ms_databaseoptions.hpp

/*
##############################################################################
# file: ms_databaseoptions.hpp                                               #
# 'msparser' toolkit                                                         #
# Encapsulates "mascot.dat"-file that describes most important parameters    #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2003 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Archive:: /Mowse/ms_mascotresfile/include/ms_databaseoptions.hpp     $ #
#     $Author: villek@matrixscience.com $ #
#       $Date: 2018-07-30 16:23:53 +0100 $ #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/
 
#ifndef MS_DATABASEOPTIONS_HPP
#define MS_DATABASEOPTIONS_HPP
 
 
#include <string>
#include <vector>
 
 
namespace matrix_science {
    enum DATABASE_TYPE
    {
        AA=0, 
        NA=1, 
        SL=2, 
        SLREF=3, 
    };
 
 
    class MS_MASCOTRESFILE_API ms_databaseoptions
    {
        friend class ms_datfile;
        friend class ms_databases;
 
    public:
 
        enum {
            NUM_THREADS_AUTO_DETECT = -1 
        };
 
 
        ms_databaseoptions();
 
        ms_databaseoptions(const ms_databaseoptions& src);
 
        ~ms_databaseoptions();
 
        void defaultValues();
 
        void copyFrom(const ms_databaseoptions* right);
 
#ifndef SWIG
        ms_databaseoptions& operator=(const ms_databaseoptions& right);
#endif
        bool isActive() const;
 
        void setActive(const bool value);
 
        std::string getName() const;
 
        void setName(const char* name);
 
        std::string getPath() const;
 
        void setPath(const char* path);
 
        int getDBType() const;
 
        void setDBType(const int type);
 
        bool isMemoryMapFiles() const;
 
        void setMemoryMapFiles(const bool flag);
 
        int getNumberOfThreads() const;
 
        void setNumberOfThreads(const int number);
 
        bool isLockMemory() const;
 
        void setLockMemory(const bool flag);
 
        bool isLocalRefFile() const;
 
        void setLocalRefFile(const bool flag);
 
        int getAccessionParseRuleIndex() const;
 
        void setAccessionParseRuleIndex(const int index);
 
        int getDescriptionParseRuleIndex() const;
 
        void setDescriptionParseRuleIndex(const int index);
 
        int getAccessionRefParseRuleIndex() const;
 
        void setAccessionRefParseRuleIndex(const int index);
 
        int getTaxonomyParseRuleIndex() const;
 
        void setTaxonomyParseRuleIndex(const int index);
 
        bool isBlastIndexFiles() const;
 
        void setBlastIndexFiles(const bool flag);
 
        void setPreceedingComments(const std::string &str);
 
        const std::string& getPreceedingComments() const;
 
    private:
        std::string getStringValue() const;
 
        bool        active_;
        std::string name_;
        std::string path_;
        int         type_;
        int         __numEntries_;  // no longer used
        int         __uniqueID_;    // no longer used
        bool        mmapFiles_;
        bool        __useBlastIndexFiles_;    // no longer used - was also blocks
        int         numThreads_;
        bool        lockMemory_;
        bool        hasRefFile_;
        int         accessionParseRule_;
        int         descriptionParseRule_;
        int         accessionRefParseRule_;
        int         taxonomyParseRule_;
        std::string comment_;
    }; // class ms_databaseoptions
 
 
    class MS_MASCOTRESFILE_API ms_databases: public ms_customproperty
    {
        friend class ms_datfile;
    public:
        ms_databases();
 
        ms_databases(const ms_databases& src);
 
        ~ms_databases();
 
        void defaultValues();
 
        void copyFrom(const ms_databases* right);
 
#ifndef SWIG
        ms_databases& operator=(const ms_databases& right);
#endif
        bool isSectionAvailable() const;
 
        void setSectionAvailable(const bool value);
 
        int getNumberOfDatabases() const;
 
        const ms_databaseoptions* getDatabase(const int index) const;
 
        void clearDatabases();
 
        void appendDatabase(const ms_databaseoptions* item);
 
        int findDatabase(const char* dbName, const bool searchInactive = false) const;
 
        bool updateDatabaseByNumber(const int num, const ms_databaseoptions db);
 
        bool updateDatabaseByName(const char* name, const ms_databaseoptions db);
 
        bool deleteDatabaseByNumber(const int num);
 
        bool deleteDatabaseByName(const char* name);
 
#ifdef SUPPRESS_MS_CUSTOMPROPERTY_INHERITANCE
#include "suppress_ms_customproperty.hpp"
#endif
 
    private:
        void appendDatabase(const ms_databaseoptions* item, const char *propVal);
        void setFollowingComments(const std::string &str);
        const std::string& getFollowingComments() const;
 
        bool sectionAvailable_;
        std::vector< ms_databaseoptions* > dbases_;
        std::string followingComments_;
    }; // class ms_databases // end of config_group
} // namespace matrix_science
 
#endif // MS_DATABASEOPTIONS_HPP
 
/*------------------------------- End of File -------------------------------*/