Package adams.data.io.input

Class MultiColumnSpreadSheetSampleDataReader

  • All Implemented Interfaces:
    adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.io.FileFormatHandler, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<adams.data.io.input.AbstractReportReader>, adams.core.SizeOfHandler, adams.core.Stoppable, adams.core.StoppableWithFeedback, adams.data.io.input.ReportReader<SampleData>, SampleDataReader, adams.db.DatabaseConnectionHandler, adams.db.DatabaseConnectionProvider, adams.db.DatabaseConnectionUser, Serializable, Comparable
    public class MultiColumnSpreadSheetSampleDataReader
extends AbstractSampleDataReader
    Reads sample data from a spreadsheet (format depends on reader), reference values stored in the specified range of columns and the column headers representing the reference value names. 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
    min-user-mode: Expert
 
    -input <adams.core.io.PlaceholderFile> (property: input)
    The file to read and turn into a report.
    default: ${CWD}
 
    -offline <boolean> (property: offline)
    If set to true, the database won't get queried, e.g., for obtaining the
    parent ID.
    default: false
 
    -format <java.lang.String> (property: format)
    The type of spectrum to use (used internally to determine the database ID
    of the spectrum).
    default: NIR
 
    -reader <adams.data.io.input.SpreadSheetReader> (property: reader)
    The spreadsheet reader to use.
    default: adams.data.io.input.CsvSpreadSheetReader -data-row-type adams.data.spreadsheet.DenseDataRow -spreadsheet-type adams.data.spreadsheet.DefaultSpreadSheet
 
    -col-id <adams.data.spreadsheet.SpreadSheetColumnIndex> (property: columnSampleID)
    The column containing the sample ID.
    default: ID
    example: An index is a number starting with 1; column names (case-sensitive) as well as the following placeholders can be used: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); column names can be surrounded by double quotes.
 
    -cols-sampledata <adams.data.spreadsheet.SpreadSheetColumnRange> (property: columnsSampleData)
    The columns with the reference values; header represents the reference name.
    default:
    example: A range is a comma-separated list of single 1-based indices or sub-ranges of indices ('start-end'); 'inv(...)' inverts the range '...'; column names (case-sensitive) as well as the following placeholders can be used: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); column names can be surrounded by double quotes.
 
    -cols-numeric <adams.data.spreadsheet.SpreadSheetColumnRange> (property: columnsNumeric)
    The columns with numeric reference values.
    default:
    example: A range is a comma-separated list of single 1-based indices or sub-ranges of indices ('start-end'); 'inv(...)' inverts the range '...'; column names (case-sensitive) as well as the following placeholders can be used: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); column names can be surrounded by double quotes.
 
    -cols-bool <adams.data.spreadsheet.SpreadSheetColumnRange> (property: columnsBoolean)
    The columns with boolean reference values.
    default:
    example: A range is a comma-separated list of single 1-based indices or sub-ranges of indices ('start-end'); 'inv(...)' inverts the range '...'; column names (case-sensitive) as well as the following placeholders can be used: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); column names can be surrounded by double quotes.
 
    -row-finder <adams.data.spreadsheet.rowfinder.RowFinder> (property: rowFinder)
    The row finder to use for locating the rows to import.
    default: adams.data.spreadsheet.rowfinder.AllFinder
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected adams.data.spreadsheet.SpreadSheetColumnIndex m_ColumnSampleID
      the column name to get the sample ID from.
      protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsBoolean
      the range of columns with boolean sample data.
      protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsNumeric
      the range of columns with numeric sample data.
      protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsSampleData
      the range of columns with the sample data.
      protected adams.data.io.input.SpreadSheetReader m_Reader
      the spreadsheet reader.
      protected adams.data.spreadsheet.rowfinder.RowFinder m_RowFinder
      for locating the rows to import.

      • Fields inherited from class adams.data.io.input.AbstractReportReader

        m_Input, m_Stopped

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

        m_OptionManager

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

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Field Detail

      • m_Reader

        protected adams.data.io.input.SpreadSheetReader m_Reader
        the spreadsheet reader.

      • m_ColumnSampleID

        protected adams.data.spreadsheet.SpreadSheetColumnIndex m_ColumnSampleID
        the column name to get the sample ID from.

