Package adams.data.spreadsheetrowgenerator

Class AbstractSpreadSheetRowGenerator

  • All Implemented Interfaces:
    adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<AbstractSpreadSheetRowGenerator>, adams.core.SizeOfHandler, Serializable, Comparable
    Direct Known Subclasses:
    SampleDataOnlyRowGenerator, SimpleRowGenerator
    public abstract class AbstractSpreadSheetRowGenerator
extends adams.core.option.AbstractOptionHandler
implements Comparable, adams.core.CleanUpHandler, adams.core.ShallowCopySupporter<AbstractSpreadSheetRowGenerator>
    Abstract base class for schemes that turn spectra into spreadsheet row objects.
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String COL_DBID  
      static String COL_SAMPLEID  
      protected boolean m_AddDatabaseID
      whether to add the database ID.
      protected boolean m_AddSampleID
      whether to add the sample ID.
      protected adams.data.spreadsheet.SpreadSheet m_OutputHeader
      the generated header.
      protected boolean m_TolerateHeaderChanges
      whether to tolerate header changes.

      • Fields inherited from class adams.core.option.AbstractOptionHandler

        m_OptionManager

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

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      String addDatabaseIDTipText()
      Returns the tip text for this property.
      String addSampleIDTipText()
      Returns the tip text for this property.
      protected abstract void checkHeader​(Spectrum data)
      Checks whether the number of waves are the same.
      protected void checkInput​(Spectrum data)
      Checks the input spectrum.
      String checkSetup()
      Checks whether the setup is consistent.
      void cleanUp()
      Cleans up data structures, frees up memory.
      int compareTo​(Object o)
      Compares this object with the specified object for order.
      void defineOptions()
      Adds options to the internal list of options.
      void destroy()
      Frees up memory in a "destructive" non-reversible way.
      boolean equals​(Object o)
      Returns whether the two objects are the same.
      adams.data.spreadsheet.Row generate​(Spectrum data)
      Returns the generated data, generates it if necessary.
      protected abstract void generateHeader​(Spectrum data)
      Generates the header of the output data.
      protected abstract adams.data.spreadsheet.Row generateOutput​(Spectrum data)
      Generates the actual data.
      boolean getAddDatabaseID()
      Returns whether the database ID is added.
      boolean getAddSampleID()
      Returns whether the sample ID is added.
      adams.data.spreadsheet.SpreadSheet getOutputHeader()
      Returns the current header.
      boolean getTolerateHeaderChanges()
      Returns whether to tolerate header changes and merely re-generating the header instead of throwing an exception.
      protected String interpretePosition​(adams.data.spreadsheet.SpreadSheet data, String position)
      Interpretes the position string based on the given dataset.
      protected void postProcessHeader​(Spectrum data)
      Adds IDs, notes, additional fields to header.
      protected adams.data.spreadsheet.Row postProcessOutput​(Spectrum data, adams.data.spreadsheet.Row row)
      For adding IDs, notes, additional fields to the data.
      protected void reset()
      Resets the generator (but does not clear the input data!).
      void setAddDatabaseID​(boolean value)
      Sets whether the database ID is added to the data or not.
      void setAddSampleID​(boolean value)
      Sets whether the sample ID is added to the data or not.
      void setTolerateHeaderChanges​(boolean value)
      Sets whether to tolerate header changes and merely re-generating the header instead of throwing an exception.
      AbstractSpreadSheetRowGenerator shallowCopy()
      Returns a shallow copy of itself, i.e., based on the commandline options.
      AbstractSpreadSheetRowGenerator shallowCopy​(boolean expand)
      Returns a shallow copy of itself, i.e., based on the commandline options.
      String tolerateHeaderChangesTipText()
      Returns the tip text for this property.

      • Methods inherited from class adams.core.option.AbstractOptionHandler

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, globalInfo, initialize, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

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

        configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel

    • Field Detail

      • m_OutputHeader

        protected adams.data.spreadsheet.SpreadSheet m_OutputHeader
        the generated header.

      • m_AddDatabaseID

        protected boolean m_AddDatabaseID
        whether to add the database ID.

      • m_AddSampleID

        protected boolean m_AddSampleID
        whether to add the sample ID.

      • m_TolerateHeaderChanges

        protected boolean m_TolerateHeaderChanges
        whether to tolerate header changes.

    • Constructor Detail

      • AbstractSpreadSheetRowGenerator

        public AbstractSpreadSheetRowGenerator()

    • Method Detail

      • defineOptions

        public void defineOptions()
        Adds options to the internal list of options.
        Specified by:
        defineOptions in interface adams.core.option.OptionHandler
        Overrides:
        defineOptions in class adams.core.option.AbstractOptionHandler

      • reset

        protected void reset()
        Resets the generator (but does not clear the input data!). Derived classes must call this method in set-methods of parameters to assure the invalidation of previously generated data.
        Overrides:
        reset in class adams.core.option.AbstractOptionHandler

      • cleanUp

        public void cleanUp()
        Cleans up data structures, frees up memory. Sets the input data to null.
        Specified by:
        cleanUp in interface adams.core.CleanUpHandler

      • destroy

        public void destroy()
        Frees up memory in a "destructive" non-reversible way.

