Package adams.db

Class SpectrumF

  • All Implemented Interfaces:
    adams.core.logging.LoggingSupporter, adams.core.SizeOfHandler, adams.db.DatabaseConnectionProvider, adams.db.DatabaseConnectionUser, adams.db.DataProvider<Spectrum>, SpectrumIntf, adams.db.TableInterface, Serializable
    public class SpectrumF
extends adams.db.AbstractTableFacade
implements SpectrumIntf
    Facade for spectrum tables.
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected SpectrumIntf m_DB
      the backend.
      protected static adams.db.FacadeManager<SpectrumF> m_TableManager
      the facade manager.

      • Fields inherited from class adams.db.AbstractTableFacade

        m_DatabaseConnection, m_Debug, m_TableName

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Constructor Summary

      Constructors 
      Constructor Description
      SpectrumF​(adams.db.AbstractDatabaseConnection dbcon, String tableName)
      Constructor.

    • Field Detail

      • m_TableManager

        protected static adams.db.FacadeManager<SpectrumF> m_TableManager
        the facade manager.

    • Constructor Detail

      • SpectrumF

        public SpectrumF​(adams.db.AbstractDatabaseConnection dbcon,
                 String tableName)
        Constructor.
        Parameters:
        dbcon - the database context to use
        tableName - the name of the table

    • Method Detail

      • init

        public boolean init()
        Initialise table & sub-tables.
        Specified by:
        init in interface SpectrumIntf
        Returns:
        success?

      • exists

        public boolean exists​(int id)
        Checks whether the container exists in the database.
        Specified by:
        exists in interface adams.db.DataProvider<Spectrum>
        Specified by:
        exists in interface SpectrumIntf
        Parameters:
        id - the database ID of the data container
        Returns:
        true if the container exists

      • exists

        public boolean exists​(String id,
                      String format)
        Checks whether the container exists in the database.
        Specified by:
        exists in interface SpectrumIntf
        Parameters:
        id - the ID of the data container
        Returns:
        true if the container exists

      • load

        public Spectrum load​(int auto_id)
        Load a spectrum with given database ID. Get from cache if available
        Specified by:
        load in interface adams.db.DataProvider<Spectrum>
        Specified by:
        load in interface SpectrumIntf
        Parameters:
        auto_id - the database ID
        Returns:
        Spectrum, or null if not found

      • load

        public Spectrum load​(String sample_id,
                     String format)
        Load a spectrum with given sample ID and type. Get from cache if available
        Specified by:
        load in interface SpectrumIntf
        Parameters:
        sample_id - the sample ID
        format - the format
        Returns:
        Spectrum, or null if not found

      • loadRaw

        public Spectrum loadRaw​(int auto_id)
        Load a data container with given auto_id, without passing it through the global filter.
        Specified by:
        loadRaw in interface SpectrumIntf
        Parameters:
        auto_id - the databae ID
        Returns:
        the data container, or null if not found

      • loadRaw

        public Spectrum loadRaw​(String sample_id,
                        String format)
        Load a spectrum with given sample ID and type, without filtering through the global container filter.
        Specified by:
        loadRaw in interface SpectrumIntf
        Parameters:
        sample_id - the sample ID
        format - the format
        Returns:
        Spectrum, or null if not found

      • loadFromDB

        public Spectrum loadFromDB​(int auto_id,
                           String rlike,
                           boolean raw)
        Load a spectrum from DB with given auto_id.
        Specified by:
        loadFromDB in interface SpectrumIntf
        Parameters:
        auto_id - the databae ID
        rlike - regex for chrom name
        raw - whether to return the raw spectrum or filter it through the global container filter
        Returns:
        Spectrum, or null if not found

      • loadFromDB

        public Spectrum loadFromDB​(String sample_id,
                           String format,
                           boolean raw)
        Load a spectrum from DB with given sample_id and format.
        Specified by:
        loadFromDB in interface SpectrumIntf
        Parameters:
        sample_id - the sample ID
        format - the format
        raw - whether to return the raw spectrum or filter it through the global container filter
        Returns:
        Spectrum, or null if not found