      • m_ColumnsSampleData

        protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsSampleData
        the range of columns with the sample data.

      • m_ColumnsNumeric

        protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsNumeric
        the range of columns with numeric sample data.

      • m_ColumnsBoolean

        protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsBoolean
        the range of columns with boolean sample data.

      • m_RowFinder

        protected adams.data.spreadsheet.rowfinder.RowFinder m_RowFinder
        for locating the rows to import.

    • Constructor Detail

      • MultiColumnSpreadSheetSampleDataReader

        public MultiColumnSpreadSheetSampleDataReader()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        Returns:
        a description suitable for displaying in the gui

      • 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 AbstractSampleDataReader

      • getFormatDescription

        public String getFormatDescription()
        Returns a string describing the format (used in the file chooser).
        Specified by:
        getFormatDescription in interface adams.core.io.FileFormatHandler
        Specified by:
        getFormatDescription in class adams.data.io.input.AbstractReportReader<SampleData>
        Returns:
        a description suitable for displaying in the file chooser

      • getFormatExtensions

        public String[] getFormatExtensions()
        Returns the extension(s) of the format.
        Specified by:
        getFormatExtensions in interface adams.core.io.FileFormatHandler
        Specified by:
        getFormatExtensions in class adams.data.io.input.AbstractReportReader<SampleData>
        Returns:
        the extension(s) (without the dot!)

      • setReader

        public void setReader​(adams.data.io.input.SpreadSheetReader value)
        Sets the spreadsheet reader to use.
        Parameters:
        value - the reader

      • getReader

        public adams.data.io.input.SpreadSheetReader getReader()
        Returns the spreadsheet reader in use.
        Returns:
        the reader

      • readerTipText

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

      • setColumnSampleID

        public void setColumnSampleID​(adams.data.spreadsheet.SpreadSheetColumnIndex value)
        Sets the column with the sample ID.
        Parameters:
        value - the column

      • getColumnSampleID

        public adams.data.spreadsheet.SpreadSheetColumnIndex getColumnSampleID()
        Returns the column with the sample ID.
        Returns:
        the column

      • columnSampleIDTipText

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

      • setColumnsSampleData

        public void setColumnsSampleData​(adams.data.spreadsheet.SpreadSheetColumnRange value)
        Sets the range of columns with the reference values.
        Parameters:
        value - the columns

      • getColumnsSampleData

        public adams.data.spreadsheet.SpreadSheetColumnRange getColumnsSampleData()
        Returns the columns with the reference values.
        Returns:
        the columns

      • columnsSampleDataTipText

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

      • setColumnsNumeric

        public void setColumnsNumeric​(adams.data.spreadsheet.SpreadSheetColumnRange value)
        Sets the range of columns with numeric reference values.
        Parameters:
        value - the columns

      • getColumnsNumeric

        public adams.data.spreadsheet.SpreadSheetColumnRange getColumnsNumeric()
        Returns the columns with numeric reference values.
        Returns:
        the columns

      • columnsNumericTipText

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

      • setColumnsBoolean

        public void setColumnsBoolean​(adams.data.spreadsheet.SpreadSheetColumnRange value)
        Sets the range of columns with boolean reference values.
        Parameters:
        value - the columns

      • getColumnsBoolean

        public adams.data.spreadsheet.SpreadSheetColumnRange getColumnsBoolean()
        Returns the columns with boolean reference values.
        Returns:
        the columns

      • columnsBooleanTipText

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

      • setRowFinder

        public void setRowFinder​(adams.data.spreadsheet.rowfinder.RowFinder value)
        Sets the row finder to use for locating the rows to import.
        Parameters:
        value - the finder

      • getRowFinder

        public adams.data.spreadsheet.rowfinder.RowFinder getRowFinder()
        Returns the row finder to use for locating the rows to import.
        Returns:
        the finder

      • rowFinderTipText

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

      • newInstance

        public SampleData newInstance()
        Returns a new instance of the report class in use.
        Specified by:
        newInstance in class adams.data.io.input.AbstractReportReader<SampleData>
        Returns:
        the new (empty) report

      • readData

        protected List<SampleData> readData()
        Performs the actual reading.
        Specified by:
        readData in class adams.data.io.input.AbstractReportReader<SampleData>
        Returns:
        the reports that were read