        Calls cleanUp() and cleans up the options.
        Specified by:
        destroy in interface adams.core.Destroyable
        Overrides:
        destroy in class adams.core.option.AbstractOptionHandler

      • setAddDatabaseID

        public void setAddDatabaseID​(boolean value)
        Sets whether the database ID is added to the data or not.
        Parameters:
        value - true if database ID should be added

      • getAddDatabaseID

        public boolean getAddDatabaseID()
        Returns whether the database ID is added.
        Returns:
        true if database ID is added

      • addDatabaseIDTipText

        public String addDatabaseIDTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setAddSampleID

        public void setAddSampleID​(boolean value)
        Sets whether the sample ID is added to the data or not.
        Parameters:
        value - true if sample ID should be added

      • getAddSampleID

        public boolean getAddSampleID()
        Returns whether the sample ID is added.
        Returns:
        true if sample ID is added

      • addSampleIDTipText

        public String addSampleIDTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setTolerateHeaderChanges

        public void setTolerateHeaderChanges​(boolean value)
        Sets whether to tolerate header changes and merely re-generating the header instead of throwing an exception.
        Parameters:
        value - true if to tolerate header changes

      • getTolerateHeaderChanges

        public boolean getTolerateHeaderChanges()
        Returns whether to tolerate header changes and merely re-generating the header instead of throwing an exception.
        Returns:
        true if to tolerate header changes

      • tolerateHeaderChangesTipText

        public String tolerateHeaderChangesTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getOutputHeader

        public adams.data.spreadsheet.SpreadSheet getOutputHeader()
        Returns the current header.
        Returns:
        the header, can be null

      • checkSetup

        public String checkSetup()
        Checks whether the setup is consistent.

        Default implementation does nothing.
        Returns:
        null if everything OK, otherwise the error message

      • generate

        public adams.data.spreadsheet.Row generate​(Spectrum data)
        Returns the generated data, generates it if necessary.
        Parameters:
        data - the spectrum to turn into a row
        Returns:
        the generated data

      • checkInput

        protected void checkInput​(Spectrum data)
        Checks the input spectrum.

        The default implementation only checks whether there is any data set.
        Parameters:
        data - the data to process

      • checkHeader

        protected abstract void checkHeader​(Spectrum data)
        Checks whether the number of waves are the same.
        Parameters:
        data - the input data

      • generateHeader

        protected abstract void generateHeader​(Spectrum data)
        Generates the header of the output data.
        Parameters:
        data - the input data

      • interpretePosition

        protected String interpretePosition​(adams.data.spreadsheet.SpreadSheet data,
                                    String position)
        Interpretes the position string based on the given dataset. "first", "second", "third", "last-2", "last-1" and "last" and "last+1" are valid as well.
        Parameters:
        data - the data to base the intepretation on
        position - the position string
        Returns:
        the numeric position string

      • postProcessHeader

        protected void postProcessHeader​(Spectrum data)
        Adds IDs, notes, additional fields to header.
        Parameters:
        data - the input data

      • generateOutput

        protected abstract adams.data.spreadsheet.Row generateOutput​(Spectrum data)
        Generates the actual data.
        Parameters:
        data - the input data to transform
        Returns:
        the generated data

      • postProcessOutput

        protected adams.data.spreadsheet.Row postProcessOutput​(Spectrum data,
                                                       adams.data.spreadsheet.Row row)
        For adding IDs, notes, additional fields to the data.
        Parameters:
        data - the input data
        row - the generated row
        Returns:
        the processed row

      • compareTo

        public int compareTo​(Object o)
        Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

        Only compares the commandlines of the two objects.
        Specified by:
        compareTo in interface Comparable
        Parameters:
        o - the object to be compared.
        Returns:
        a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.
        Throws:
        ClassCastException - if the specified object's type prevents it from being compared to this object.

      • equals

        public boolean equals​(Object o)
        Returns whether the two objects are the same.

        Only compares the commandlines of the two objects.
        Overrides:
        equals in class Object
        Parameters:
        o - the object to be compared
        Returns:
        true if the object is the same as this one

      • shallowCopy

        public AbstractSpreadSheetRowGenerator shallowCopy​(boolean expand)
        Returns a shallow copy of itself, i.e., based on the commandline options.
        Specified by:
        shallowCopy in interface adams.core.ShallowCopySupporter<AbstractSpreadSheetRowGenerator>
        Parameters:
        expand - whether to expand variables to their current values
        Returns:
        the shallow copy