      • getDatabaseID

        public int getDatabaseID​(String sample_id,
                         String format)
        Returns the database ID for given sample ID and type. Get from cache if available
        Specified by:
        getDatabaseID in interface SpectrumIntf
        Parameters:
        sample_id - the sample ID
        format - the format
        Returns:
        the database ID, Constants.NO_ID

      • getValues

        public List<String> getValues​(String[] fields,
                              SpectrumIDConditions cond)
        returns all the specified fields in the database, separated by TABs.
        Specified by:
        getValues in interface SpectrumIntf
        Parameters:
        fields - the field names
        cond - the conditions for the retrieval
        Returns:
        list of tab-separated values

      • getValues

        public List<String> getValues​(String[] fields,
                              String where,
                              SpectrumIDConditions cond)
        returns all the specified fields in the database, separated by TABs.
        Specified by:
        getValues in interface SpectrumIntf
        Parameters:
        fields - the field names
        where - the where clause, can be null
        cond - the conditions for the retrieval
        Returns:
        list of tab-separated values

      • getValues

        public List<String> getValues​(String[] fields,
                              String tables,
                              String where,
                              SpectrumIDConditions cond)
        returns all the specified fields in the database, separated by TABs.
        Specified by:
        getValues in interface SpectrumIntf
        Parameters:
        fields - the field names
        tables - the involved tables
        where - the where clause, can be null
        cond - the conditions for the retrieval
        Returns:
        list of tab-separated values

      • add

        public Integer add​(Spectrum sp)
        Adds a spectrum to the database. Returns the created auto-id, and sets in Spectrum. Wave numbers get stored.
        Specified by:
        add in interface adams.db.DataProvider<Spectrum>
        Specified by:
        add in interface SpectrumIntf
        Parameters:
        sp - spectrum Header
        Returns:
        new ID, or null if fail

      • add

        public Integer add​(Spectrum sp,
                   boolean storeWaveNo)
        Adds a spectrum to the database. Returns the created auto-id, and sets in Spectrum.
        Specified by:
        add in interface SpectrumIntf
        Parameters:
        sp - spectrum Header
        storeWaveNo - whether to store the wave numbers as well
        Returns:
        new ID, or null if fail

      • bulkAdd

        public boolean bulkAdd​(Spectrum[] sp,
                       boolean storeWaveNo,
                       int batchSize,
                       boolean autoCommit,
                       boolean newConnection)
        Stores the spectra in the database.
        Specified by:
        bulkAdd in interface SpectrumIntf
        Parameters:
        sp - the spectra to add
        storeWaveNo - whether to store the wave numbers as well
        batchSize - the maximum number of records in one batch
        autoCommit - whether to use auto-commit or not (turning off may impact other transactions!)
        newConnection - uses a separate database connection just for this connection (then no auto-commit doesn't affect the rest)
        Returns:
        true if successfully inserted/updated

      • stopBulkAdd

        public void stopBulkAdd()
        Interrupts a currently running bulk store, if possible.
        Specified by:
        stopBulkAdd in interface SpectrumIntf

      • remove

        public boolean remove​(String sample_id,
                      String format,
                      boolean keepReport)
        Removes the spectrum and its sample data.
        Specified by:
        remove in interface SpectrumIntf
        Parameters:
        sample_id - the sample ID of the spectrum
        format - the format of the spectrum (eg NIR)
        keepReport - if true does not delete associated report
        Returns:
        true if no error

      • remove

        public boolean remove​(int id,
                      boolean keepReport)
        Removes the spectrum and its sample data.
        Specified by:
        remove in interface adams.db.DataProvider<Spectrum>
        Specified by:
        remove in interface SpectrumIntf
        Parameters:
        id - the ID of the spectrum to remove from the database
        keepReport - if true does not delete associated report
        Returns:
        true if no error

      • getSingleton

        public static SpectrumF getSingleton​(adams.db.AbstractDatabaseConnection dbcon)
        Returns the singleton of the facade.
        Parameters:
        dbcon - the database connection to get the singleton for
        Returns:
        the singleton