {

class SamHeaderValidator {

    // ctor & dtor
    public:
        SamHeaderValidator(const SamHeader& header);
        ~SamHeaderValidator(void);

    // SamHeaderValidator interface
    public:
        // validates SamHeader data, returns true/false accordingly
        // prints error & warning messages to stderr when @verbose is true
        bool Validate(bool verbose = false);

    // internal methods
    private:

        // validate header metadata
        bool ValidateMetadata(void);
        bool ValidateVersion(void);
        bool ContainsOnlyDigits(const std::string& s);
        bool ValidateSortOrder(void);
        bool ValidateGroupOrder(void);

        // validate sequence dictionary
        bool ValidateSequenceDictionary(void);
        bool ContainsUniqueSequenceNames(void);
        bool CheckNameFormat(const std::string& name);
        bool ValidateSequence(const SamSequence& seq);
        bool CheckLengthInRange(const std::string& length);

        // validate read group dictionary
        bool ValidateReadGroupDictionary(void);
        bool ContainsUniqueIDsAndPlatformUnits(void);
        bool ValidateReadGroup(const SamReadGroup& rg);
        bool CheckReadGroupID(const std::string& id);
        bool CheckSequencingTechnology(const std::string& technology);

        // validate program data
        bool ValidateProgramChain(void);
        bool ContainsUniqueProgramIds(void);
        bool ValidatePreviousProgramIds(void);

        // error reporting
        void AddError(const std::string& message);
        void AddWarning(const std::string& message);
        void PrintErrorMessages(void);
        void PrintWarningMessages(void);

    // data members
    private:

        // SamHeader being validated
        const SamHeader& m_header;

        // error reporting helpers
        static const std::string ERROR_PREFIX;
        static const std::string WARN_PREFIX;
        static const std::string NEWLINE;

        // error reporting messages
        std::vector<std::string> m_errorMessages;
        std::vector<std::string> m_warningMessages;
};

} // namespace Internal
} // namespace BamTools

#endif // SAM_HEADER_VALIDATOR_P_H